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Conserved domains on  [gi|4505939|ref|NP_000928|]
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DNA-directed RNA polymerase II subunit RPB1 [Homo sapiens]

Protein Classification

DNA-directed RNA polymerase II subunit RPB1( domain architecture ID 11553359)

DNA-directed RNA polymerase II subunit RPB1, together with RPB2, forms the active site, DNA entry channel and RNA exit channel of RNAP II, a large multi-subunit complex responsible for the synthesis of mRNA

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
19-876 0e+00

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


:

Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 1611.06  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    19 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 97
Cdd:cd02733    1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    98 GFLVKTMKVLRCVCffcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltk 177
Cdd:cd02733   79 GFLTKILKILRCVC------------------------------------------------------------------ 92
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   178 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02733   93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   258 LSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 337
Cdd:cd02733  138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   338 SLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAK 417
Cdd:cd02733  218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   418 YIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 497
Cdd:cd02733  298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   498 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQP 577
Cdd:cd02733  378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   578 AILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISY 657
Cdd:cd02733  458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   658 LEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 737
Cdd:cd02733  533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   738 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 817
Cdd:cd02733  613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692
                        810       820       830       840       850
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939   818 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd02733  693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1058-1476 0e+00

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


:

Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 821.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1058 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1137
Cdd:cd02584    1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1138 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1215
Cdd:cd02584   81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1216 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1295
Cdd:cd02584  161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1296 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1375
Cdd:cd02584  234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1376 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1455
Cdd:cd02584  310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
                        410       420
                 ....*....|....*....|.
gi 4505939  1456 ENIMLGQLAPAGTGCFDLLLD 1476
Cdd:cd02584  390 ENIMLGQLAPIGTGCFDLLLD 410
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
896-1079 3.06e-96

RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


:

Pssm-ID: 461511  Cd Length: 188  Bit Score: 308.27  E-value: 3.06e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     896 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 972
Cdd:pfam04992    1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     973 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1051
Cdd:pfam04992   81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
                          170       180
                   ....*....|....*....|....*...
gi 4505939    1052 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1079
Cdd:pfam04992  161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
Herpes_BLLF1 super family cl37540
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
1854-1959 4.83e-15

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


The actual alignment was detected with superfamily member pfam05109:

Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 81.12  E-value: 4.83e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1854 TP--TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1931
Cdd:pfam05109  517 TPnaTSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVG 596
                           90       100
                   ....*....|....*....|....*...
gi 4505939    1932 PTSPKGSTYSPTSPGyspTSPTYSLTSP 1959
Cdd:pfam05109  597 ETSPQANTTNHTLGG---TSSTPVVTSP 621
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
1491-1610 3.19e-10

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


:

Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 59.46  E-value: 3.19e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     1491 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1563
Cdd:smart01104   15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 4505939     1564 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1610
Cdd:smart01104   91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
 
Name Accession Description Interval E-value
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
19-876 0e+00

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 1611.06  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    19 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 97
Cdd:cd02733    1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    98 GFLVKTMKVLRCVCffcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltk 177
Cdd:cd02733   79 GFLTKILKILRCVC------------------------------------------------------------------ 92
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   178 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02733   93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   258 LSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 337
Cdd:cd02733  138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   338 SLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAK 417
Cdd:cd02733  218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   418 YIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 497
Cdd:cd02733  298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   498 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQP 577
Cdd:cd02733  378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   578 AILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISY 657
Cdd:cd02733  458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   658 LEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 737
Cdd:cd02733  533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   738 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 817
Cdd:cd02733  613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692
                        810       820       830       840       850
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939   818 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd02733  693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
18-895 0e+00

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 992.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:PRK08566    9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     97 VGFLVKTMKVLRCVCFFCSKLLVDSNnpKIKDIL-----AKSKGQPKKRLT-HVYDLCKGKNICeggeemdnkfgveqPe 170
Cdd:PRK08566   87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------P- 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    171 gdedltkekgHggCGRYQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:PRK08566  150 ----------H--CGEKQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 329
Cdd:PRK08566  212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    330 QKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRG 409
Cdd:PRK08566  291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    410 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 487
Cdd:PRK08566  371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    488 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 567
Cdd:PRK08566  450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    568 STWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKhiSPGDTKVVVENGELIMGILCKKSLGT 647
Cdd:PRK08566  530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    648 SAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEP 727
Cdd:PRK08566  608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    728 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 807
Cdd:PRK08566  688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    808 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVV 887
Cdd:PRK08566  768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847

                  ....*...
gi 4505939    888 QLRYGEDG 895
Cdd:PRK08566  848 QFKYGEDG 855
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
18-897 0e+00

DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.


Pssm-ID: 274106 [Multi-domain]  Cd Length: 868  Bit Score: 940.68  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:TIGR02390    4 IGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      97 VGFLVKTMKVLRCVCFFCSKLLV-----DSNNPKIKDILAKSkGQPKKRL-THVYDLCKGKNICEGGEEMDNKFGVEQPe 170
Cdd:TIGR02390   82 VGFAKEIYKILRATCRKCGRITLteeeiEQYLEKINKLKEEG-GDLASTLiEKIVKEAAKRMKCPHCGEEQKKIKFEKP- 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     171 gdedltkekghggcgryqprirrsglelyaewKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:TIGR02390  160 --------------------------------TYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVL 207
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:TIGR02390  208 TVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARH 287
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     331 KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGN 410
Cdd:TIGR02390  288 RSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGP 367
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     411 SQYPGAKYIIRDNGDRIDLRFHPKPSDL-HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVT 489
Cdd:TIGR02390  368 DSWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVC 447
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     490 TPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLST 569
Cdd:TIGR02390  448 PPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAG 526
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     570 WDGKVPQPAILKPRPLWTGKQIFSLIIPGHINC-IRTHSTHPDDEDSgpyKHISPGDTKVVVENGELIMGILCKKSLGTS 648
Cdd:TIGR02390  527 YFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFeGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAE 603
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     649 AGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPT 728
Cdd:TIGR02390  604 KGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPL 683
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     729 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 808
Cdd:TIGR02390  684 PGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLP 763
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     809 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQ 888
Cdd:TIGR02390  764 HFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQ 843

                   ....*....
gi 4505939     889 LRYGEDGLA 897
Cdd:TIGR02390  844 FKYGEDGVD 852
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1058-1476 0e+00

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 821.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1058 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1137
Cdd:cd02584    1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1138 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1215
Cdd:cd02584   81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1216 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1295
Cdd:cd02584  161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1296 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1375
Cdd:cd02584  234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1376 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1455
Cdd:cd02584  310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
                        410       420
                 ....*....|....*....|.
gi 4505939  1456 ENIMLGQLAPAGTGCFDLLLD 1476
Cdd:cd02584  390 ENIMLGQLAPIGTGCFDLLLD 410
RNA_pol_Rpb1_5 pfam04998
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
830-1427 3.85e-176

RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.


Pssm-ID: 398596 [Multi-domain]  Cd Length: 516  Bit Score: 545.03  E-value: 3.85e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     830 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL 909
Cdd:pfam04998    1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     910 KPSNKAFEKKFRFDYTNERALrrtlqedlvkdvlsnahiqnelEREFERMREDREVLRVIFptgdskvvlpcnllrmiwn 989
Cdd:pfam04998   81 EFSDLKLEDKFKNDLLDDLLL----------------------LSEFSLSYKKEILVRDSK------------------- 119
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     990 aqkifhinprlpsdlhpikvvegvkelskklvivNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLL 1069
Cdd:pfam04998  120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1070 GEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSAR 1149
Cdd:pfam04998  166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1150 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVAR--------ISPWLLRVELDRKHM 1221
Cdd:pfam04998  246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1222 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQGI 1301
Cdd:pfam04998  326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGL---RRVDELFMEEDPKLAILVASLLGNITLRGI 402
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1302 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1380
Cdd:pfam04998  403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*..
gi 4505939    1381 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPL 1427
Cdd:pfam04998  470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
246-546 4.54e-172

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 524.78  E-value: 4.54e-172
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      246 EWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNElpGL 325
Cdd:smart00663    1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      326 PRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQEL 405
Cdd:smart00663   79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      406 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 484
Cdd:smart00663  159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
                           250       260       270       280       290       300
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505939      485 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 546
Cdd:smart00663  234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
15-354 3.70e-142

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 444.04  E-value: 3.70e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      15 LRTIKRVQFGVLSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 92
Cdd:pfam04997    1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      93 PVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQ--PKKRLTHVYDLCKGKNICEGGEEMDnkfgveqpe 170
Cdd:pfam04997   79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     171 gdedltkekghGGCGRYQPRIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:pfam04997  150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:pfam04997  217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296
                          330       340
                   ....*....|....*....|....
gi 4505939     331 KSGRPLKSLKQRLKGKEGRVRGNL 354
Cdd:pfam04997  297 KSKRPLKSISQRLKGKEGRFRGNL 320
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
896-1079 3.06e-96

RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


Pssm-ID: 461511  Cd Length: 188  Bit Score: 308.27  E-value: 3.06e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     896 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 972
Cdd:pfam04992    1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     973 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1051
Cdd:pfam04992   81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
                          170       180
                   ....*....|....*....|....*...
gi 4505939    1052 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1079
Cdd:pfam04992  161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
1052-1479 2.20e-88

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 294.06  E-value: 2.20e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1052 RRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1131
Cdd:PRK04309   27 REKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1132 KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaeDqewvnvYYEMpdfdvarispwL 1211
Cdd:PRK04309  107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------T 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1212 LRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKMQEEEEVVDKmdddvflrciesn 1291
Cdd:PRK04309  157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK------------- 213
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1292 mLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:PRK04309  214 -IRNIKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGI 274
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:PRK04309  275 EAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDEL 354
                         410       420
                  ....*....|....*....|....*...
gi 4505939   1452 KGVSENIMLGQLAPAGTGCFDLLLDAEK 1479
Cdd:PRK04309  355 KGVTENIIVGQPIPLGTGDVELTMDPPL 382
RNA_pol_rpoA2 TIGR02389
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1054-1476 5.76e-85

DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274105 [Multi-domain]  Cd Length: 367  Bit Score: 283.48  E-value: 5.76e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1054 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1133
Cdd:TIGR02389   14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1134 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlLR 1213
Cdd:TIGR02389   94 PSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VI 143
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1214 VELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeklVLRIRIMNSDenkmQEEEEVVDKMDDDVF--LRCIEsN 1291
Cdd:TIGR02389  144 IELDEEQLKERGITVDDVEKAIKK------------------AKLGKVIEID----MDNNTITIKPGNPSLkeLRKLK-E 200
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1292 MLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:TIGR02389  201 KIKNLHIKGIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGI 262
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:TIGR02389  263 EAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDEL 342
                          410       420
                   ....*....|....*....|....*
gi 4505939    1452 KGVSENIMLGQLAPAGTGCFDLLLD 1476
Cdd:TIGR02389  343 KGVIENIIVGQPIPLGTGDVDLVMD 367
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
20-948 2.36e-64

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 241.22  E-value: 2.36e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    20 RVQFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 77
Cdd:COG0086    9 AIKIGLASPEKI--RSWSYGEVKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    78 MTECP---GHFGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKIK--DILAKSKGQPKkrl 141
Cdd:COG0086   82 VTLSKvrrERMGHIELAMPVFHIWGlkslpsrigllLDMSLRDLERVLYFESYVVIDPGDTPLEkgQLLTEDEYREI--- 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   142 thvydlckgknICEGGEEMDNKFG---VEQPEGDEDLTKEKGhggcgryqprirrsglELYAEWKHVNedSQEKKIllsp 218
Cdd:COG0086  159 -----------LEEYGDEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK---- 205
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   219 ervhEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGA 298
Cdd:COG0086  206 ----KLIKRLKVVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKA 277
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   299 AAHVIAEDVKLLQFHVATMVDNELPGlpRAMQKSG-RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQ 377
Cdd:COG0086  278 PDIIVRNEKRMLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQ 355
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   378 VGVPRSIAanmtfAEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqtgykverhm 450
Cdd:COG0086  356 CGLPKKMA-----LELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------- 410
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   451 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 522
Cdd:COG0086  411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLST 477
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   523 RMIVTPQSNRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKVPQPAILKPRPLWTGKQ---- 590
Cdd:COG0086  478 NNILSPANGKPIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgki 552
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   591 --------IFSLIIP---GHINcirthsthpddedsgpykhispgdtKVvvengelimgiLCKKSLGTsagsLVHISYLE 659
Cdd:COG0086  553 vettvgryLVNEILPqevPFYN-------------------------QV-----------INKKHIEV----IIRQMYRR 592
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   660 MGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTyqdiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfEN 739
Cdd:COG0086  593 CGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YN 661
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   740 QVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpe 818
Cdd:COG0086  662 KVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS-------------- 727
                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   819 srgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGedgla 897
Cdd:COG0086  728 -------NFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEG----- 794
                        970       980       990      1000      1010
                 ....*....|....*....|....*....|....*....|....*....|.
gi 4505939   898 GESVEfqnlaTLKpsnkafekkfrfdytnERALRRTLQEDlVKDVLSNAHI 948
Cdd:COG0086  795 GEVIE-----PLK----------------ERILGRVAAED-VVDPGTGEVL 823
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
1854-1959 4.83e-15

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 81.12  E-value: 4.83e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1854 TP--TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1931
Cdd:pfam05109  517 TPnaTSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVG 596
                           90       100
                   ....*....|....*....|....*...
gi 4505939    1932 PTSPKGSTYSPTSPGyspTSPTYSLTSP 1959
Cdd:pfam05109  597 ETSPQANTTNHTLGG---TSSTPVVTSP 621
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
764-1117 3.92e-12

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 71.95  E-value: 3.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    764 NNFKS---------MVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 830
Cdd:PRK02597  111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    831 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGESVEFQNlatl 909
Cdd:PRK02597  167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    910 kpsnkafekkfrfdytneRALRRTLQEDLVKDvlsnahiqnelerefermreDREVLrvifptgdskvvlpcnllrmiwn 989
Cdd:PRK02597  238 ------------------RLLGRVLAEDVVDP--------------------EGEVI----------------------- 256
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    990 AQKIFHINPRLPsdlhpiKVVE--GVKElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDW 1067
Cdd:PRK02597  257 AERNTAIDPDLA------KKIEkaGVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYGW 300
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 4505939   1068 LLgeieskfnqAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1117
Cdd:PRK02597  301 SL---------AHNHLvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
1491-1610 3.19e-10

