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Conserved domains on  [gi|27597090|ref|NP_003161|]
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transcription elongation factor SPT6 [Homo sapiens]

Protein Classification

DLD and SH2_Nterm_SPT6_like domain-containing protein( domain architecture ID 13390031)

protein containing domains DLD, S1_like, SH2_Nterm_SPT6_like, and SH2_Cterm_SPT6_like

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1308-1512 4.98e-98

SH2 domain;


:

Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 314.09  E-value: 4.98e-98
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090   1308 ADHKQEEDMKRKQQRTTYIKRVIAHPSFHNINFKQAEKMMETMDQGDVIIRPSSKGENHLTVTWKVSDGIYQHVDVREEG 1387
Cdd:pfam14633    2 ADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLELD 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090   1388 KENAFSLGATLWINSEEFEDLDEIVARYVQPMASFARDLLNHKYYQDcsgGDRKKLEELLIKTKKEKPTFIPYFICACKE 1467
Cdd:pfam14633   82 KENEFSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFKD---GTKEEVEEWLREEKKANPKRSPYAFCLSHK 158
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 27597090   1468 LPGKFLLGYQPRGKPRI--EYVTVTPEGFRYRGQIFPTVNGLFRWFK 1512
Cdd:pfam14633  159 HPGYFLLSFKANKNSRVhhWYVKVTPDGFRLRGQQFPDVDALCNGFK 205
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
775-931 1.40e-77

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage


:

Pssm-ID: 258777  Cd Length: 150  Bit Score: 253.25  E-value: 1.40e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    775 QGKGIRVLGIAFSSAR-DHPVFCALVNGEGEVTDFLRLphftkrrtAWREEEREKKAQDIETLKKFLLNKKPHVVTVAGE 853
Cdd:pfam14639    1 QGKIPRVLGVAFGSGRfDDAIICVLVNGEGEVTDFLKL--------AWREFDRENKAQFEETLKKFLLSKKPHVIGVSGE 72
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27597090    854 NRDAQMLIEDVKRIVHELDQGQQLSSIGVELVDNELAILYMNSKKSEAEFRDYPPVLRQAVSLARRIQDPLIEFAQVC 931
Cdd:pfam14639   73 NRDAQKFYEDVQRVLHELEQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
HHH_7 pfam14635
Helix-hairpin-helix motif;
935-1038 9.06e-60

Helix-hairpin-helix motif;


:

Pssm-ID: 291309  Cd Length: 104  Bit Score: 200.08  E-value: 9.06e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    935 EDILCLKFHPLQEHVVKEELLNALYCEFINRVNEVGVDVNRAIAHPYSQALIQYVCGLGPRKGTHLLKILKQNNTRLESR 1014
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80
                           90       100
                   ....*....|....*....|....
gi 27597090   1015 TQLVTMCHMGPKVFMNCAGFLKID 1038
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
Tex super family cl34417
Transcriptional accessory protein Tex/SPT6 [Transcription];
564-1130 8.76e-34

Transcriptional accessory protein Tex/SPT6 [Transcription];


