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Conserved domains on  [gi|1824096841|gb|QIQ08543|]
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DNA-dependent RNA polymerase subunit RPB2 [Carcinus maenas virus 1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rpoB_arch super family cl37306
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 706-1039 1.90e-33

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


The actual alignment was detected with superfamily member TIGR03670:

Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 137.47  E-value: 1.90e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLF-SH------TEQRVVV------FVIPQDKILG---KAVTSNLDyVDGtgvikcgtLVTNDTN 769
Cdd:TIGR03670  212 NIEDALIMNKASIERGLArSTffrtyeAEERRYPggqedrFEIPEPDVRGyrgEEAYKHLD-EDG--------IVYPEVE 282

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  770 VLVNSVLFGMDD--HFnLTTYDNPLLLA------------------DKLngFKTERVEAfNNNVKLYFSKLHFLTEGDKL 829
Cdd:TIGR03670  283 VKGGDVLIGKTSppRF-LEELREFGLVTerrrdtsvtvrhgekgivDKV--IITETEEG-NKLVKVRVRDLRIPELGDKF 358

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  830 TSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYEELklsGGGGGDITIKRT--------------- 893
Cdd:TIGR03670  359 ASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGqLLEMI---AGKVAALEGRRVdgtpfegepeeelrk 435

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  894 ---------------FSGITGKCIGAHEW-GLLAYIALDQIASNKKYiciptQTNR---QTFTGQPKEGRSQEGGFRVGV 954
Cdd:TIGR03670  436 ellklgfkpdgkevmYDGITGEKLEAEIFiGVIYYQKLHHMVADKIH-----ARSRgpvQVLTRQPTEGRAREGGLRFGE 510

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  955 LEVASIRASGSLQFLRDRMSTNSDQIKVLICSRCKMLQhLEKKRRRRWWCSFCGVYTRPVPLTVSKCMKFIFQLLAFLNI 1034
Cdd:TIGR03670  511 MERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIA-WEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGI 589


                   ....*
gi 1824096841 1035 KITLN 1039
Cdd:TIGR03670  590 SPRLE 594
RNA_pol_Rpb2_3 super family cl38165
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 369-417 1.66e-03

RNA polymerase Rpb2, 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). Domain 3, s also known as the fork domain and is proximal to catalytic site.


The actual alignment was detected with superfamily member pfam04565:

Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 37.89  E-value: 1.66e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1824096841  369 HLGKISSSINNVG--NKVDRLRFYDNSSALFVCPHNSPDGRKIGLIKQLSV 417
Cdd:pfam04565   14 HLRRVNSPRGGLFreMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLAL 64
 
Name Accession Description Interval E-value
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 706-1039 1.90e-33

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 137.47  E-value: 1.90e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLF-SH------TEQRVVV------FVIPQDKILG---KAVTSNLDyVDGtgvikcgtLVTNDTN 769
Cdd:TIGR03670  212 NIEDALIMNKASIERGLArSTffrtyeAEERRYPggqedrFEIPEPDVRGyrgEEAYKHLD-EDG--------IVYPEVE 282

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  770 VLVNSVLFGMDD--HFnLTTYDNPLLLA------------------DKLngFKTERVEAfNNNVKLYFSKLHFLTEGDKL 829
Cdd:TIGR03670  283 VKGGDVLIGKTSppRF-LEELREFGLVTerrrdtsvtvrhgekgivDKV--IITETEEG-NKLVKVRVRDLRIPELGDKF 358

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  830 TSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYEELklsGGGGGDITIKRT--------------- 893
Cdd:TIGR03670  359 ASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGqLLEMI---AGKVAALEGRRVdgtpfegepeeelrk 435

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  894 ---------------FSGITGKCIGAHEW-GLLAYIALDQIASNKKYiciptQTNR---QTFTGQPKEGRSQEGGFRVGV 954
Cdd:TIGR03670  436 ellklgfkpdgkevmYDGITGEKLEAEIFiGVIYYQKLHHMVADKIH-----ARSRgpvQVLTRQPTEGRAREGGLRFGE 510