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 59.46  E-value: 3.19e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     1491 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1563
Cdd:smart01104   15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 4505939     1564 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1610
Cdd:smart01104   91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
1853-1967 1.68e-06

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 52.83  E-value: 1.68e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1853 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1929
Cdd:COG3469   89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168
                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 4505939  1930 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSD 1967
Cdd:COG3469  169 TTTTTSASTTPSATTTATATTASGATTPSATTTATTTG 206
PHA03291 PHA03291
envelope glycoprotein I; Provisional
1858-1962 1.01e-05

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 50.34  E-value: 1.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1858 PKYSPTSPKYSPTSPKYSPTSpTYSPTTPKYSPTSPTYSPTSPvyTPTSPKySPTSPTYSPTSPKYSPTSPTYSPTSPkg 1937
Cdd:PHA03291  181 SADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTASPETTP--TPSTTT-SPPSTTIPAPSTTIAAPQAGTTPEAE-- 254
                          90       100
                  ....*....|....*....|....*
gi 4505939   1938 STYSPTSPGYSPTSPTYSLTSPAIS 1962
Cdd:PHA03291  255 GTPAPPTPGGGEAPPANATPAPEAS 279
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
1865-1960 5.88e-05

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 44.43  E-value: 5.88e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     1865 PKYSPTSPKYSPTSPTysPTTPKYSPTSPTYSpTSPVYTPTS---PKYSPTSPTYSPTSPKY--SPTSPTYSPTSPKGST 1939
Cdd:smart01104   15 PAWGSRTPGTAAGGAP--TARGGSGSRTPAWG-GAGSRTPAWggaGPTGSRTPAWGGASAWGnkSSEGSASSWAAGPGGA 91
                            90       100
                    ....*....|....*....|.
gi 4505939     1940 YSPTSPGYSPTSPTYSLTSPA 1960
Cdd:smart01104   92 YGAPTPGYGGTPSAYGPATPG 112
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
1870-1942 1.46e-04

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 46.43  E-value: 1.46e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4505939    1870 TSPKYSPTSPTYSPTTPKYSPTSptySPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP 1942
Cdd:TIGR00601   75 SKPKTGTGKVAPPAATPTSAPTP---TPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS 144
 
Name Accession Description Interval E-value
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
19-876 0e+00

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 1611.06  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    19 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 97
Cdd:cd02733    1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    98 GFLVKTMKVLRCVCffcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltk 177
Cdd:cd02733   79 GFLTKILKILRCVC------------------------------------------------------------------ 92
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   178 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02733   93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   258 LSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 337
Cdd:cd02733  138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   338 SLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAK 417
Cdd:cd02733  218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   418 YIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 497
Cdd:cd02733  298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   498 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQP 577
Cdd:cd02733  378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   578 AILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISY 657
Cdd:cd02733  458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   658 LEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 737
Cdd:cd02733  533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   738 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 817
Cdd:cd02733  613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692
                        810       820       830       840       850
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939   818 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd02733  693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
15-895 0e+00

A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.


Pssm-ID: 259846 [Multi-domain]  Cd Length: 861  Bit Score: 1006.77  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    15 LRTIKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKP 93
Cdd:cd02582    1 PKRIKGIKFGLLSPEEIRKMSVVE--IITPDTyDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARP 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    94 VFHVGFLVKTMKVLRCVCFFCSKLLV-DSNNPKIKDILAKSKG---QPKKRL-THVYDLCKGKNICeggeemdnkfgveq 168
Cdd:cd02582   79 VIHVGFAKHIYDLLRATCRSCGRILLpEEEIEKYLERIRRLKEkwpELVKRViEKVKKKAKKRKVC-------------- 144
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   169 PegdedltkekgHggCGRYQPRIRrsgLELYAEWKHVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWM 248
Cdd:cd02582  145 P-----------H--CGAPQYKIK---LEKPTTFYEEKEEGEVK---LTPSEIRERLEKIPDEDLELLGIDPKTARPEWM 205
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   249 IVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRA 328
Cdd:cd02582  206 VLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPA 285
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   329 MQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRR 408
Cdd:cd02582  286 RHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLN 365
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   409 GNSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNL 486
Cdd:cd02582  366 GPDKWPGANYVIRPDGRRIRLRYVNR-EELaeRLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNL 444
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   487 SVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMF 566
Cdd:cd02582  445 AVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSA 524
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   567 LStWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHisPGDTKVVVENGELIMGILCKKSLG 646
Cdd:cd02582  525 AG-YDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEGKAKVCSGCSECKDEDC--PNDGYVVIKNGKLLEGVIDKKAIG 601
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   647 T-SAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNEL 725
Cdd:cd02582  602 AeQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGEL 681
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   726 EPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHR 805
Cdd:cd02582  682 EPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNR 761
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   806 TLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQ 885
Cdd:cd02582  762 TLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGN 841
                        890
                 ....*....|
gi 4505939   886 VVQLRYGEDG 895
Cdd:cd02582  842 IIQFKYGEDG 851
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
18-895 0e+00

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 992.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:PRK08566    9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     97 VGFLVKTMKVLRCVCFFCSKLLVDSNnpKIKDIL-----AKSKGQPKKRLT-HVYDLCKGKNICeggeemdnkfgveqPe 170
Cdd:PRK08566   87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------P- 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    171 gdedltkekgHggCGRYQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:PRK08566  150 ----------H--CGEKQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 329
Cdd:PRK08566  212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    330 QKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRG 409
Cdd:PRK08566  291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    410 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 487
Cdd:PRK08566  371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    488 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 567
Cdd:PRK08566  450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    568 STWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKhiSPGDTKVVVENGELIMGILCKKSLGT 647
Cdd:PRK08566  530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    648 SAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEP 727
Cdd:PRK08566  608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    728 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 807
Cdd:PRK08566  688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    808 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVV 887
Cdd:PRK08566  768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847

                  ....*...
gi 4505939    888 QLRYGEDG 895
Cdd:PRK08566  848 QFKYGEDG 855
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
18-897 0e+00

DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.


Pssm-ID: 274106 [Multi-domain]  Cd Length: 868  Bit Score: 940.68  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:TIGR02390    4 IGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      97 VGFLVKTMKVLRCVCFFCSKLLV-----DSNNPKIKDILAKSkGQPKKRL-THVYDLCKGKNICEGGEEMDNKFGVEQPe 170
Cdd:TIGR02390   82 VGFAKEIYKILRATCRKCGRITLteeeiEQYLEKINKLKEEG-GDLASTLiEKIVKEAAKRMKCPHCGEEQKKIKFEKP- 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     171 gdedltkekghggcgryqprirrsglelyaewKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:TIGR02390  160 --------------------------------TYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVL 207
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:TIGR02390  208 TVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARH 287
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     331 KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGN 410
Cdd:TIGR02390  288 RSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGP 367
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     411 SQYPGAKYIIRDNGDRIDLRFHPKPSDL-HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVT 489
Cdd:TIGR02390  368 DSWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVC 447
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     490 TPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLST 569
Cdd:TIGR02390  448 PPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAG 526
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     570 WDGKVPQPAILKPRPLWTGKQIFSLIIPGHINC-IRTHSTHPDDEDSgpyKHISPGDTKVVVENGELIMGILCKKSLGTS 648
Cdd:TIGR02390  527 YFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFeGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAE 603
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     649 AGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPT 728
Cdd:TIGR02390  604 KGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPL 683
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     729 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 808
Cdd:TIGR02390  684 PGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLP 763
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     809 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQ 888
Cdd:TIGR02390  764 HFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQ 843

                   ....*....
gi 4505939     889 LRYGEDGLA 897
Cdd:TIGR02390  844 FKYGEDGVD 852
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
14-1481 0e+00

bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 914.03  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     14 PLRTIKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 92
Cdd:PRK14977    5 AVKAIDGIIFGLISPADARKIGFAE--ITAPEAyDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAE 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     93 PVFHVGFLVKTMKVLRCVCFFCSKLLV---DSNNPK-IKDILAKSKGQPKKRLThvydlckgkniceggEEMDNKFGvEQ 168
Cdd:PRK14977   83 PVIHIAFIDNIKDLLNSTCHKCAKLKLpqeDLNVFKlIEEAHAAARDIPEKRID---------------DEIIEEVR-DQ 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    169 PEGDEDLTKEKGHggCGRYQPRirrsgLELYAEWKHVNEDSQEKKILLsPERVHEIFKRISDEECFVLGMEPRYARPEWM 248
Cdd:PRK14977  147 VKVYAKKAKECPH--CGAPQHE-----LEFEEPTIFIEKTEIEEHRLL-PIEIRDIFEKIIDDDLELIGFDPKKARPEWA 218
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    249 IVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRA 328
Cdd:PRK14977  219 VLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQA 298
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    329 MQK-SGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVR 407
Cdd:PRK14977  299 HHKgSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVI 378
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    408 RGNSQYPGAKYIIRDNGDRIDLRFHPKPSDL-------HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS 480
Cdd:PRK14977  379 NGPDEFPGANAIRKGDGTKIRLDFLEDKGKDalreaaeQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGA 458
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    481 TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEV 560
Cdd:PRK14977  459 TFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEA 538
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    561 MNLLMfLSTWDGKVPQPAI-LKPRPLWTGKQIFSLIIPGHINCIRThSTHPDDEDSGPYKHISPGDTKVVVENGELIMGI 639
Cdd:PRK14977  539 SNIAM-LAGITDPLPEPAIkTKDGPAWTGKQLFSLFLPKDFNFEGI-AKWSAGKAGEAKDPSCLGDGYVLIKEGELISGV 616
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    640 LCKKSLGTSAG---SLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEV 716
Cdd:PRK14977  617 IDDNIIGALVEepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDL 696
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    717 IEK--------AHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVV 788
Cdd:PRK14977  697 IDQrkitrkitIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGAL 776
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    789 GQQNVE--------GKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYI 860
Cdd:PRK14977  777 GQQKRKtrigfvltGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYF 856
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    861 QRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLagesvefqnlatlkpsnkAFEKKFRFDYTN-ERALRRTLQEDLV 939
Cdd:PRK14977  857 QRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGI------------------DPQKLDHGEAFNlERIIEKQKIEDRG 918
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    940 KDVlSNAHIQnELEREFERMREDRevlrvifptgdskvvLPCNLLRMIWNAQkifhinprlPSDlhpikvvEGVKELSKK 1019
Cdd:PRK14977  919 KGA-SKDEIE-ELAKEYTKTFNAN---------------LPKLLADAIHGAE---------LKE-------DELEAICAE 965
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1020 LvivngddplsrqaqenatllfnihlrstlcsrrmaeefrlsgeafdwLLGeieskFNQAIAHPGEMVGALAAQSLGEPA 1099
Cdd:PRK14977  966 G-----------------------------------------------KEG-----FEKAKVEPGQAIGIISAQSIAEPG 993
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1100 TQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYdP 1179
Cdd:PRK14977  994 TQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN-A 1072
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1180 NPQSTVVAEDQEWVNVYYEMPDFdvarispwllrVELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeKLVlri 1259
Cdd:PRK14977 1073 NEIKLIKPDKRALENGCIPMERF-----------AEIEAALAKGKKFEMELEDDLIIL----------------DLV--- 1122
                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1260 rimnsdenkmqeeeEVVDKMDDDVFLRCIeSNMLTDMTLQGIEQISKVYMHLPQTDNKKkiiitedgefkalqEWILETD 1339
Cdd:PRK14977 1123 --------------EAADRDKPLATLIAI-RNKILDKPVKGVPDIERAWVELVEKDGRD--------------EWIIQTS 1173
                        1370      1380      1390      1400      1410      1420      1430      1440
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1340 GVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAI----- 1414
Cdd:PRK14977 1174 GSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIglqaa 1253
                        1450      1460      1470      1480      1490      1500
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4505939   1415 -TRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCK 1481
Cdd:PRK14977 1254 gVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
26-880 0e+00

Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.


Pssm-ID: 259847 [Multi-domain]  Cd Length: 816  Bit Score: 897.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    26 LSPDELKRMSVTEggIKYPE--TTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKT 103
Cdd:cd02583    1 LSPEDIIRLSEVE--VTNRNlyDIETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAI 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   104 MKVLRCVCFFCSKLLVDSNnpKIKDILAKSKGQPKKRLTH------VYDLCKGKNICeggeemdnkfgveqPEgdedltk 177
Cdd:cd02583   79 INILQCICKTCSRVLLPEE--EKRKFLKRLRRPNLDNLQKkalkkkILEKCKKVRKC--------------PH------- 135
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   178 ekghggCGRYqprirrsglelyaewKHVNEDsqekkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02583  136 ------CGLL---------------KKAQED-------LNPLKVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPP 187
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   258 LSVRPAVVMQG-SARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSgRPL 336
Cdd:cd02583  188 LCIRPSVVMDEkSGTNEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPK-KPI 266
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   337 KSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGA 416
Cdd:cd02583  267 RGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGA 346
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   417 KYII-RDNGDRIDLRF-HPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNA 494
Cdd:cd02583  347 NFVIkRDGGKKKFLKYgNRRKIARELKIGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNA 426
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   495 DFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwDGK- 573
Cdd:cd02583  427 DFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCSYML--DGEi 504
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   574 ---VPQPAILKPRPLWTGKQIFSLII-PGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGT-S 648
Cdd:cd02583  505 kidLPPPAILKPVELWTGKQIFSLLLrPNKKSPVLVNLEAKEKSYTKKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSgS 584
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   649 AGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPT 728
Cdd:cd02583  585 KNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQ 664
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   729 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 808
Cdd:cd02583  665 PGCTAEQTLEAKISGELSKIREDAGKACLKELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLP 744
                        810       820       830       840       850       860       870
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505939   809 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVR 880
Cdd:cd02583  745 HFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1058-1476 0e+00

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 821.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1058 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1137
Cdd:cd02584    1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1138 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1215
Cdd:cd02584   81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1216 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1295
Cdd:cd02584  161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1296 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1375
Cdd:cd02584  234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1376 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1455
Cdd:cd02584  310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
                        410       420
                 ....*....|....*....|.
gi 4505939  1456 ENIMLGQLAPAGTGCFDLLLD 1476
Cdd:cd02584  390 ENIMLGQLAPIGTGCFDLLLD 410
RNAP_I_RPA1_N cd01435
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
22-876 0e+00

Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.