The actual alignment was detected with superfamily member COG2183:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 140.93  E-value: 8.76e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  564 AEPLELAKDYVCS--QFPTPEAVLEGARYMVALQIAREPLVRQVLRQTFQERAKLnITPTKKGRKDVD---EAHYAYSfk 638
Cdd:COG2183  135 GDPEAEAAKYINEekGVADVEAALDGARDILAERISEDAELRGKLRELLWKEGVL-VSKVKKGKEEEGakfRDYFDYS-- 211
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  639 ylknKPVKELRDDQFLKICLAEDEGLLTTDISIDlkgvegygnDQTYFEEIKQFYyrdeFSHQVQEWNRQRTMAIERALQ 718
Cdd:COG2183  212 ----EPLKKIPSHRILALNRGEKEGVLKVKLEPD---------EEEAEAYIARRF----IKDQGRPADEWLKEAVRDAYK 274
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  719 QFLYVQMAKELKNKLLAEAKEYVIKACSRKLYNWLRVAPYrpdqqveedddfmdenqgKGIRVLGIafssarDhPVF--- 795
Cdd:COG2183  275 RLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPA------------------GGKVVLGL------D-PGFrtg 329
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  796 --CALVNGEGEVTD----FlrlPHftkrrtawreEEREKKAQDIETLKKFLlnKKPHVVTVAGEN----RDAQMLIEDVK 865
Cdd:COG2183  330 ckVAVVDETGKLLDtatiY---PH----------PPQNKWEEAAKTLAALI--KKYKVELIAIGNgtasRETEQFVAELI 394
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  866 RivhelDQGQQLSSIGVelvdNEL-AILYMNSKKSEAEFRDYPPVLRQAVSLARRIQDPLIEFaqVcssdedilclKFHP 944
Cdd:COG2183  395 K-----ELDLKVQYVIV----SEAgASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAEL--V----------KIDP 453
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  945 -------LQeHVVKEELLN-AL-----YCefinrVNEVGVDVNRAiahpySQALIQYVCGLGPRkgthllkiLKQN---- 1007
Cdd:COG2183  454 ksigvgqYQ-HDVNQKKLKrSLdavveDC-----VNAVGVDLNTA-----SAPLLSYVSGLNPT--------LAKNivay 514
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090 1008 ---NTRLESRTQL--VTMchMGPKVFMNCAGFLKIDTASlgdstdsyiEVLDGSRVHPETYEWARKMAvDALEYDesaed 1082
Cdd:COG2183  515 rdeNGAFKSRKELlkVPR--LGPKAFEQAAGFLRIRDGD---------NPLDNSAVHPESYPVVEKIL-KDLGVS----- 577
                        570       580       590       600
                 ....*....|....*....|....*....|....*....|....*...
gi 27597090 1083 anpagaLEEILENPERLKDLDLDAFAEELerqgYGDkhITLYDIRAEL 1130
Cdd:COG2183  578 ------VKDLIGNKELLKKLDPEKYADEL----FGL--PTLRDILKEL 613
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
347-422 2.53e-24

Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins.


:

Pssm-ID: 464230  Cd Length: 115  Bit Score: 99.17  E-value: 2.53e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    347 SFSRKGPSTIQKIKEALGFMRNQHFEVPFIAFYRKEYVE-----------PELHINDLWRVWQWDEKWTQLRIRKENLTR 415
Cdd:pfam14641   27 DFERLLEPFKEAVGNVLEFISKDNLEVPFIWQHRRDYLLhsekdgfeighKLLNEDDLWRIVQLDIKFHSLIEKRNNLEK 106

                   ....*..
gi 27597090    416 LFEKMQA 422
Cdd:pfam14641  107 LYEKLGI 113
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1227-1282 4.32e-09

Ribosomal protein S1-like RNA-binding domain;


:

Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 54.53  E-value: 4.32e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 27597090    1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEKFSADLTCR 1282
Cdd:smart00316   17 GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1308-1512 4.98e-98

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 314.09  E-value: 4.98e-98
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090   1308 ADHKQEEDMKRKQQRTTYIKRVIAHPSFHNINFKQAEKMMETMDQGDVIIRPSSKGENHLTVTWKVSDGIYQHVDVREEG 1387
Cdd:pfam14633    2 ADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLELD 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090   1388 KENAFSLGATLWINSEEFEDLDEIVARYVQPMASFARDLLNHKYYQDcsgGDRKKLEELLIKTKKEKPTFIPYFICACKE 1467
Cdd:pfam14633   82 KENEFSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFKD---GTKEEVEEWLREEKKANPKRSPYAFCLSHK 158
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 27597090   1468 LPGKFLLGYQPRGKPRI--EYVTVTPEGFRYRGQIFPTVNGLFRWFK 1512
Cdd:pfam14633  159 HPGYFLLSFKANKNSRVhhWYVKVTPDGFRLRGQQFPDVDALCNGFK 205
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
775-931 1.40e-77