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  955 LEVASIRASGSLQFLRDRMSTNSDQIKVLICSRCKMLQhLEKKRRRRWWCSFCGVYTRPVPLTVSKCMKFIFQLLAFLNI 1034
Cdd:TIGR03670  511 MERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIA-WEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGI 589


                   ....*
gi 1824096841 1035 KITLN 1039
Cdd:TIGR03670  590 SPRLE 594
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 706-1029 2.78e-32

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 133.93  E-value: 2.78e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLF-SH------TEQR------VVVFVIPQDKILG---KAVTSNLDyVDGtgvikcgtLVTNDTN 769
Cdd:PRK07225   218 NIEDALIMNKASIERGLGrSHffrtyeGEERrypggqEDRFEIPDKDVRGyrgEEAYRHLD-EDG--------LVNPETE 288

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  770 VLVNSVLFGMD---------DHFNL----------TTYDNPLLLADKLngFKTERVEAfNNNVKLYFSKLHFLTEGDKLT 830
Cdd:PRK07225   289 VKEGDVLIGKTspprfleepDDFGIspekrretsvTMRSGEEGIVDTV--ILTETEEG-SRLVKVRVRDLRIPELGDKFA 365

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  831 SRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLGvyEELKLSGGGGGDITIKRT----------------- 893
Cdd:PRK07225   366 SRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVG--HVLEMIGGKVGSLEGRRVdgtafsgedeedlreal 443

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  894 -------------FSGITGKCIGAHEW-GLLAYIALDQIASNKKYiciptQTNR---QTFTGQPKEGRSQEGGFRVGVLE 956
Cdd:PRK07225   444 eklgfehtgkevmYDGITGEKIEAEIFvGVIYYQKLHHMVANKLH-----ARSRgpvQVLTRQPTEGRAREGGLRFGEME 518

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1824096841  957 VASIRASGSLQFLRDRMSTNSDQIKVLICSRCKMLQHLEKKRRRRwWCSFCGVYTRPVPLTVSkcmkFIFQLL 1029
Cdd:PRK07225   519 RDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRK-YCPICGEETDIYPVEMS----YAFKLL 586
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 706-1039 8.86e-32

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 133.85  E-value: 8.86e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLF--SHTE-------------QRVVVFVIPQDKIlgkavtSNLDYVDGTGVIKCGTLVTNDtNV 770
Cdd:cd00653    491 NFEDAIIINKSSVDRGFFrsIHYKkyeielrktkngpEEITRGDIPNVSE------EKLKNLDEDGIIRPGARVEPG-DI 563

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  771 LVN----------SVLFGMDDHfnlTTYDNPLLLADKLNG-------FKTERVEAFNNNVKLYFSKLHFLTEGDKLTSRH 833
Cdd:cd00653    564 LVGkitpkgetesTPIFGEKAR---DVRDTSLKYPGGEKGivddvkiFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRH 640

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  834 GQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYEELK-LSG---GGGGDIT---------IKRTF----- 894
Cdd:cd00653    641 GQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGqLLESLLgKAGallGKFGDATpfdgaeeedISELLgeagl 720

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  895 ---------SGITGKCIGAHEW-GLLAYIALDQIASNKkyicI------PtqtnRQTFTGQPKEGRSQEGGFRVGVLEVA 958
Cdd:cd00653    721 nyygkevlyDGRTGEPLEAPIFvGPVYYQRLKHMVDDK----IharstgP----YSLLTRQPLKGRSRGGGQRFGEMERD 792

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  959 SIRASGSLQFLRDRMSTNSDQIKVLICSRCKMLQHLEkkrrrrwWCSFCGVYTRPVPLTVSKCMKFIFQLLAFLNIKITL 1038
Cdd:cd00653    793 ALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN-------LCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865