Pssm-ID: 259844 [Multi-domain]  Cd Length: 779  Bit Score: 631.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    22 QFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFL 100
Cdd:cd01435    1 SFSFYSAEEIRKLSVKE--ITNPVTfDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFF 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   101 VKTMKVLRCVCFFCSKLLVdsnnPKIKDILAKSKGQPkkrlthvydLCKGKNiceggeemdnkfgveqpegdedltkekg 180
Cdd:cd01435   79 DLLYKLLRGSCFYCHRFRI----SKWEVKLFVAKLKL---------LDKGLL---------------------------- 117
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   181 hggcgryqprirrsglelyaewkhvnedsQEKKILLSPervheifkrisdeecfvlgmepryarPEWMIVTVLPVPPLSV 260
Cdd:cd01435  118 -----------------------------VEAAELDFG--------------------------YDMFFLDVLLVPPNRF 142
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   261 RPAVVMQGSArnqddLTHK----LADIVKINNQLR------RNEQNGAAAHVIAEDVKL---------LQFHVATMVDNE 321
Cdd:cd01435  143 RPPSFLGDKV-----FENPqnvlLSKILKDNQQIRdllasmRQAESQSKLDLISGKTNSeklinawlqLQSAVNELFDST 217
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   322 LPGLPRAMQKSGrplksLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDR 401
Cdd:cd01435  218 KAPKSGKKSPPG-----IKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEE 292
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   402 LQELVRRGNSQYPGAKYIIRDNGDRIDLRFH--------------PKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKM 467
Cdd:cd01435  293 LRQAVINGPDVYPGANAIEDEDGRLILLSALseerrkalakllllLSSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLHKP 372
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   468 SMMGHRVRILPWS-TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 546
Cdd:cd01435  373 SIMAHKVRVLPGEkTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGV 452
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   547 KFTKRDVFLERGEVMNLLMF-LSTWDG-------KVPQPAILKPRPLWTGKQIFSLIIpghINCIRTHStHPDDEDS--- 615
Cdd:cd01435  453 LLTSRDTFFTREEYQQLVYAaLRPLFTsdkdgriKLLPPAILKPKPLWTGKQVISTIL---KNLIPGNA-PLLNLSGkkk 528
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   616 ------GPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGI 689
Cdd:cd01435  529 tkkkvgGGKWGGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGI 608
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   690 GDSIADSKTYQDIQNTIKKAKQDVIEVIEKAhnneleptpgntlrqtFENQVNRILNDARDKTGSSAQKSLSEYNNFKSM 769
Cdd:cd01435  609 EDLLLTPKADEKRRKILRKAKKLGLEAAAEF----------------LGLKLNKVTSSIIKACLPKGLLKPFPENNLQLM 672
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   770 VVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLID 849
Cdd:cd01435  673 VQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLID 752
                        890       900
                 ....*....|....*....|....*..
gi 4505939   850 TAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd01435  753 TAVKTSRSGYLQRCLIKHLEGLKVNYD 779
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
26-876 2.85e-180

Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.


Pssm-ID: 259843 [Multi-domain]  Cd Length: 528  Bit Score: 556.66  E-value: 2.85e-180
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    26 LSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLvkt 103
Cdd:cd00399    1 MSPEEIRKWSVAK--VIKPETIDnrTLKAERGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFI--- 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   104 mkvlrcvcffcskllvdsnnpkikdilakskgqpkkrlTHVYDLCKgkniceggeemdnkfgveqpegdedltkekghgg 183
Cdd:cd00399   76 --------------------------------------KKVPSFLG---------------------------------- 83
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   184 cgryqprirrsglelyaewkhvnedsqekkillspervheifkrisdeecfvlgmepryarPEWMIVTVLPVPPLSVRPA 263
Cdd:cd00399   84 -------------------------------------------------------------PEWMILTCLPVPPPCLRPS 102
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   264 VVmqgsarnqddlthkladivkinnqlrrneqngaaahvIAEDVKLLQFHVATMVDNELPGLPRAMqKSGRPLKSLKQRL 343
Cdd:cd00399  103 VI-------------------------------------IEERWRLLQEHVDTYLDNGIAGQPQTQ-KSGRPLRSLAQRL 144
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   344 KGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMtfaeivtpfnidrlqelvrrgnsqypgakyiirdn 423
Cdd:cd00399  145 KGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------- 189
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   424 gdridlrfhpkpsdlhlqtgykverhmcDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNL 503
Cdd:cd00399  190 ----------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNL 241
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   504 HLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKrdvflergevmnllmflstwdgkvpqpailkpr 583
Cdd:cd00399  242 HVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTL--------------------------------- 288
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   584 plwtGKQIFSLIIPGhincirthsthpddedsgpykhispgdtkvvvengelimgilckkslgtsagSLVHISYLEMGHD 663
Cdd:cd00399  289 ----GKQIVSAALPG----------------------------------------------------GLLHTVTRELGPE 312
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   664 ITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNR 743
Cdd:cd00399  313 KAAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILD 392
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   744 ILNDARDKTGSSAQKSL---SEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESR 820
Cdd:cd00399  393 FLNEARDKAGSAASVNLdlvSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAK 472
                        810       820       830       840       850
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 4505939   821 GFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd00399  473 GFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
RNA_pol_Rpb1_5 pfam04998
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
830-1427 3.85e-176

RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.


Pssm-ID: 398596 [Multi-domain]  Cd Length: 516  Bit Score: 545.03  E-value: 3.85e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     830 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL 909
Cdd:pfam04998    1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     910 KPSNKAFEKKFRFDYTNERALrrtlqedlvkdvlsnahiqnelEREFERMREDREVLRVIFptgdskvvlpcnllrmiwn 989
Cdd:pfam04998   81 EFSDLKLEDKFKNDLLDDLLL----------------------LSEFSLSYKKEILVRDSK------------------- 119
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     990 aqkifhinprlpsdlhpikvvegvkelskklvivNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLL 1069
Cdd:pfam04998  120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1070 GEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSAR 1149
Cdd:pfam04998  166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1150 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVAR--------ISPWLLRVELDRKHM 1221
Cdd:pfam04998  246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1222 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQGI 1301
Cdd:pfam04998  326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGL---RRVDELFMEEDPKLAILVASLLGNITLRGI 402
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1302 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1380
Cdd:pfam04998  403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*..
gi 4505939    1381 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPL 1427
Cdd:pfam04998  470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
246-546 4.54e-172

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 524.78  E-value: 4.54e-172
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      246 EWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNElpGL 325
Cdd:smart00663    1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      326 PRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQEL 405
Cdd:smart00663   79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      406 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 484
Cdd:smart00663  159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
                           250       260       270       280       290       300
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505939      485 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 546
Cdd:smart00663  234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
15-354 3.70e-142

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 444.04  E-value: 3.70e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      15 LRTIKRVQFGVLSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 92
Cdd:pfam04997    1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      93 PVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQ--PKKRLTHVYDLCKGKNICEGGEEMDnkfgveqpe 170
Cdd:pfam04997   79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     171 gdedltkekghGGCGRYQPRIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:pfam04997  150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:pfam04997  217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296
                          330       340
                   ....*....|....*....|....
gi 4505939     331 KSGRPLKSLKQRLKGKEGRVRGNL 354
Cdd:pfam04997  297 KSKRPLKSISQRLKGKEGRFRGNL 320
RNA_pol_Rpb1_2 pfam00623
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
356-521 1.05e-97

RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.


Pssm-ID: 395498  Cd Length: 166  Bit Score: 311.54  E-value: 1.05e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     356 GKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKP 435
Cdd:pfam00623    1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     436 SDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEI 515
Cdd:pfam00623   81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160

                   ....*.
gi 4505939     516 QELAMV 521
Cdd:pfam00623  161 EELMLV 166
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
896-1079 3.06e-96

RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


Pssm-ID: 461511  Cd Length: 188  Bit Score: 308.27  E-value: 3.06e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     896 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 972
Cdd:pfam04992    1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     973 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1051
Cdd:pfam04992   81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
                          170       180
                   ....*....|....*....|....*...
gi 4505939    1052 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1079
Cdd:pfam04992  161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
RNAP_IV_RPD1_N cd10506
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
57-880 3.96e-91

Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.


Pssm-ID: 259849 [Multi-domain]  Cd Length: 744  Bit Score: 314.34  E-value: 3.96e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    57 LMDPRQGVIERTGRCQTC-AGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCffcskllvdsnnPKIKDILAKSKG 135
Cdd:cd10506   20 VTNPRLGLPNESGQCTTCgAKDNKKCEGHFGVIKLPVTIYHPYFISEVAQILNKIC------------PGCKSIKQKKKK 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   136 QPKKRLTHVY-DLCKGKniceggeemdnkfgvEQPEGdEDLTKekghggcgryqprirrsglelyaewkhvnedsqekki 214
Cdd:cd10506   88 PPRETLPPDYwDFIPKD---------------GQQEE-SCVTK------------------------------------- 114
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   215 lLSPERVHEIFKRISDEECFVLGMEpRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNE 294
Cdd:cd10506  115 -NLPILSLAQVKKILKEIDPKLIAK-GLPRQEGLFLKCLPVPPNCHRVTEFTHGFSTGSRLIFDERTRAYKKLVDFIGTA 192
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   295 QNGAAAHviaedvkllqfhvatmvdnelpglpramqKSGrpLKSLKQrlkgkegrvrgNLMGKRVDFSARTVITPDPNLS 374
Cdd:cd10506  193 NESAASK-----------------------------KSG--LKWMKD-----------LLLGKRSGHSFRSVVVGDPYLE 230
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   375 IDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGnsqyPGAKYII--RDNGDRIDLRFHPKpsdlhLQTGYKVERHMCD 452
Cdd:cd10506  231 LNEIGIPCEIAERLTVSERVSSWNRERLQEYCDLT----LLLKGVIgvRRNGRLVGVRSHNT-----LQIGDVIHRPLVD 301
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   453 GDIVIFNRQPTLHKMSMMGHRVRILPW-STFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSN 531
Cdd:cd10506  302 GDVVLVNRPPSIHQHSLIALSVKVLPTnSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSG 381
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   532 RPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTwdgKVPQPAILK--PR--PLWTGKQIFSLIIPGHINCirths 607
Cdd:cd10506  382 QNLLSLTQDSLLAAHLMTERGVFLDKAQMQQLQMLCPS---QLPPPAIIKspPSngPLWTGKQLFQMLLPTDLDY----- 453
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   608 thpddedSGPykhispgDTKVVVENGELIMGiLCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTI 687
Cdd:cd10506  454 -------SFP-------SNLVFISDGELISS-SGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSV 518
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   688 GIGD------SIADSKTYQDIQNTIKKAKQ----DVIEV----IEKAHNNELEPTPGNTLRQTFENQVN-RILNDARDK- 751
Cdd:cd10506  519 SLSDlylssdSYSRQKMIEEISLGLREAEIacniKQLLVdsrkDFLSGSGEENDVSSDVERVIYERQKSaALSQASVSAf 598
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   752 ------TGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKrIPFGFKH---------RTLPHFIKDDY- 815
Cdd:cd10506  599 kqvfrdIQNLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVK-LSYRIPRqlscaawnsQKSPRVIEKDGs 677
                        810       820       830       840       850       860       870
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   816 ----GPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDtavKTAET-GYIQRRLIKSMESVMVKYDATVR 880
Cdd:cd10506  678 ecteSYIPYGVVESSFLDGLNPLECFVHSITSRDSSFS---SNADLpGTLFRKLMFFMRDIYVAYDGTVR 744
RNAP_A'' cd06528
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
1054-1477 2.07e-90

A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.