                   .
gi 1824096841 1039 N 1039
Cdd:cd00653    866 K 866
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 706-862 1.06e-19

RNA polymerase Rpb2, 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 represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 92.21  E-value: 1.06e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLF------SHTEQRV-------VVFVIPQDKILgkavtsNLDYVDGTGVIKCGTLVTNDtNVLV 772
Cdd:pfam00562   83 NQEDAIIINKSSVDRGFFtsihikEIEARKTklgpieeITRDIPNVSEE------ALKKLDEDGIVRVGAEVKPG-DILV 155

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  773 NSV-----------LFGMDDhfnLTTYDNPLLLADKLNGFkTERVEAFNNN------VKLYFSKLHFLTEGDKLTSRHGQ 835
Cdd:pfam00562  156 GKVgpteltkllraIFGEKA---RDVKDTSLKVPPGEEGV-VDDVIVFELPpggikmVKVYIRQKRKPEVGDKFASRHGQ 231

                          170       180
                   ....*....|....*....|....*..
gi 1824096841  836 KGVVCQIGNAEDMPFDGEGNVPDIIIN 862
Cdd:pfam00562  232 KGVVSRILPQEDMPFTEDGIPPDIILN 258
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 706-978 8.20e-14

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 76.30  E-value: 8.20e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLFS--HTE------------QRVVVFVIPQdkiLGKAVTSNLDyvdGTGVIKCGTLVtNDTNVL 771
Cdd:COG0085    622 NYEDAIIISERLVKDDVLTsiHIEeyeieardtklgPEEITRDIPN---VSEEALRNLD---EDGIIRIGAEV-KGGDIL 694

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  772 VNSV-----------------LFGM--------------------DDHFNLTTYDNPLLLADklngfkterveaFNNNVK 814
Cdd:COG0085    695 VGKVtpkgeteltpeerllraIFGEkarevrdtslrvphgekgkvIDVKVFSREEGDELPPG------------VNKLVR 762

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  815 LYFSKLHFLTEGDKLTSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYEEL--KLSGGGGgdITIK 891
Cdd:COG0085    763 VYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGqVLETHlgWAAALLG--RRVA 840

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  892 RT-FSGITGKCIgaheWGLLA-------------------------------YIALDQIASNK-------KYICIpTQtn 932
Cdd:COG0085    841 TPvFDGAPEEEI----RELLEkaglppdgkevlydgrtgepfdnpvtvgymyYLKLHHMVDDKiharstgPYSLI-TQ-- 913

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 1824096841  933 rqtftgQPKEGRSQEGGFRVGVLEVASIRASGSLQFLRDRMSTNSD 978
Cdd:COG0085    914 ------QPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD 953
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 369-417 1.66e-03

RNA polymerase Rpb2, 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). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 37.89  E-value: 1.66e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1824096841  369 HLGKISSSINNVG--NKVDRLRFYDNSSALFVCPHNSPDGRKIGLIKQLSV 417
Cdd:pfam04565   14 HLRRVNSPRGGLFreMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLAL 64
 
Name Accession Description Interval E-value
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 706-1039 1.90e-33

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 137.47  E-value: 1.90e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLF-SH------TEQRVVV------FVIPQDKILG---KAVTSNLDyVDGtgvikcgtLVTNDTN 769
Cdd:TIGR03670  212 NIEDALIMNKASIERGLArSTffrtyeAEERRYPggqedrFEIPEPDVRGyrgEEAYKHLD-EDG--------IVYPEVE 282

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  770 VLVNSVLFGMDD--HFnLTTYDNPLLLA------------------DKLngFKTERVEAfNNNVKLYFSKLHFLTEGDKL 829
Cdd:TIGR03670  283 VKGGDVLIGKTSppRF-LEELREFGLVTerrrdtsvtvrhgekgivDKV--IITETEEG-NKLVKVRVRDLRIPELGDKF 358