Pssm-ID: 132725 [Multi-domain]  Cd Length: 363  Bit Score: 298.78  E-value: 2.07e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1054 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1133
Cdd:cd06528   10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1134 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyyDpnpqstvvaedqewvnvYYEMPdfdvarispwlLR 1213
Cdd:cd06528   90 PSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI--D-----------------LFNMR-----------IT 139
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1214 VELDRKHMTDRKLTMEQIAEKINAGFGDDlncIFNDDNAEKLVLRIrimnsDENKMQEEEEVVDKmdddvflrciesnmL 1293
Cdd:cd06528  140 IELDEEMLEDRGITVDDVLKAIEKLKKGK---VGEEGDVTLIVLKA-----EEPSIKELRKLAEK--------------I 197
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1294 TDMTLQGIEQISKVymhlpqtdnkkkIIITEDGefkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEA 1373
Cdd:cd06528  198 LNTKIKGIKGIKRV------------IVRKEED------EYVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEA 259
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1374 VRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKG 1453
Cdd:cd06528  260 ARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRG 339
                        410       420
                 ....*....|....*....|....
gi 4505939  1454 VSENIMLGQLAPAGTGCFDLLLDA 1477
Cdd:cd06528  340 VIENIIVGQPIPLGTGDVELTMDP 363
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
1052-1479 2.20e-88

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 294.06  E-value: 2.20e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1052 RRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1131
Cdd:PRK04309   27 REKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1132 KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaeDqewvnvYYEMpdfdvarispwL 1211
Cdd:PRK04309  107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------T 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1212 LRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKMQEEEEVVDKmdddvflrciesn 1291
Cdd:PRK04309  157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK------------- 213
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1292 mLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:PRK04309  214 -IRNIKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGI 274
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:PRK04309  275 EAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDEL 354
                         410       420
                  ....*....|....*....|....*...
gi 4505939   1452 KGVSENIMLGQLAPAGTGCFDLLLDAEK 1479
Cdd:PRK04309  355 KGVTENIIVGQPIPLGTGDVELTMDPPL 382
RNA_pol_rpoA2 TIGR02389
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1054-1476 5.76e-85

DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274105 [Multi-domain]  Cd Length: 367  Bit Score: 283.48  E-value: 5.76e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1054 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1133
Cdd:TIGR02389   14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1134 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlLR 1213
Cdd:TIGR02389   94 PSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VI 143
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1214 VELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeklVLRIRIMNSDenkmQEEEEVVDKMDDDVF--LRCIEsN 1291
Cdd:TIGR02389  144 IELDEEQLKERGITVDDVEKAIKK------------------AKLGKVIEID----MDNNTITIKPGNPSLkeLRKLK-E 200
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1292 MLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:TIGR02389  201 KIKNLHIKGIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGI 262
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:TIGR02389  263 EAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDEL 342
                          410       420
                   ....*....|....*....|....*
gi 4505939    1452 KGVSENIMLGQLAPAGTGCFDLLLD 1476
Cdd:TIGR02389  343 KGVIENIIVGQPIPLGTGDVDLVMD 367
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
20-1135 2.98e-76

DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274103 [Multi-domain]  Cd Length: 1140  Bit Score: 278.09  E-value: 2.98e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      20 RVQFGVLSPDELKRMSvtEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 77
Cdd:TIGR02386    1 AIKISIASPDTIRNWS--YGEVKKPETInyRTLKPEKDGLFCEKifgptkdwecycgkykkiryKGVV-----CERCGVE 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939      78 MTECP---GHFGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKI--KDILAkskgqpkkrL 141
Cdd:TIGR02386   74 VTESKvrrERMGHIELAAPVAHIWYfkglpsrigllLDITAKELESVLYFENYVVLDPGDTKLdkKEVLD---------E 144
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     142 THVYDLCK----GKNICEGGEemdnkfGVEQPEGDEDLTKEkghggcgryqprIRRSGLELyaewKHVNEDSQEKKILls 217
Cdd:TIGR02386  145 TEYREVLKrygdGFRAGMGAE------AIKELLEKIDLDKE------------IEELKIQL----RESKSDQKRKKLL-- 200
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     218 pervheifKRISDEECFVLGMepryARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNG 297
Cdd:TIGR02386  201 --------KRLEIVEAFKDSG----NRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG 268
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     298 AAAHVIAEDVKLLQFHVATMVDNELPGLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQ 377
Cdd:TIGR02386  269 APEIIVRNEKRMLQEAVDALFDNGRRGKP-VVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQ 347
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     378 VGVPRSIAAnmtfaEIVTPFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqtgy 444
Cdd:TIGR02386  348 CGLPKKMAL-----ELFKPFIIKRLIDrelaaniksakkMIEQEDPEvWDVLEDVIKE---------HP----------- 402
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     445 kverhmcdgdiVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRM 524
Cdd:TIGR02386  403 -----------VLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNN 471
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     525 IVTPQSNRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVmnllmFLSTWDGKVPQPAILKPRP----LWT--GKQ 590
Cdd:TIGR02386  472 ILNPKDGKPIVTPSQDMvlglyyLTTEKPGAKGEgkIFSNVDEA-----IRAYDNGKVHLHALIGVRTsgeiLETtvGRV 546
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     591 IFSLIIPghincirthsthpddeDSGPYKHISPgdtkvvvengelimgILCKKSLgtsaGSLVHISYLEMGHDITRLFYS 670
Cdd:TIGR02386  547 IFNEILP----------------EGFPYINDNE---------------PLSKKEI----SSLIDLLYEVHGIEETAEMLD 591
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     671 NIQTVINNWLLIEGHTIGIGDSIadskTYQDIQNTIKKAKQDVIEVIEKAHNNELepTPGNTLRQTFEnqvnrILNDARD 750
Cdd:TIGR02386  592 KIKALGFKYATKSGTTISASDIV----VPDEKYEILKEADKEVAKIQKFYNKGLI--TDEERYRKVVS-----IWSETKD 660
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     751 KTGSSAQKSLS----EYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfven 825
Cdd:TIGR02386  661 KVTDAMMKLLKkdtyKFNPIFMMADSGARGNISQFRQLAGMRGlMAKPSGDIIELPIKS--------------------- 719
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     826 SYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKY-DATVRNSInQVVQLRYGEDglagESVEfq 904
Cdd:TIGR02386  720 SFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREeDCGTEEGI-EVEAIVEGKD----EIIE-- 792
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     905 nlaTLKpsnkafekkfrfdytnERALRRTLQEDLVKDVLSNAHIQ-NELerefermrEDREVLRVIFPTGDSKV----VL 979
Cdd:TIGR02386  793 ---SLK----------------DRIVGRYSAEDVYDPDTGKLIAEaNTL--------ITEEIAEKIENSGIEKVkvrsVL 845
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     980 PCNLLRMIwnAQKIFHINprlpsdlhpikvvegvkelskklvivngddpLSRQAqenatlLFNIhlrstlcsrrmaeefr 1059
Cdd:TIGR02386  846 TCESEHGV--CQKCYGRD-------------------------------LATGK------LVEI---------------- 870
                         1130      1140      1150      1160      1170      1180      1190
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4505939    1060 lsgeafdwllgeieskfnqaiahpGEMVGALAAQSLGEPATQMTLNTFHYAGVSA--KNVTLGVPRLKELINiSKKPK 1135
Cdd:TIGR02386  871 ------------------------GEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDITQGLPRVKELFE-ARTPK 923
RNA_pol_Rpb1_7 pfam04990
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
1164-1299 2.04e-75

RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561).


Pssm-ID: 461510 [Multi-domain]  Cd Length: 136  Bit Score: 246.29  E-value: 2.04e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1164 TTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA---RISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFG 1240
Cdd:pfam04990    1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDVEdldRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKEEFG 80
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939    1241 DDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQ 1299
Cdd:pfam04990   81 NDLFVIFSDDNAEKLVIRIRIINDEKEK---DEEQEDKAEDDVFLKRLEANMLDSLTLR 136
RNAP_III_Rpc1_C cd02736
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1075-1471 3.71e-72

Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.


Pssm-ID: 132723 [Multi-domain]  Cd Length: 300  Bit Score: 244.05  E-value: 3.71e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1075 KFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLgqSARDAERA 1154
Cdd:cd02736    1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLE--NDRDEKSA 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1155 KDILCRLEHTTLRKVTANTAIYYDPNpqstvvaedqewvNVYyempdfdvarispwlLRVELDRKHMTDRKLTMEQIAEK 1234
Cdd:cd02736   79 RIVKGRIEKTYLGEVASYIEEVYSPD-------------DCY---------------ILIKLDKKIIEKLQLSKSNLYFL 130
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1235 INagfgddlncifnddnaeklvlririmnsdenkmqeeeevvdkmdddvFLRciesNMLTDMTLQGIEQISKVYMHLPQT 1314
Cdd:cd02736  131 LQ-----------------------------------------------SLK----RKLPDVVVSGIPEVKRAVINKDKK 159
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1315 DNKKKIIItEDGEFKAlqewILETDGVslmrvlsekdvDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVN 1394
Cdd:cd02736  160 KGKYKLLV-EGYGLRA----VMNTPGV-----------IGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSID 223
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4505939  1395 YRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCF 1471
Cdd:cd02736  224 PRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
PRK14897 PRK14897
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
1053-1474 4.51e-69

unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional


Pssm-ID: 237853 [Multi-domain]  Cd Length: 509  Bit Score: 242.41  E-value: 4.51e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1053 RMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISK 1132
Cdd:PRK14897  151 KAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARK 230
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1133 KPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVtANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlL 1212
Cdd:PRK14897  231 KPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDV-ADIIT---------------------------DIAEMS---V 279
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1213 RVELDRKHMTDRKLTMEQIAEKInagfgddlncifnddnaEKLVLRIRIMNSDENKMQEEEEVVDKmdddvfLRCIESNm 1292
Cdd:PRK14897  280 VVELDEEKMKERLIEYDDILAAI-----------------SKLTFKTVEIDDGIIRLKPQQPSFKK------LYLLAEK- 335
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1293 LTDMTLQGIEQISKVymhlpqtdnkkkIIITEDGEfkalQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIE 1372
Cdd:PRK14897  336 VKSLTIKGIKGIKRA------------IARKENDE----RRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIE 399
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1373 AVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMK 1452
Cdd:PRK14897  400 AARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLA 479
                         410       420
                  ....*....|....*....|..
gi 4505939   1453 GVSENIMLGQLAPAGTGCFDLL 1474
Cdd:PRK14897  480 GVAENIIVGQPITLGTGAVSLV 501
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
20-948 2.36e-64

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 241.22  E-value: 2.36e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    20 RVQFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 77
Cdd:COG0086    9 AIKIGLASPEKI--RSWSYGEVKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    78 MTECP---GHFGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKIK--DILAKSKGQPKkrl 141
Cdd:COG0086   82 VTLSKvrrERMGHIELAMPVFHIWGlkslpsrigllLDMSLRDLERVLYFESYVVIDPGDTPLEkgQLLTEDEYREI--- 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   142 thvydlckgknICEGGEEMDNKFG---VEQPEGDEDLTKEKGhggcgryqprirrsglELYAEWKHVNedSQEKKIllsp 218
Cdd:COG0086  159 -----------LEEYGDEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK---- 205
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   219 ervhEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGA 298
Cdd:COG0086  206 ----KLIKRLKVVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKA 277
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   299 AAHVIAEDVKLLQFHVATMVDNELPGlpRAMQKSG-RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQ 377
Cdd:COG0086  278 PDIIVRNEKRMLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQ 355
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   378 VGVPRSIAanmtfAEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqtgykverhm 450
Cdd:COG0086  356 CGLPKKMA-----LELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------- 410
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   451 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 522
Cdd:COG0086  411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLST 477
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   523 RMIVTPQSNRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKVPQPAILKPRPLWTGKQ---- 590
Cdd:COG0086  478 NNILSPANGKPIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgki 552
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   591 --------IFSLIIP---GHINcirthsthpddedsgpykhispgdtKVvvengelimgiLCKKSLGTsagsLVHISYLE 659
Cdd:COG0086  553 vettvgryLVNEILPqevPFYN-------------------------QV-----------INKKHIEV----IIRQMYRR 592
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   660 MGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTyqdiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfEN 739
Cdd:COG0086  593 CGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YN 661
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   740 QVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpe 818
Cdd:COG0086  662 KVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS-------------- 727
                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   819 srgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGedgla 897
Cdd:COG0086  728 -------NFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEG----- 794
                        970       980       990      1000      1010
                 ....*....|....*....|....*....|....*....|....*....|.
gi 4505939   898 GESVEfqnlaTLKpsnkafekkfrfdytnERALRRTLQEDlVKDVLSNAHI 948
Cdd:COG0086  795 GEVIE-----PLK----------------ERILGRVAAED-VVDPGTGEVL 823
RNA_pol_Rpb1_3 pfam04983
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
525-691 1.67e-61

RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.


Pssm-ID: 461507  Cd Length: 158  Bit Score: 207.48  E-value: 1.67e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     525 IVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwdgKVPQPAILKP-RPLWTGKQIFSLIIPGHINCI 603
Cdd:pfam04983    2 ILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGI----VLPHPAILKPiKPLWTGKQTFSRLLPNEINPK 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     604 RTHSTHPDDEdsgpykhiSPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIE 683
Cdd:pfam04983   78 GKPKTNEEDL--------CENDSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKS 149

                   ....*...
gi 4505939     684 GHTIGIGD 691
Cdd:pfam04983  150 GFSIGIDD 157
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
244-874 2.72e-61

Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.


Pssm-ID: 259845 [Multi-domain]  Cd Length: 659  Bit Score: 223.93  E-value: 2.72e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   244 RPEWMIVTVLPVPPLSVRPAVVMQG-----SARNqdDLTHKladIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMV 318
Cdd:cd01609  138 RPEWMILTVLPVIPPDLRPMVQLDGgrfatSDLN--DLYRR---VINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALI 212
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   319 DNELPGLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFN 398
Cdd:cd01609  213 DNGRRGKP-VTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMA-----LELFKPFV 286
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   399 IdrlQELVRRGNSQYP-GAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRIL 477
Cdd:cd01609  287 I---RELIERGLAPNIkSAKKMIERKDPEV----------------WDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLI 347
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   478 PWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDT------LTAVRKFTKr 551
Cdd:cd01609  348 EGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMvlglyyLTKERKGDK- 426
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   552 dvflerGEVMnllmfLSTWDGKVpqpailkprplwtgkqIFSLIIPghincirthsthpddedsgpykhispgdtkvvvE 631
Cdd:cd01609  427 ------GEGI-----IETTVGRV----------------IFNEILP---------------------------------E 446
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   632 NGELIMGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGD-SIADSKtyqdiQNTIKKAK 710
Cdd:cd01609  447 GLPFINKTLKKKVL----KKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDiVVPPEK-----KEIIKEAE 517
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   711 QDVIEvIEKAHNNeleptpGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEY--NNFKSMVVSGAKGSKINISQVIAVV 788
Cdd:cd01609  518 EKVKE-IEKQYEK------GLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKDpfNPIYMMADSGARGSKSQIRQLAGMR 590
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   789 G-QQNVEGKRIPfgfkhrtLPhfIKDdygpesrgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKS 867
Cdd:cd01609  591 GlMAKPSGKIIE-------LP--IKS------------NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDV 649

                 ....*..
gi 4505939   868 MESVMVK 874
Cdd:cd01609  650 AQDVIVT 656
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
22-1116 9.11e-60