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  830 TSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYEELklsGGGGGDITIKRT--------------- 893
Cdd:TIGR03670  359 ASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGqLLEMI---AGKVAALEGRRVdgtpfegepeeelrk 435

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  894 ---------------FSGITGKCIGAHEW-GLLAYIALDQIASNKKYiciptQTNR---QTFTGQPKEGRSQEGGFRVGV 954
Cdd:TIGR03670  436 ellklgfkpdgkevmYDGITGEKLEAEIFiGVIYYQKLHHMVADKIH-----ARSRgpvQVLTRQPTEGRAREGGLRFGE 510

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  955 LEVASIRASGSLQFLRDRMSTNSDQIKVLICSRCKMLQhLEKKRRRRWWCSFCGVYTRPVPLTVSKCMKFIFQLLAFLNI 1034
Cdd:TIGR03670  511 MERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIA-WEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGI 589


                   ....*
gi 1824096841 1035 KITLN 1039
Cdd:TIGR03670  590 SPRLE 594
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 706-1029 2.78e-32

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 133.93  E-value: 2.78e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLF-SH------TEQR------VVVFVIPQDKILG---KAVTSNLDyVDGtgvikcgtLVTNDTN 769
Cdd:PRK07225   218 NIEDALIMNKASIERGLGrSHffrtyeGEERrypggqEDRFEIPDKDVRGyrgEEAYRHLD-EDG--------LVNPETE 288

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  770 VLVNSVLFGMD---------DHFNL----------TTYDNPLLLADKLngFKTERVEAfNNNVKLYFSKLHFLTEGDKLT 830
Cdd:PRK07225   289 VKEGDVLIGKTspprfleepDDFGIspekrretsvTMRSGEEGIVDTV--ILTETEEG-SRLVKVRVRDLRIPELGDKFA 365

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  831 SRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLGvyEELKLSGGGGGDITIKRT----------------- 893
Cdd:PRK07225   366 SRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVG--HVLEMIGGKVGSLEGRRVdgtafsgedeedlreal 443

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  894 -------------FSGITGKCIGAHEW-GLLAYIALDQIASNKKYiciptQTNR---QTFTGQPKEGRSQEGGFRVGVLE 956
Cdd:PRK07225   444 eklgfehtgkevmYDGITGEKIEAEIFvGVIYYQKLHHMVANKLH-----ARSRgpvQVLTRQPTEGRAREGGLRFGEME 518

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1824096841  957 VASIRASGSLQFLRDRMSTNSDQIKVLICSRCKMLQHLEKKRRRRwWCSFCGVYTRPVPLTVSkcmkFIFQLL 1029
Cdd:PRK07225   519 RDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRK-YCPICGEETDIYPVEMS----YAFKLL 586
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 706-1039 8.86e-32

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 133.85  E-value: 8.86e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLF--SHTE-------------QRVVVFVIPQDKIlgkavtSNLDYVDGTGVIKCGTLVTNDtNV 770
Cdd:cd00653    491 NFEDAIIINKSSVDRGFFrsIHYKkyeielrktkngpEEITRGDIPNVSE------EKLKNLDEDGIIRPGARVEPG-DI 563

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  771 LVN----------SVLFGMDDHfnlTTYDNPLLLADKLNG-------FKTERVEAFNNNVKLYFSKLHFLTEGDKLTSRH 833
Cdd:cd00653    564 LVGkitpkgetesTPIFGEKAR---DVRDTSLKYPGGEKGivddvkiFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRH 640

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  834 GQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYEELK-LSG---GGGGDIT---------IKRTF----- 894
Cdd:cd00653    641 GQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGqLLESLLgKAGallGKFGDATpfdgaeeedISELLgeagl 720