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 229.04  E-value: 9.11e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     22 QFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLM-------------------DPR-QGViertGRCQTCAGNMT 79
Cdd:PRK09603 1400 QLTLASPEKI--HSWSYGEVKKPETInyRTLKPERDGLFcmkifgptkdyeclcgkykKPRfKDI----GTCEKCGVAIT 1473
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     80 ECP---GHFGHIELAKPVFHVGFL------------VKtMKVLRCVCFFCSKLLV---------DSNNPKIK-DILAKSK 134
Cdd:PRK09603 1474 HSKvrrFRMGHIELATPVAHIWYVnslpsrigtllgVK-MKDLERVLYYEAYIVKepgeaaydnEGTKLVMKyDILNEEQ 1552
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    135 GQP-KKRLTHvydlcKGKNICEGGEEMdnKFGVEQPEGDEDLTKekghggcgryqprirrsgleLYAEWKHVNEDSQEKK 213
Cdd:PRK09603 1553 YQNiSRRYED-----RGFVAQMGGEAI--KDLLEEIDLITLLQS--------------------LKEEVKDTNSDAKKKK 1605
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    214 ILlspervheifKRISDEECFVLGMEpryaRPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRN 293
Cdd:PRK09603 1606 LI----------KRLKVVESFLNSGN----RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRL 1671
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    294 EQNGAAAHVIAEDVKLLQFHVATMVDNelpGLPRAMQKSG--RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDP 371
Cdd:PRK09603 1672 MELGAPEIIVRNEKRMLQEAVDVLFDN---GRSTNAVKGAnkRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGP 1748
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    372 NLSIDQVGVPRSIAanmtfAEIVTPFNIDRLQElvrRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHM 450
Cdd:PRK09603 1749 NLKMDECGLPKNMA-----LELFKPHLLSKLEE---RGYaTTLKQAKRMIEQKSNEV----------------WECLQEI 1804
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    451 CDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQS 530
Cdd:PRK09603 1805 TEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPAS 1884
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    531 NRPVMGIVQDTLTAVRKFT--KRDVFLER---GEVMNLLMFLST--WDGKVPQPAILKPRPLWT--GKQIFSLIIPGHIn 601
Cdd:PRK09603 1885 GKAVAIPSQDMVLGLYYLSleKSGVKGEHklfSSVNEIITAIDTkeLDIHAKIRVLDQGNIIATsaGRMIIKSILPDFI- 1963
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    602 cirthsthPDDEDSGPYKhispgdtkvvvengelimgilcKKSLGTsagsLVHISYLEMGHDITRLFYSNIQTVINNWll 681
Cdd:PRK09603 1964 --------PTDLWNRPMK----------------------KKDIGV----LVDYVHKVGGIGITATFLDNLKTLGFRY-- 2007
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    682 ieGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEViekahnnELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLS 761
Cdd:PRK09603 2008 --ATKAGISISMEDIITPKDKQKMVEKAKVEVKKI-------QQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIA 2078
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    762 E----YNNFKSMVVSGAKGSKINISQVIAVVGqqnVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFF 837
Cdd:PRK09603 2079 KdkegFNSIYMMADSGARGSAAQIRQLSAMRG---LMTK--PDGSIIET----------PIISNFKE-----GLNVLEYF 2138
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    838 FHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYdatvrnsinqvvqlrygEDGLAGESVEFQNLATLKPSNKAFE 917
Cdd:PRK09603 2139 NSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVS-----------------DDCGTHEGIEITDIAVGSELIEPLE 2201
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    918 kkfrfdytnERALRRTLQEDLVKDvlsnahIQNElerefermredrevlrvifptgdskVVLPCNLLRMIWNAQKIfhin 997
Cdd:PRK09603 2202 ---------ERIFGRVLLEDVIDP------ITNE-------------------------ILLYADTLIDEEGAKKV---- 2237
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    998 prlpsdlhpikvvegvKELSKKLVIVNgdDPLSRQAQENatllfnihlrstLCSRrmaeefrlsgeAFDWLLGEieskfn 1077
Cdd:PRK09603 2238 ----------------VEAGIKSITIR--TPVTCKAPKG------------VCAK-----------CYGLNLGE------ 2270
                        1130      1140      1150
                  ....*....|....*....|....*....|....*....
gi 4505939   1078 QAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKN 1116
Cdd:PRK09603 2271 GKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
PRK14898 PRK14898
DNA-directed RNA polymerase subunit A''; Provisional
1100-1478 2.65e-57

DNA-directed RNA polymerase subunit A''; Provisional


Pssm-ID: 237854 [Multi-domain]  Cd Length: 858  Bit Score: 215.53  E-value: 2.65e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1100 TQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyyDP 1179
Cdd:PRK14898  541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAI--DL 618
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1180 NPQStvvaedqewvnvyyempdfdvarispwlLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRI 1259
Cdd:PRK14898  619 WTQS----------------------------IKVELDEETLADRGLTIESVEEAIEKKLGVKID-------RKGTVLYL 663
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1260 RImnsdenkmqEEEEVVDkmdddvFLRCIESnmLTDMTLQGIEQISKVYMHLPQTDNKkkiiitedgefkalQEWILETD 1339
Cdd:PRK14898  664 KP---------KTPSYKA------LRKRIPK--IKNIVLKGIPGIERVLVKKEEHEND--------------EEYVLYTQ 712
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1340 GVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGV 1419
Cdd:PRK14898  713 GSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGV 792
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939   1420 NRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAE 1478
Cdd:PRK14898  793 AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDRE 851
RNAP_I_Rpa1_C cd02735
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1075-1474 3.10e-55

Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.


Pssm-ID: 132722 [Multi-domain]  Cd Length: 309  Bit Score: 195.49  E-value: 3.10e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1075 KFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKE-LINISKKPKTPSLTV-FLLGQSARDAE 1152
Cdd:cd02735    1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREiLMTASKNIKTPSMTLpLKNGKSAERAE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1153 RAK---------DILCRLEHTTLRKVTANTAIyydpnPQStvvaedQEWVNVYYEMPdfdvarispwllrveLDRKhmtd 1223
Cdd:cd02735   81 TLKkrlsrvtlsDVVEKVEVTEILKTIERVFK-----KLL------GKWCEVTIKLP---------------LSSP---- 130
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1224 rKLTMEQIAEKInagfgddlncifnddnAEKLVLRirimnsdenkmqeeeEVvdkmdddvflrciesnmltdmtlQGIEQ 1303
Cdd:cd02735  131 -KLLLLSIVEKL----------------ARKAVIR---------------EI-----------------------PGITR 155
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1304 ISKVYmhlpqTDNKKKiiitedgefkalQEWILETDGVSL--MRVLSEKdVDPVRTTSNDIVEIFTVLGIEAVRKALERE 1381
Cdd:cd02735  156 CFVVE-----EDKGGK------------TKYLVITEGVNLaaLWKFSDI-LDVNRIYTNDIHAMLNTYGIEAARRAIVKE 217
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1382 LYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVnRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLG 1461
Cdd:cd02735  218 ISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVG 296
                        410
                 ....*....|...
gi 4505939  1462 QLAPAGTGCFDLL 1474
Cdd:cd02735  297 KPVNGGTGLFDLL 309
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
16-1469 3.11e-54

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 211.02  E-value: 3.11e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     16 RTIKRVQFGVLSPDELKRMS------VTEGGIKYPETTEGGR--PKLGGLMDPRQGVIER------TGR-CQTCAGNMTE 80
Cdd:PRK14844 1446 QSFNEVSISIASPESIKRMSygeiedVSTANYRTFKVEKGGLfcPKIFGPVNDDECLCGKykkrrhRGRiCEKCGVEVTS 1525
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     81 CP---GHFGHIELAKPVFHVGFLvKTMKvlrcvcffcSKL--LVDSNNPKIKDILAKSKGQPKKRLTHVYDlcKGKNICE 155
Cdd:PRK14844 1526 SKvrrERMGHIELASPVAHIWFL-KSLP---------SRIgaLLDMSLRDIENILYSDNYIVIDPLVSPFE--KGEIISE 1593
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    156 GG-EEMDNKFGVEQ---PEGDED----LTKEKGHggcgryqpRIRRsglELYAEWKHVNEDSQEKKILlspervheifKR 227
Cdd:PRK14844 1594 KAyNEAKDSYGIDSfvaMQGVEAirelLTRLDLH--------EIRK---DLRLELESVASEIRRKKII----------KR 1652
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    228 ISDEECFVLGMEpryaRPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDV 307
Cdd:PRK14844 1653 LRIVENFIKSGN----RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEK 1728
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    308 KLLQFHVATMVDNELPGlpRAMQKSGRP--LKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIA 385
Cdd:PRK14844 1729 RMLQEAVDSLFDNSRRN--ALVNKAGAVgyKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMA 1806
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    386 anmtfAEIVTPFNIDRLQELVRRGNSQYpgAKYIIRDNgdridlrfHPKPSDLHLQTgykVERHMcdgdiVIFNRQPTLH 465
Cdd:PRK14844 1807 -----LELFKPFVYSKLKMYGMAPTIKF--ASKLIRAE--------KPEVWDMLEEV---IKEHP-----VLLNRAPTLH 1863
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    466 KMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAV 545
Cdd:PRK14844 1864 RLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGI 1943
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    546 RKFT----KRD---VFLERGEVMNllmflSTWDGKVpqpailkprplwtgkqifsliipgHINC-IRTHSTHPDDEDSGP 617
Cdd:PRK14844 1944 YYLTlqepKEDdlpSFGAFCEVEH-----SLSDGTL------------------------HIHSsIKYRMEYINSSGETH 1994
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    618 YKHISPGDTKVVV-------EN--GELIMGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIG 688
Cdd:PRK14844 1995 YKTICTTPGRLILwqifpkhENlgFDLINQVLTVKEI----TSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFS 2070
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    689 IGDSIADSKTYQDIQNT---IKKAK---QDVIEVIEKAHNNELEptpgntlrqTFENQVNRILNDARDKTgsSAQKSLSE 762
Cdd:PRK14844 2071 RCDMVIPETKATHVDHArgeIKKFSmqyQDGLITRSERYNKVID---------EWSKCTDMIANDMLKAI--SIYDGNSK 2139
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    763 YNNFKSMVVSGAKGSKiniSQVIAVVGQQNVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFFFHAMG 842
Cdd:PRK14844 2140 YNSVYMMVNSGARGST---SQMKQLAGMRGLMTK--PSGEIIET----------PIISNFRE-----GLNVFEYFNSTHG 2199
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    843 GREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVefqnlatlkpsnkafekkfr 921
Cdd:PRK14844 2200 ARKGLADTALKTANSGYLTRRLVDvSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESV-------------------- 2259
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    922 fdytnerALRRTLQEDLVKDVlsnahIQNELEREFERMREDRevlrvifptgdskvvlpcnllrmiwnaqkifhinprlp 1001
Cdd:PRK14844 2260 -------VLGRTAANDIYNPV-----TKELLVKAGELIDEDK-------------------------------------- 2289
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1002 sdlhpikvvegVKELS-KKLVIVNGDDPLSRQAQENAtllfnihlrSTLCSRRmaeefrlsgeafDWLLGEIESKfnqai 1080
Cdd:PRK14844 2290 -----------VKQINiAGLDVVKIRSPLTCEISPGV---------CSLCYGR------------DLATGKIVSI----- 2332
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1081 ahpGEMVGALAAQSLGEPATQMTLNTFHYAGVsaknVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDA-ERAKDILC 1159
Cdd:PRK14844 2333 ---GEAVGVIAAQSVGEPGTQLTMRTFHIGGV----MTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIViSRSCEVVL 2405
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1160 -------RLEHTtlrkVTANTAIYYDPNPQSTVVAEDQEW-------------VNVYYEMPD------------------ 1201
Cdd:PRK14844 2406 idslgseKLKHS----VPYGAKLYVDEGGSVKIGDKVAEWdpytlpiitektgTVSYQDLKDgisitevmdestgisskv 2481
                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1202 -------FDVARISPWLLRVELDRKHMTdrkltmeqIAEKINAGFGDDLNCIFNDDNAEK-----LVLRI---------- 1259
Cdd:PRK14844 2482 vkdwklySGGANLRPRIVLLDDNGKVMT--------LASGVEACYFIPIGAVLNVQDGQKvhagdVITRTpresvktrdi 2553
                        1370      1380      1390      1400      1410      1420      1430      1440
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1260 -----RIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGI-EQISKVYMHLpqtdNKKKIIITEDGEFkaLQE 1333
Cdd:PRK14844 2554 tgglpRVIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKRSILIKPVdEQISPVEYLV----SRSKHVIVNEGDF--VRK 2627
                        1450      1460      1470      1480      1490      1500      1510      1520
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1334 WILETDGvslmrvlsekdvDPvrttsnDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLC----------- 1402
Cdd:PRK14844 2628 GDLLMDG------------DP------DLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILkqmlqkveitd 2689
                        1530      1540      1550      1560      1570      1580      1590      1600
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1403 --DTMTCRGHlmAITRHGVNRQDTG------------PLMK---------------CSFEETVDVLMEAAAHGESDPMKG 1453
Cdd:PRK14844 2690 pgDTMYLVGE--SIDKLEVDRENDAmsnsgkrpahylPILQgitrasletssfisaASFQETTKVLTEAAFCGKSDPLSG 2767
                        1610
                  ....*....|....*.
gi 4505939   1454 VSENIMLGQLAPAGTG 1469
Cdd:PRK14844 2768 LKENVIVGRLIPAGTG 2783
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
244-1135 9.82e-54