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  895 ---------SGITGKCIGAHEW-GLLAYIALDQIASNKkyicI------PtqtnRQTFTGQPKEGRSQEGGFRVGVLEVA 958
Cdd:cd00653    721 nyygkevlyDGRTGEPLEAPIFvGPVYYQRLKHMVDDK----IharstgP----YSLLTRQPLKGRSRGGGQRFGEMERD 792

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  959 SIRASGSLQFLRDRMSTNSDQIKVLICSRCKMLQHLEkkrrrrwWCSFCGVYTRPVPLTVSKCMKFIFQLLAFLNIKITL 1038
Cdd:cd00653    793 ALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN-------LCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865


                   .
gi 1824096841 1039 N 1039
Cdd:cd00653    866 K 866
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 706-1039 6.36e-30

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 128.54  E-value: 6.36e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLFSHT--------EQRVVV-----FVIPQDKILG---KAVTSNLD---------YVDGTGVI-- 758
Cdd:PRK08565   716 NIEDAIIMNKASIERGLARSTffrtyeteERKYPGgqedkIEIPEPNVRGyrgEEYYRKLDedgivspevEVKGGDVLig 795

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  759 --------------KCGTLVTNDTNVLVNSVLFGMDDHfnlttydnpLLLADKLNGFKTerveafnnnVKLYFSKLHFLT 824
Cdd:PRK08565   796 ktspprfleeleelSLGLQERRDTSVTVRHGEKGIVDT---------VLITESPEGNKL---------VKVRVRDLRIPE 857

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  825 EGDKLTSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYEELklsGGGGGDITIKR----------- 892
Cdd:PRK08565   858 LGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGqLLESI---AGKVAALEGRFvdatpfygepe 934

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  893 -------------------TFSGITGKCIGAHEW-GLLAYIALDQIASNKkyICIPTQTNRQTFTGQPKEGRSQEGGFRV 952
Cdd:PRK08565   935 eelrkellklgykpdgtevMYDGRTGEKIKAPIFiGVVYYQKLHHMVADK--IHARARGPVQILTRQPTEGRAREGGLRF 1012

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  953 GVLEVASIRASGSLQFLRDRMSTNSDQIKVLICSRCKMLQhLEKKRRRRWWCSFCGVYTRPVPLTVSKCMKFIFQLLAFL 1032
Cdd:PRK08565  1013 GEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIA-WYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSM 1091


                   ....*..
gi 1824096841 1033 NIKITLN 1039
Cdd:PRK08565  1092 GISPRLK 1098
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 706-862 1.06e-19

RNA polymerase Rpb2, 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 represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 92.21  E-value: 1.06e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLF------SHTEQRV-------VVFVIPQDKILgkavtsNLDYVDGTGVIKCGTLVTNDtNVLV 772
Cdd:pfam00562   83 NQEDAIIINKSSVDRGFFtsihikEIEARKTklgpieeITRDIPNVSEE------ALKKLDEDGIVRVGAEVKPG-DILV 155

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  773 NSV-----------LFGMDDhfnLTTYDNPLLLADKLNGFkTERVEAFNNN------VKLYFSKLHFLTEGDKLTSRHGQ 835
Cdd:pfam00562  156 GKVgpteltkllraIFGEKA---RDVKDTSLKVPPGEEGV-VDDVIVFELPpggikmVKVYIRQKRKPEVGDKFASRHGQ 231

                          170       180
                   ....*....|....*....|....*..
gi 1824096841  836 KGVVCQIGNAEDMPFDGEGNVPDIIIN 862
Cdd:pfam00562  232 KGVVSRILPQEDMPFTEDGIPPDIILN 258
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 706-978 8.20e-14

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 76.30  E-value: 8.20e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLFS--HTE------------QRVVVFVIPQdkiLGKAVTSNLDyvdGTGVIKCGTLVtNDTNVL 771
Cdd:COG0085    622 NYEDAIIISERLVKDDVLTsiHIEeyeieardtklgPEEITRDIPN---VSEEALRNLD---EDGIIRIGAEV-KGGDIL 694