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 208.19  E-value: 9.82e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    244 RPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELP 323
Cdd:PRK14906  311 DPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRR 390
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    324 GLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFNIDRLQ 403
Cdd:PRK14906  391 GRP-VTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMA-----LELFKPFVMKRLV 464
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    404 ELVRRGNSQypGAKYIIrdngdridlrfhpkpsDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFR 483
Cdd:PRK14906  465 ELEYAANIK--AAKRAV----------------DRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIK 526
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    484 LNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFT-KRDVFLERGEVmn 562
Cdd:PRK14906  527 LHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTtERDGFEGEGRT-- 604
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    563 llmFLSTWDGkvpqpailkprplwtgkqifsliipghincIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMgilCK 642
Cdd:PRK14906  605 ---FADFDDA------------------------------LNAYDARADLDLQAKIVVRLSRDMTVRGSYGDLEE---TK 648
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    643 --KSLGTSAGSLV----------HISYLEMGHDITRLfysnIQTVINNWLLIEGHTI---------------GIGDSIAD 695
Cdd:PRK14906  649 agERIETTVGRIIfnqvlpedypYLNYKMVKKDIGRL----VNDCCNRYSTAEVEPIldgikktgfhyatraGLTVSVYD 724
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    696 SKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPtpgntlrQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAK 775
Cdd:PRK14906  725 ATIPDDKPEILAEADEKVAAIDEDYEDGFLSE-------RERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGAR 797
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    776 GSKINISQVIAVVG-QQNVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFHAMGGREGLIDTAVKT 854
Cdd:PRK14906  798 GNIKQIRQLAGMRGlMADMKGEII-------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRT 856
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    855 AETGYIQRRLiksmesVMVKYDATVRNsinqvvqlrygEDGLAGESVEfqnlatlkpsnkafekkfrFDYTNERAlrrTL 934
Cdd:PRK14906  857 ADSGYLTRRL------VDVAQDVIVRE-----------EDCGTDEGVT-------------------YPLVKPKG---DV 897
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    935 QEDLVKDVLSNAHIQNELErefermredrevlrVIFPTGDskvvlpcnllrmiwnaqkifhinprlpsdlhpikvvegvk 1014
Cdd:PRK14906  898 DTNLIGRCLLEDVCDPNGE--------------VLLSAGD---------------------------------------- 923
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1015 elskklvIVNGDDPLSRQAQENATllfNIHLRSTLCSRrmaEEFRLSGEAFDWLLgeieskfnqAIAHP---GEMVGALA 1091
Cdd:PRK14906  924 -------YIESMDDLKRLVEAGVT---KVQIRTLMTCH---AEYGVCQKCYGWDL---------ATRRPvniGTAVGIIA 981
                         890       900       910       920
                  ....*....|....*....|....*....|....*....|....
gi 4505939   1092 AQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIsKKPK 1135
Cdd:PRK14906  982 AQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEA-RKPK 1024
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
244-1137 1.33e-53

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 206.84  E-value: 1.33e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    244 RPEWMIVTVLPVPPLSVRPAVVMQG-----SARNqdDLTHKLadivkI--NNQLRR------------NEQngaaahvia 304
Cdd:PRK00566  223 KPEWMILDVLPVIPPDLRPLVQLDGgrfatSDLN--DLYRRV-----InrNNRLKRllelgapeiivrNEK--------- 286
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    305 edvKLLQFHVATMVDNELPGlpRAMQ-KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRS 383
Cdd:PRK00566  287 ---RMLQEAVDALFDNGRRG--RPVTgPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKK 361
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    384 IAanmtfAEIVTPFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqtgykverhm 450
Cdd:PRK00566  362 MA-----LELFKPFIMKKLVErglattiksakkMVEREDPEvWDVLEEVIKE---------HP----------------- 410
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    451 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPwstfrLnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 522
Cdd:PRK00566  411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHP-----L---VCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSS 477
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    523 RMIVTPQSNRPVmgIV--QD------TLTAVRKFTKrdvflerGEVMnllMFLSTWD-------GKVPQPAILKPRP--- 584
Cdd:PRK00566  478 NNILSPANGKPI--IVpsQDmvlglyYLTREREGAK-------GEGM---VFSSPEEalrayenGEVDLHARIKVRItsk 545
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    585 --LWT--GKQIFSLIIPGHIncirthsthpddedsgPYkhispgdtkvvvENGELIMGilcKKSLgtsaGSLVHISYLEM 660
Cdd:PRK00566  546 klVETtvGRVIFNEILPEGL----------------PF------------INVNKPLK---KKEI----SKIINEVYRRY 590
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    661 GHDITRLFYSNIQTVINNWLLIEGHTIGIGD-SIADSKtyQDIqntIKKAKQDVIEvIEKAHNNELeptpgntlrQTFE- 738
Cdd:PRK00566  591 GLKETVIFLDKIKDLGFKYATRSGISIGIDDiVIPPEK--KEI---IEEAEKEVAE-IEKQYRRGL---------ITDGe 655
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    739 --NQVNRILNDARDKTGSSAQKSLSEYNN-FKS---MVVSGAKGSKINISQVIAVVG-QQNVEGKRIPfgfkhrtLPhfI 811
Cdd:PRK00566  656 ryNKVIDIWSKATDEVAKAMMKNLSKDQEsFNPiymMADSGARGSASQIRQLAGMRGlMAKPSGEIIE-------TP--I 726
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    812 KddygpesrgfveNSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLiksmesVMVKYDATVRN----SINQVV 887
Cdd:PRK00566  727 K------------SNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRL------VDVAQDVIVREddcgTDRGIE 788
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    888 QLRYGEDGLAGESVEfqnlatlkpsnkafekkfrfdytnERALRRTLQEDLVKDVLSNahiqnelerefermredrevlr 967
Cdd:PRK00566  789 VTAIIEGGEVIEPLE------------------------ERILGRVLAEDVVDPETGE---------------------- 822
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    968 VIFPTGDskvvlpcnLLRMIWnAQKIfhinprlpsdlhpikVVEGVKElskklvivngddplsrqaqenatllfnIHLRS 1047
Cdd:PRK00566  823 VIVPAGT--------LIDEEI-ADKI---------------EEAGIEE---------------------------VKIRS 851
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1048 TL-CsrrmaeefrlsgeafdwllgeiESKF---------NQAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVsa 1114
Cdd:PRK00566  852 VLtC----------------------ETRHgvcakcygrDLATGKLvniGEAVGVIAAQSIGEPGTQLTMRTFHTGGV-- 907
                         970       980
                  ....*....|....*....|...
gi 4505939   1115 kNVTLGVPRLKELINiSKKPKTP 1137
Cdd:PRK00566  908 -DITGGLPRVAELFE-ARKPKGP 928
RNA_pol_Rpb1_4 pfam05000
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
717-823 2.50e-45

RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.


Pssm-ID: 398598  Cd Length: 108  Bit Score: 159.45  E-value: 2.50e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     717 IEKA-HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEG 795
Cdd:pfam05000    1 ITDAeRYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
                           90       100
                   ....*....|....*....|....*...
gi 4505939     796 KRIPFGFKHRTLPHFIKDDYGPESRGFV 823
Cdd:pfam05000   81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
243-540 4.52e-42

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 165.31  E-value: 4.52e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    243 ARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNEL 322
Cdd:PRK02625  240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    323 PGlPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFNIDRl 402
Cdd:PRK02625  320 RG-RTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMA-----IELFQPFVIHR- 392
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    403 qeLVRRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWST 481
Cdd:PRK02625  393 --LIRQGIvNNIKAAKKLIQRADPEV----------------WQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRA 454
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939    482 FRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQD 540
Cdd:PRK02625  455 IQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQD 513
rpoC1 CHL00018
RNA polymerase beta' subunit
86-514 7.16e-40

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 159.30  E-value: 7.16e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     86 GHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNpkiKDILAKSKGqpkkrlTHVYDLCKGKNIc 154
Cdd:CHL00018  105 GYIKLACPVTHVWYlkrlpsyianlLDKPLKELEGLVYCDFSFARPIAK---KPTFLRLRG------LFEYEIQSWKYS- 174
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    155 eggeemDNKFgVEQPEGDEDLTKEKGHGGcgryqPRIRR--SGLEL-------YAEWKHVNEDSQ------EKKILLspe 219
Cdd:CHL00018  175 ------IPLF-FSTQGFDTFRNREISTGA-----GAIREqlADLDLriiidnsLVEWKELGEEGStgneweDRKIGR--- 239
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    220 RVHEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRR--NEQNG 297
Cdd:CHL00018  240 RKDFLVRRIKLAKHFIR----TNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDllTTSRS 315
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    298 AAAHVIAEDVKLLQFHVATMVDNELPGLPraMQKS-GRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSID 376
Cdd:CHL00018  316 TPGELVMCQKKLLQEAVDALLDNGIRGQP--MRDGhNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLH 393
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    377 QVGVPRSIAanmtfAEIVTPFNIdrlQELVRRGNSQYPG-AKYIIRDNGDRIDlrfhpkpsdlhlqtgyKVERHMCDGDI 455
Cdd:CHL00018  394 QCGLPREIA-----IELFQPFVI---RGLIRQHLASNIRaAKSKIREKEPIVW----------------EILQEVMQGHP 449
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4505939    456 VIFNRQPTLHKMSMM--------GHRVRILPwstfrlnlSVTTPYNADFDGDEMNLHLPQSLETRAE 514
Cdd:CHL00018  450 VLLNRAPTLHRLGIQafqpilveGRAICLHP--------LVCKGFNADFDGDQMAVHVPLSLEAQAE 508
RNAP_largest_subunit_C cd00630
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1361-1470 1.59e-38

Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.


Pssm-ID: 132719 [Multi-domain]  Cd Length: 158  Bit Score: 141.79  E-value: 1.59e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1361 DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM 1440
Cdd:cd00630   49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128
                         90       100       110
                 ....*....|....*....|....*....|
gi 4505939  1441 EAAAHGESDPMKGVSENIMLGQLAPAGTGC 1470
Cdd:cd00630  129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158
RNAP_largest_subunit_C cd00630
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1084-1131 4.41e-21

Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.


Pssm-ID: 132719 [Multi-domain]  Cd Length: 158  Bit Score: 91.71  E-value: 4.41e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 4505939  1084 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1131
Cdd:cd00630    1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
1854-1959 4.83e-15

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 81.12  E-value: 4.83e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1854 TP--TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1931
Cdd:pfam05109  517 TPnaTSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVG 596
                           90       100
                   ....*....|....*....|....*...
gi 4505939    1932 PTSPKGSTYSPTSPGyspTSPTYSLTSP 1959
Cdd:pfam05109  597 ETSPQANTTNHTLGG---TSSTPVVTSP 621
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
764-1117 3.92e-12

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 71.95  E-value: 3.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    764 NNFKS---------MVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 830
Cdd:PRK02597  111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    831 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGESVEFQNlatl 909
Cdd:PRK02597  167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    910 kpsnkafekkfrfdytneRALRRTLQEDLVKDvlsnahiqnelerefermreDREVLrvifptgdskvvlpcnllrmiwn 989
Cdd:PRK02597  238 ------------------RLLGRVLAEDVVDP--------------------EGEVI----------------------- 256
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    990 AQKIFHINPRLPsdlhpiKVVE--GVKElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDW 1067
Cdd:PRK02597  257 AERNTAIDPDLA------KKIEkaGVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYGW 300
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 4505939   1068 LLgeieskfnqAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1117
Cdd:PRK02597  301 SL---------AHNHLvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
rpoC2_cyan TIGR02388
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
764-1234 6.98e-12

DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274104 [Multi-domain]  Cd Length: 1227  Bit Score: 71.03  E-value: 6.98e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     764 NNFKSMVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFH 839
Cdd:TIGR02388  119 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 174
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     840 AMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqvvQLRYGEDGlaGESVEFQNlatlkpsnkafek 918
Cdd:TIGR02388  175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTERSI----VVRAMTEG--DKKISLGD------------- 235
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     919 kfrfdytneRALRRTLQEDLVkdvlsnaHIQNElerefermredrevlrVIFPTGDSkvvlpcnllrmiwnaqkifhINP 998
Cdd:TIGR02388  236 ---------RLLGRLVAEDVL-------HPEGE----------------VIVPKNTA--------------------IDP 263
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     999 RLPSDLHPIKVVEgvkelskklviVNGDDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDWllgeieskfnq 1078
Cdd:TIGR02388  264 DLAKTIETAGISE-----------VVVRSPLTCEAA-----------RS-VCRK-----------CYGW----------- 298
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1079 AIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGV-PRLKELINISKKPKT-PSLTVFllGQSARDA 1151
Cdd:TIGR02388  299 SLAHAhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVrSKIDGTVEFGKKLRTrGYRTRH--GEDAKQV 376
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1152 ERAKDILCRlehttLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDF--------------DVA-RISPWLLRVEL 1216
Cdd:TIGR02388  377 EVAGLLIIK-----PTGSITNKAQEIEVTQGSLLFVEDGQTVDAGQLLAEIalgavrkstekatkDVAsDLAGEVKFDKV 451
                          490
                   ....*....|....*...
gi 4505939    1217 DRKHMTDRKLTMEQIAEK 1234
Cdd:TIGR02388  452 VPEEKTDRQGNTTRIAQR 469
RNAP_beta'_C cd02655
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1084-1127 5.94e-11

Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.


Pssm-ID: 132721 [Multi-domain]  Cd Length: 204  Bit Score: 63.70  E-value: 5.94e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 4505939  1084 GEMVGALAAQSLGEPATQMTLNTFHYAGVsAKNVTLGVPRLKEL 1127
Cdd:cd02655    6 GEAVGIIAAQSIGEPGTQLTMRTFHTGGV-ATDITQGLPRVEEL 48
RNAP_IV_NRPD1_C cd02737
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1084-1475 6.13e-11

Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.


Pssm-ID: 132724 [Multi-domain]  Cd Length: 381  Bit Score: 66.68  E-value: 6.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1084 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAknvtlgVPRLKELI--NISKKPKTPSLTVFL---LGQSARDAE---RAK 1155
Cdd:cd02737    1 GEPVGSLAATAISEPAYKALLDPPQSLESSP------LELLKEVLecRSKSKSKENDRRVILslhLCKCDHGFEyerAAL 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1156 DILCRLEHTTLRKVTANTAIYYDPNPQstvvaedqewvnvyyEMPDFDVARISPWLLRVELDRKHMTDRKLTmeqiaeKI 1235
Cdd:cd02737   75 EVKNHLERVTLEDLATTSMIKYSPQAT---------------EAIVGEIGDQLNTKKKGKKKAIFSTSLKIT------KF 133
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1236 NAGfgddlNCIFNDDNAEKLVLR---IRIMNSDENKmQEEEEVVDKMDDDVFlrciesNMLTDMTLQGIEQISKVYMhLP 1312
Cdd:cd02737  134 SPW-----VCHFHLDKECQKLSDgpcLTFSVSKEVS-KSSEELLDVLRDRII------PFLLETVIKGDERIKSVNI-LW 200
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1313 QTDNKKKIIITEDGEFKAlqEWILETdGVSLMRVLSEKD---------------VDPVRTTSNDIVEIFTVLGIEAVRKA 1377
Cdd:cd02737  201 EDSPSTSWVKSVGKSSRG--ELVLEV-TVEESCKKTRGNawnvvmdacipvmdlIDWERSMPYSIQQIKSVLGIDAAFEQ 277
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1378 LERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDT-----GPLMKCSFEETVDVLMEAAAHGESDPMK 1452
Cdd:cd02737  278 FVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRslkisAPFTEACFSSPIKCFLKAAKKGASDSLS 357
                        410       420
                 ....*....|....*....|....
gi 4505939  1453 GVSENIMLGQLAPAGTGC-FDLLL 1475
Cdd:cd02737  358 GVLDACAWGKEAPVGTGSkFEILW 381
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
1491-1610 3.19e-10

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 59.46  E-value: 3.19e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     1491 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1563
Cdd:smart01104   15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 4505939     1564 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1610
Cdd:smart01104   91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
PARM pfam17061
PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present ...
1854-1970 1.30e-08

PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present in most tissues, with high levels in the heart, kidney and placenta. It has been shown to be induced and expressed in prostate after castration and may have a role in cell proliferation and immortalization in prostate cancer.


Pssm-ID: 465341 [Multi-domain]  Cd Length: 296  Bit Score: 58.72  E-value: 1.30e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1854 TPTSPKY--SPTSPKYSPTSPKySPTSPTYSPTTPKYSPTSPT----------YSPTSPV-------YTPTSPKYSPTS- 1913
Cdd:pfam17061   22 TPPTATWtsSPQNTAAVTASPT-SGTHNNSVLPVTASAPTSPLpknvsvepreEESTSPAsnwegtsTDPSPPGLSPTSs 100
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505939    1914 -----PT---YSPTSPKYS-PT----SPTYSP--TSPKGSTYSPTSPgysPTSPTySLTSPAISPDDSDEEN 1970
Cdd:pfam17061  101 gvhltPTpeeHSSGTPETSvPAtgsqSPAESPtlTSPQAPASSPSSP---STSPP-EVSSASVTTNHSSTET 168
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
1431-1469 3.60e-07

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 55.77  E-value: 3.60e-07
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 4505939   1431 SFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTG 1469
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
rpoC2 CHL00117
RNA polymerase beta'' subunit; Reviewed
1084-1112 8.89e-07

RNA polymerase beta'' subunit; Reviewed


Pssm-ID: 214368 [Multi-domain]  Cd Length: 1364  Bit Score: 54.56  E-value: 8.89e-07
                          10        20
                  ....*....|....*....|....*....
gi 4505939   1084 GEMVGALAAQSLGEPATQMTLNTFHYAGV 1112
Cdd:CHL00117  315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
1853-1967 1.68e-06

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 52.83  E-value: 1.68e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1853 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1929
Cdd:COG3469   89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168
                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 4505939  1930 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSD 1967
Cdd:COG3469  169 TTTTTSASTTPSATTTATATTASGATTPSATTTATTTG 206
rpoC2 CHL00117
RNA polymerase beta'' subunit; Reviewed
761-865 1.80e-06

RNA polymerase beta'' subunit; Reviewed


Pssm-ID: 214368 [Multi-domain]  Cd Length: 1364  Bit Score: 53.40  E-value: 1.80e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    761 SEY------NNFKS---------MVVSGAKGskiNISQVIAVVG--------QqnveGKRIpfgfkhrTLPhfIKddygp 817
Cdd:CHL00117  108 SEYlkqemnPNFRMtdplnpvymMSFSGARG---NASQVHQLVGmrglmsdpQ----GQII-------DLP--IQ----- 166
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 4505939    818 esRGFVEnsylaGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLI 865
Cdd:CHL00117  167 --SNFRE-----GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLV 207
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
1871-1963 8.15e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 51.07  E-value: 8.15e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1871 SPKYSPTSPTYSpTTPKYSPTSPTYSP------------------------TSPVYTPTSPKYSPTSPTYSP-------- 1918
Cdd:pfam05109  424 APESTTTSPTLN-TTGFAAPNTTTGLPssthvptnltapastgptvstadvTSPTPAGTTSGASPVTPSPSPrdngtesk 502
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 4505939    1919 ----TSPKYSPTSPTYSPTSPKGSTYSP----TSPGYSPTSPTYSLTSP---AISP 1963
Cdd:pfam05109  503 apdmTSPTSAVTTPTPNATSPTPAVTTPtpnaTSPTLGKTSPTSAVTTPtpnATSP 558
PHA03291 PHA03291
envelope glycoprotein I; Provisional
1858-1962 1.01e-05

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 50.34  E-value: 1.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1858 PKYSPTSPKYSPTSPKYSPTSpTYSPTTPKYSPTSPTYSPTSPvyTPTSPKySPTSPTYSPTSPKYSPTSPTYSPTSPkg 1937
Cdd:PHA03291  181 SADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTASPETTP--TPSTTT-SPPSTTIPAPSTTIAAPQAGTTPEAE-- 254
                          90       100
                  ....*....|....*....|....*
gi 4505939   1938 STYSPTSPGYSPTSPTYSLTSPAIS 1962
Cdd:PHA03291  255 GTPAPPTPGGGEAPPANATPAPEAS 279
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
1875-1969 1.15e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 50.19  E-value: 1.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1875 SPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPT--YSPTSPKGSTYSPTSPGYSPTSP 1952
Cdd:PRK14950  370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTpeSAPKLTRAAIPVDEKPKYTPPAP 449
                          90
                  ....*....|....*..
gi 4505939   1953 TYSLTSPAISPDDSDEE 1969
Cdd:PRK14950  450 PKEEEKALIADGDVLEQ 466
rpoC2 CHL00117
RNA polymerase beta'' subunit; Reviewed
1431-1470 1.88e-05

RNA polymerase beta'' subunit; Reviewed


Pssm-ID: 214368 [Multi-domain]  Cd Length: 1364  Bit Score: 49.94  E-value: 1.88e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 4505939   1431 SFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGC 1470
Cdd:CHL00117 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
1855-1968 5.57e-05

Protein of unknown function (DUF1373); This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown.


Pssm-ID: 462093 [Multi-domain]  Cd Length: 212  Bit Score: 46.32  E-value: 5.57e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1855 PTSPKYSPTSPKYSPTSPKY----SPTSP-TYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPT 1929
Cdd:pfam07117   33 PLPPGQEPEPPRPEEEEGQGggggTFPFPgSPEPEPGGGGSGPMPMSASAPEPEPAKAKPQRPAPAQGHGHGGGGDSDSS 112
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 4505939    1930 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDE 1968
Cdd:pfam07117  113 GSGSGHQGSGGAGAGAGAPGHQHEQEQESSSSDDDDEDE 151
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
1854-1938 5.69e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 48.27  E-value: 5.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1854 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPkySPTSPTYSPTSPKYSPTSPTYSPT 1933
Cdd:PRK14950  370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPH--TPESAPKLTRAAIPVDEKPKYTPP 447

                  ....*
gi 4505939   1934 SPKGS 1938
Cdd:PRK14950  448 APPKE 452
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
1865-1960 5.88e-05

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 44.43  E-value: 5.88e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     1865 PKYSPTSPKYSPTSPTysPTTPKYSPTSPTYSpTSPVYTPTS---PKYSPTSPTYSPTSPKY--SPTSPTYSPTSPKGST 1939
Cdd:smart01104   15 PAWGSRTPGTAAGGAP--TARGGSGSRTPAWG-GAGSRTPAWggaGPTGSRTPAWGGASAWGnkSSEGSASSWAAGPGGA 91
                            90       100
                    ....*....|....*....|.
gi 4505939     1940 YSPTSPGYSPTSPTYSLTSPA 1960
Cdd:smart01104   92 YGAPTPGYGGTPSAYGPATPG 112
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
1852-1957 6.25e-05

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 47.83  E-value: 6.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939  1852 EYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYS------PTSPVYTPTSPKYSPTSPTYSPTSPKYSP 1925
Cdd:COG3469  109 TSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVsgtetaTGGTTTTSTTTTTTSASTTPSATTTATAT 188
                         90       100       110
                 ....*....|....*....|....*....|..
gi 4505939  1926 TSPTYSPTSPKGSTysPTSPGYSPTSPTYSLT 1957
Cdd:COG3469  189 TASGATTPSATTTA--TTTGPPTPGLPKHVLV 218
Endomucin pfam07010
Endomucin; This family consists of several mammalian endomucin proteins. Endomucin is an early ...
1868-1959 8.31e-05

Endomucin; This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.


Pssm-ID: 429246 [Multi-domain]  Cd Length: 260  Bit Score: 46.40  E-value: 8.31e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1868 SPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTS--PKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSP 1945
Cdd:pfam07010   29 ANITLSTTPSTTAETASTPKTTNLNTPTGGTSPVGTTSSelSKTSLVSTTISLTTTKKGVGTTTTDVSKNESSTTKPTVT 108
                           90
                   ....*....|....
gi 4505939    1946 GYSPTSPTYSLTSP 1959
Cdd:pfam07010  109 STPLSNAVSTLQSS 122
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
1854-1960 1.08e-04

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 46.87  E-value: 1.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1854 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPT 1933
Cdd:PTZ00436  232 AAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAA 311
                          90       100       110
                  ....*....|....*....|....*....|.
gi 4505939   1934 SPKGSTYSP----TSPGYSPTSPTYSLTSPA 1960
Cdd:PTZ00436  312 APAKAAAPPakaaAPPAKAATPPAKAAAPPA 342
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
1870-1942 1.46e-04

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 46.43  E-value: 1.46e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4505939    1870 TSPKYSPTSPTYSPTTPKYSPTSptySPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP 1942
Cdd:TIGR00601   75 SKPKTGTGKVAPPAATPTSAPTP---TPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS 144
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
1855-1966 1.79e-04

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 46.46  E-value: 1.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1855 PTSPkySPTSPKYSPTSPKYSPTSPTySPTTPKYSPTSPTYSPTSPVYTPTSPKY------SPTSPTYSPTSPKYSPTSP 1928
Cdd:PLN03209  450 PTSP--SPTAPTGVSPSVSSTSSVPA-VPDTAPATAATDAAAPPPANMRPLSPYAvyddlkPPTSPSPAAPVGKVAPSST 526
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 4505939   1929 TYSPtsPKGSTYSPTS---------PGYSPTSP--TYSLTSPAISPDDS 1966
Cdd:PLN03209  527 NEVV--KVGNSAPPTAladeqhhaqPKPRPLSPytMYEDLKPPTSPTPS 573
PRK14898 PRK14898
DNA-directed RNA polymerase subunit A''; Provisional
1060-1104 1.87e-04

DNA-directed RNA polymerase subunit A''; Provisional


Pssm-ID: 237854 [Multi-domain]  Cd Length: 858  Bit Score: 46.42  E-value: 1.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 4505939   1060 LSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTL 1104
Cdd:PRK14898   33 VTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
PHA03291 PHA03291
envelope glycoprotein I; Provisional
1853-1961 1.94e-04

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 46.10  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1853 YTPTSPKYSPTSPKYSPTSpKYSPTSPTYSP--------TTPKYSPTSPTysptspvyTPTSPKYSPTSPTYSPTSPKYS 1924
Cdd:PHA03291  183 DGSCDPALPLSAPRLGPAD-VFVPATPRPTPrttaspetTPTPSTTTSPP--------STTIPAPSTTIAAPQAGTTPEA 253
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 4505939   1925 PTSPtySPTSPKGSTYSPTSPGYSPTSPTYSLTSPAI 1961
Cdd:PHA03291  254 EGTP--APPTPGGGEAPPANATPAPEASRYELTVTQI 288
PHA03291 PHA03291
envelope glycoprotein I; Provisional
1865-1952 2.55e-04

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 45.72  E-value: 2.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1865 PKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSpVYTPTSPKYSPTSPTySP--TSPKYSPTSPTYSPTSPKGSTYSP 1942
Cdd:PHA03291  167 PAEGTLAAPPLGEGSADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTA-SPetTPTPSTTTSPPSTTIPAPSTTIAA 244
                          90
                  ....*....|
gi 4505939   1943 TSPGYSPTSP 1952
Cdd:PHA03291  245 PQAGTTPEAE 254
PLN02217 PLN02217
probable pectinesterase/pectinesterase inhibitor
1869-1966 3.33e-04

probable pectinesterase/pectinesterase inhibitor


Pssm-ID: 215130 [Multi-domain]  Cd Length: 670  Bit Score: 45.85  E-value: 3.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1869 PTSPKYSPTSPTYSPTTPKYS--PTSPTYSPTSPVyTPTSPKYSPtsPTYSPTSPKYSPT---SPTYSPtsPKGSTYSPT 1943
Cdd:PLN02217  556 PYIPGLFAGNPGSTNSTPTGSaaSSNTTFSSDSPS-TVVAPSTSP--PAGHLGSPPATPSkivSPSTSP--PASHLGSPS 630
                          90       100
                  ....*....|....*....|...
gi 4505939   1944 SPGYSPTSPTYSLTSPAISPDDS 1966
Cdd:PLN02217  631 TTPSSPESSIKVASTETASPESS 653
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
1515-1621 5.37e-04

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 41.74  E-value: 5.37e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     1515 PAMTP-WNQGA--TPAYGAWSPSVGSGMTPGAAGFSPSAASdASGFSPGYSPAWSPTpgspgspgpsspyipSPGGAMSP 1591
Cdd:smart01104    1 GGRTPaWGASGskTPAWGSRTPGTAAGGAPTARGGSGSRTP-AWGGAGSRTPAWGGA---------------GPTGSRTP 64
                            90       100       110
                    ....*....|....*....|....*....|
gi 4505939     1592 SYSPTSPAYEPRSPGGYTPQSPSYSPTSPS 1621
Cdd:smart01104   65 AWGGASAWGNKSSEGSASSWAAGPGGAYGA 94
GATA-N pfam05349
GATA-type transcription activator, N-terminal; GATA transcription factors mediate cell ...
1861-1969 5.40e-04

GATA-type transcription activator, N-terminal; GATA transcription factors mediate cell differentiation in a diverse range of tissues. Mutation are often associated with certain congenital human disorders. The six classical vertebrate GATA proteins, GATA-1 to GATA-6, are highly homologous and have two tandem zinc fingers. The classical GATA transcription factors function transcription activators. In lower metazoans GATA proteins carry a single canonical zinc finger. This family represents the N-terminal domain of the family of GATA transcription activators.