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  772 VNSV-----------------LFGM--------------------DDHFNLTTYDNPLLLADklngfkterveaFNNNVK 814
Cdd:COG0085    695 VGKVtpkgeteltpeerllraIFGEkarevrdtslrvphgekgkvIDVKVFSREEGDELPPG------------VNKLVR 762

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  815 LYFSKLHFLTEGDKLTSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYEEL--KLSGGGGgdITIK 891
Cdd:COG0085    763 VYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGqVLETHlgWAAALLG--RRVA 840

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  892 RT-FSGITGKCIgaheWGLLA-------------------------------YIALDQIASNK-------KYICIpTQtn 932
Cdd:COG0085    841 TPvFDGAPEEEI----RELLEkaglppdgkevlydgrtgepfdnpvtvgymyYLKLHHMVDDKiharstgPYSLI-TQ-- 913

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 1824096841  933 rqtftgQPKEGRSQEGGFRVGVLEVASIRASGSLQFLRDRMSTNSD 978
Cdd:COG0085    914 ------QPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD 953
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 810-980 2.31e-11

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 68.15  E-value: 2.31e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  810 NNNVKLYFSKLHFLTEGDKLTSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYE-ELKLSGGGGGD 887
Cdd:TIGR02013  824 NKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGqILEtHLGWAGKRLGR 903

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  888 ITIKR---TFSGITGKCIGAH--EWGL------------------------------LAYIALDQI--ASNKKYICIptq 930
Cdd:TIGR02013  904 KGVPIatpVFDGASEEEIKEYleKAGLprdgkvrlydgrtgeqfdrpvtvgymymlkLHHLVDDKMhaRSTGPYSLV--- 980

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1824096841  931 tnrqtfTGQPKEGRSQEGGFRVGVLEVASIRASGSLQFLRDRMSTNSDQI 980
Cdd:TIGR02013  981 ------TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1024
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 706-878 2.50e-07

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 55.10  E-value: 2.50e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  706 NMEDGIIVNKASVERGLFSHTEQRVVVFVIPQDKILGKAVTSNLDYV--------DGTGVIKCGTLV-TND---TNVLVN 773
Cdd:CHL00207   661 NFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVseyslknlDENGIISIGSKVlAGDilvGKITPK 740

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824096841  774 S------------VLFGMDdhfNLTTYDNPLLLADKLNGFKTErVEAF------------NNNVKLYFSKLHFLTEGDKL 829
Cdd:CHL00207   741 GesdqlpegkllrAIFGEK---AKDVKDTSLRMPNGGYGRVIK-VEIFsrskgdelkfgyYLKIRVFIAQIRKIQVGDKL 816

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1824096841  830 TSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG-VYEEL 878
Cdd:CHL00207   817 AGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGqLFECL 866
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
812-873 7.09e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 53.86  E-value: 7.09e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1824096841  812 NVKLYFSKLHFLTEGDKLTSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLG 873
Cdd:PRK14844  1070 SVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVG 1131
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 813-862 9.42e-07

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 53.18  E-value: 9.42e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1824096841  813 VKLYFSKLHFLTEGDKLTSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIIN 862
Cdd:PRK00405   870 VKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLN 919
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
813-880 1.13e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 53.00  E-value: 1.13e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1824096841  813 VKLYFSKLHFLTEGDKLTSRHGQKGVVCQIGNAEDMPFDGEGNVPDIIINGNSTLKRLSLGVYEELKL 880
Cdd:PRK09603  1078 VKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHL 1145
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 369-417 1.66e-03

RNA polymerase Rpb2, 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). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 37.89  E-value: 1.66e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1824096841  369 HLGKISSSINNVG--NKVDRLRFYDNSSALFVCPHNSPDGRKIGLIKQLSV 417
Cdd:pfam04565   14 HLRRVNSPRGGLFreMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLAL 64
 
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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