Pssm-ID: 461628 [Multi-domain]  Cd Length: 174  Bit Score: 42.81  E-value: 5.40e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1861 SPTSPKYSPTSPKY---SPTSPTYSPTT--PKYSPTSPtYSPTSPVYTPTSPKYS-PTSPTYSPTSPKYSPTSPTYSPts 1934
Cdd:pfam05349   10 NHGQAAYDHDSGGFlhsAASSPVYVPTTrvPSMLPTLP-YLQGCGSSQQSHPVSShSGWAQAGAESSSYNPGSPHPSP-- 86
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 4505939    1935 pkGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEE 1969
Cdd:pfam05349   87 --RFSYSHSPPGSNGTSRDAAYQSPLLISAGGREQ 119
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
1854-1936 7.05e-04

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 44.68  E-value: 7.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1854 TPTSPKYSPTS-PKYSPTSPKySPTSPTYSPTTPKYSPTSPTYSPTS--------PVYTP--------------TSPKYS 1910
Cdd:PTZ00449  710 TPGTPFTTPRPlPPKLPRDEE-FPFEPIGDPDAEQPDDIEFFTPPEEertffhetPADTPlpdilaeefkeediHAETGE 788
                          90       100
                  ....*....|....*....|....*..
gi 4505939   1911 PTSPTYSPTSP-KYSPTSPTYSPTSPK 1936
Cdd:PTZ00449  789 PDEAMKRPDSPsEHEDKPPGDHPSLPK 815
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
1857-1959 8.33e-04

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 43.79  E-value: 8.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1857 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1936
Cdd:PTZ00436  249 APAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPA 328
                          90       100
                  ....*....|....*....|...
gi 4505939   1937 GSTyspTSPGYSPTSPTYSLTSP 1959
Cdd:PTZ00436  329 KAA---TPPAKAAAPPAKAAAAP 348
Pneumo_att_G pfam05539
Pneumovirinae attachment membrane glycoprotein G;
1854-1970 9.16e-04

Pneumovirinae attachment membrane glycoprotein G;


Pssm-ID: 114270 [Multi-domain]  Cd Length: 408  Bit Score: 43.88  E-value: 9.16e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1854 TPTSPKysptsPKYSPTSPKYSPT-SPTYSPTTPkySPTSPTySPTSPVYTPTspkysPTSPTySPTSPKYSPTSPTYSP 1932
Cdd:pfam05539  226 TSSNPE-----PQTEPPPSQRGPSgSPQHPPSTT--SQDQST-TGDGQEHTQR-----RKTPP-ATSNRRSPHSTATPPP 291
                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 4505939    1933 TSPKGSTYSPTspgYSPTSPTYSLTSPAISPDDSDEEN 1970
Cdd:pfam05539  292 TTKRQETGRPT---PRPTATTQSGSSPPHSSPPGVQAN 326
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
1855-1960 1.03e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 44.15  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1855 PTSP--KYSPTSPkysPTSPKYSPTSPTYSPTTpkySPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPK------YSPT 1926
Cdd:PLN03209  437 PLSPyaRYEDLKP---PTSPSPTAPTGVSPSVS---STSSVPAVPDTAPATAATDAAAPPPANMRPLSPYavyddlKPPT 510
                          90       100       110
                  ....*....|....*....|....*....|....
gi 4505939   1927 SPTysPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 1960
Cdd:PLN03209  511 SPS--PAAPVGKVAPSSTNEVVKVGNSAPPTALA 542
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
1857-1960 1.03e-03

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 43.79  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1857 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1936
Cdd:PTZ00436  228 APAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPA 307
                          90       100
                  ....*....|....*....|....*...
gi 4505939   1937 GSTYSP----TSPGYSPTSPTYSLTSPA 1960
Cdd:PTZ00436  308 KAAAAPakaaAPPAKAAAPPAKAATPPA 335
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
1862-1943 1.12e-03

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 43.73  E-value: 1.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1862 PTSPKYSPTSPKYSPTS-PTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTY 1940
Cdd:TIGR00601   77 PKTGTGKVAPPAATPTSaPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSER 156

                   ...
gi 4505939    1941 SPT 1943
Cdd:TIGR00601  157 ETT 159
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
1857-1937 1.23e-03

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 43.40  E-value: 1.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1857 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1936
Cdd:PTZ00436  270 PPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAAPV 349

                  .
gi 4505939   1937 G 1937
Cdd:PTZ00436  350 G 350
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
1857-1960 1.24e-03

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 43.40  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1857 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1936
Cdd:PTZ00436  221 APAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPA 300
                          90       100
                  ....*....|....*....|....*...
gi 4505939   1937 GSTYSP----TSPGYSPTSPTYSLTSPA 1960
Cdd:PTZ00436  301 KAAAAPakaaAAPAKAAAPPAKAAAPPA 328
KAR9 pfam08580
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ...
1853-1962 1.50e-03

Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localizes at the shmoo tip in mating cells and at the tip of the growing bud in anaphase.


Pssm-ID: 430088 [Multi-domain]  Cd Length: 684  Bit Score: 43.67  E-value: 1.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1853 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTP---------------KYSPTSPT-YSPTSPVYTPTSPKYSPTSPTY 1916
Cdd:pfam08580  503 GFLSTPSNTATSETPTPALRPPSRPQPPPPGNRPrwnastntndldvghNFKPLTLTtPSPTPSRSSRSSSTLPPVSPLS 582
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 4505939    1917 SPTSPKYSPTSPTYSPTSPKGSTYSPTSPGySPTSPTYSLTSPAIS 1962
Cdd:pfam08580  583 RDKSRSPAPTCRSVSRASRRRASRKPTRIG-SPNSRTSLLDEPPYP 627
PHA03269 PHA03269
envelope glycoprotein C; Provisional
1855-1959 1.59e-03

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 43.56  E-value: 1.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1855 PTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTySPTSPKYSPtsPTYSPTS 1934
Cdd:PHA03269   46 PHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAVAPQLAA-APKPDAAEA--FTSAAQA 122
                          90       100
                  ....*....|....*....|....*.
gi 4505939   1935 PKGSTYSPTSP-GYSPTSPTYSLTSP 1959
Cdd:PHA03269  123 HEAPADAGTSAaSKKPDPAAHTQHSP 148
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
1856-1942 1.97e-03

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 42.63  E-value: 1.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1856 TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSP 1935
Cdd:PTZ00436  262 APPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPP 341

                  ....*..
gi 4505939   1936 KGSTYSP 1942
Cdd:PTZ00436  342 AKAAAAP 348
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
1855-1959 2.19e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 43.14  E-value: 2.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1855 PTSPKY--SPTSPKySPTSPKySPTSP-----TYSPTTPKySPTSPTySPTSP-----VYTPTSPKYSPTSPT------- 1915
Cdd:PTZ00449  621 PKSPKRpeSPKSPK-RPPPPQ-RPSSPerpegPKIIKSPK-PPKSPK-PPFDPkfkekFYDDYLDAAAKSKETkttvvld 696
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 4505939   1916 ------------YSPTSPKYSPTS-PTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSP 1959
Cdd:PTZ00449  697 esfesilketlpETPGTPFTTPRPlPPKLPRDEEFPFEPIGDPDAEQPDDIEFFTPP 753
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
1854-1968 2.31e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 42.99  E-value: 2.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1854 TPTSPKYSPTSPK-----YSPTSPKYSPTSPTYS----------------PTTP--KYS----PTSPTYSPTSPVYTPTS 1906
Cdd:PLN03209  387 IPTPPSSSPASSKsvdavAKPAEPDVVPSPGSASnvpevepaqveakktrPLSPyaRYEdlkpPTSPSPTAPTGVSPSVS 466
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4505939   1907 pkySPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP---TSPGYSPTSPTYSLTSPAISPDDSDE 1968
Cdd:PLN03209  467 ---STSSVPAVPDTAPATAATDAAAPPPANMRPLSPyavYDDLKPPTSPSPAAPVGKVAPSSTNE 528
KAR9 pfam08580
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ...
1854-1970 2.39e-03

Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localizes at the shmoo tip in mating cells and at the tip of the growing bud in anaphase.


Pssm-ID: 430088 [Multi-domain]  Cd Length: 684  Bit Score: 42.89  E-value: 2.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1854 TPTSPKYSPTSPKYSPTSP---------------KYSPTSPTY-SPTTPKYSPTSPTYSPTSPVYTPTSPKYSPT----- 1912
Cdd:pfam08580  518 TPALRPPSRPQPPPPGNRPrwnastntndldvghNFKPLTLTTpSPTPSRSSRSSSTLPPVSPLSRDKSRSPAPTcrsvs 597
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4505939    1913 SPTYSPTSPK----YSPTSPTY--SPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN 1970
Cdd:pfam08580  598 RASRRRASRKptriGSPNSRTSllDEPPYPKLTLSKGLPRTPRNRQSYAGTSPSRSVSVSSGLG 661
CytochromB561_N pfam09786
Cytochrome B561, N terminal; Members of this family are found in the N terminal region of ...
1855-1941 2.52e-03

Cytochrome B561, N terminal; Members of this family are found in the N terminal region of cytochrome B561, as well as in various other putative uncharacterized proteins.


Pssm-ID: 462899  Cd Length: 579  Bit Score: 42.89  E-value: 2.52e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1855 PTSPKYSPTSPKYSPTSPKYSP--TSPTYSPTTPKYSPTSP-TYSPTSPVYTPTSPkySPTSPTYSpTSPKYSP--TSPT 1929
Cdd:pfam09786  145 PLHQSVSPSSSESRKGGDKSPAgsGKKLRSFSTSSKSPASPsVYLRGSPVPLNSSP--LPSDRNYE-NSVQSSPeiDSAV 221
                           90
                   ....*....|..
gi 4505939    1930 YSPTSPKGSTYS 1941
Cdd:pfam09786  222 STPWSRKRATIG 233
2A1904 TIGR00927
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ...
1852-1967 2.99e-03

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273344 [Multi-domain]  Cd Length: 1096  Bit Score: 42.68  E-value: 2.99e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1852 EYTPTSPKyspTSPKYSPTSPK--YSPTSPTY------SPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKY 1923
Cdd:TIGR00927  109 ENTPSPPR---RTAKITPTTPKnnYSPTAAGTervkedTPATPSRALNHYISTSGRQRVKSYTPKPRGEVKSSSPTQTRE 185
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 4505939    1924 SPTSPTYSPTSPKGSTYSPTSPGYSPTSPTyslTSPAISPDDSD 1967
Cdd:TIGR00927  186 KVRKYTPSPLGRMVNSYAPSTFMTMPRSHG---ITPRTTVKDSE 226
Pneumo_att_G pfam05539
Pneumovirinae attachment membrane glycoprotein G;
1855-1951 3.73e-03

Pneumovirinae attachment membrane glycoprotein G;


Pssm-ID: 114270 [Multi-domain]  Cd Length: 408  Bit Score: 41.96  E-value: 3.73e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1855 PTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYS-PTSPVYTPTSPKYSPTSPTYSPTspkYSPTSPTYSPT 1933
Cdd:pfam05539  237 PPSQRGPSGSPQHPPSTTSQDQSTTGDGQEHTQRRKTPPATSnRRSPHSTATPPPTTKRQETGRPT---PRPTATTQSGS 313
                           90
                   ....*....|....*...
gi 4505939    1934 SPKGStySPTSPGYSPTS 1951
Cdd:pfam05539  314 SPPHS--SPPGVQANPTT 329
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
1854-1945 5.18e-03

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 39.04  E-value: 5.18e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939     1854 TP----TSPKYSPTSPkysPTSPKYSP-TSPTYSPT---TP------KYSPTSPTYSPTSPVY-----TPTSPKYSPTSP 1914
Cdd:smart01104   14 TPawgsRTPGTAAGGA---PTARGGSGsRTPAWGGAgsrTPawggagPTGSRTPAWGGASAWGnksseGSASSWAAGPGG 90
                            90       100       110
                    ....*....|....*....|....*....|.
gi 4505939     1915 TYSPTSPKYSPTSPTYSPTSPKGSTYSPTSP 1945
Cdd:smart01104   91 AYGAPTPGYGGTPSAYGPATPGGGAMAGSAS 121
Hamartin pfam04388
Hamartin protein; This family includes the hamartin protein which is thought to function as a ...
1876-1955 5.49e-03

Hamartin protein; This family includes the hamartin protein which is thought to function as a tumour suppressor. The hamartin protein interacts with the tuberin protein pfam03542. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterized by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. TSC1 encodes a protein, hamartin, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. The TSC2 gene codes for tuberin pfam03542. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking.


Pssm-ID: 461287 [Multi-domain]  Cd Length: 730  Bit Score: 41.58  E-value: 5.49e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939    1876 PTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTsPTYSPTSPKGSTYSPTSPGYSPTSPTYS 1955
Cdd:pfam04388  276 PTASPYTDQQSSYGSSTSTPSSTPRLQLSSSSGTSPPYLSPPSIRLKTDSF-PLWSPSSVCGMTTPPTSPGMVPTTPSEL 354
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
1854-1952 8.61e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 41.21  E-value: 8.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939   1854 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKyspTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTyspt 1933
Cdd:PTZ00449  728 DEEFPFEPIGDPDAEQPDDIEFFTPPEEERTFFH---ETPADTPLPDILAEEFKEEDIHAETGEPDEAMKRPDSPS---- 800
                          90
                  ....*....|....*....
gi 4505939   1934 spkgsTYSPTSPGYSPTSP 1952
Cdd:PTZ00449  801 -----EHEDKPPGDHPSLP 814
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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