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage


Pssm-ID: 258777  Cd Length: 150  Bit Score: 253.25  E-value: 1.40e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    775 QGKGIRVLGIAFSSAR-DHPVFCALVNGEGEVTDFLRLphftkrrtAWREEEREKKAQDIETLKKFLLNKKPHVVTVAGE 853
Cdd:pfam14639    1 QGKIPRVLGVAFGSGRfDDAIICVLVNGEGEVTDFLKL--------AWREFDRENKAQFEETLKKFLLSKKPHVIGVSGE 72
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27597090    854 NRDAQMLIEDVKRIVHELDQGQQLSSIGVELVDNELAILYMNSKKSEAEFRDYPPVLRQAVSLARRIQDPLIEFAQVC 931
Cdd:pfam14639   73 NRDAQKFYEDVQRVLHELEQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
HHH_7 pfam14635
Helix-hairpin-helix motif;
935-1038 9.06e-60

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 200.08  E-value: 9.06e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    935 EDILCLKFHPLQEHVVKEELLNALYCEFINRVNEVGVDVNRAIAHPYSQALIQYVCGLGPRKGTHLLKILKQNNTRLESR 1014
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80
                           90       100
                   ....*....|....*....|....
gi 27597090   1015 TQLVTMCHMGPKVFMNCAGFLKID 1038
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
SH2_Nterm_SPT6_like cd09918
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ...
1331-1415 1.76e-45

N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198174  Cd Length: 85  Bit Score: 158.55  E-value: 1.76e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090 1331 AHPSFHNINFKQAEKMMETMDQGDVIIRPSSKGENHLTVTWKVSDGIYQHVDVREEGKENAFSLGATLWINSEEFEDLDE 1410
Cdd:cd09918    1 RHPLFKNVNYKQAEAYLKSKDVGEVVIRPSSKGVDHLTVTWKVADGVYQHIDIEELNKENPFSLGKELIIGGEEYEDLDE 80

                 ....*
gi 27597090 1411 IVARY 1415
Cdd:cd09918   81 IIARF 85
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
564-1130 8.76e-34

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 140.93  E-value: 8.76e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  564 AEPLELAKDYVCS--QFPTPEAVLEGARYMVALQIAREPLVRQVLRQTFQERAKLnITPTKKGRKDVD---EAHYAYSfk 638
Cdd:COG2183  135 GDPEAEAAKYINEekGVADVEAALDGARDILAERISEDAELRGKLRELLWKEGVL-VSKVKKGKEEEGakfRDYFDYS-- 211
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  639 ylknKPVKELRDDQFLKICLAEDEGLLTTDISIDlkgvegygnDQTYFEEIKQFYyrdeFSHQVQEWNRQRTMAIERALQ 718
Cdd:COG2183  212 ----EPLKKIPSHRILALNRGEKEGVLKVKLEPD---------EEEAEAYIARRF----IKDQGRPADEWLKEAVRDAYK 274
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  719 QFLYVQMAKELKNKLLAEAKEYVIKACSRKLYNWLRVAPYrpdqqveedddfmdenqgKGIRVLGIafssarDhPVF--- 795
Cdd:COG2183  275 RLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPA------------------GGKVVLGL------D-PGFrtg 329
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  796 --CALVNGEGEVTD----FlrlPHftkrrtawreEEREKKAQDIETLKKFLlnKKPHVVTVAGEN----RDAQMLIEDVK 865
Cdd:COG2183  330 ckVAVVDETGKLLDtatiY---PH----------PPQNKWEEAAKTLAALI--KKYKVELIAIGNgtasRETEQFVAELI 394
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  866 RivhelDQGQQLSSIGVelvdNEL-AILYMNSKKSEAEFRDYPPVLRQAVSLARRIQDPLIEFaqVcssdedilclKFHP 944
Cdd:COG2183  395 K-----ELDLKVQYVIV----SEAgASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAEL--V----------KIDP 453
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  945 -------LQeHVVKEELLN-AL-----YCefinrVNEVGVDVNRAiahpySQALIQYVCGLGPRkgthllkiLKQN---- 1007
Cdd:COG2183  454 ksigvgqYQ-HDVNQKKLKrSLdavveDC-----VNAVGVDLNTA-----SAPLLSYVSGLNPT--------LAKNivay 514
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090 1008 ---NTRLESRTQL--VTMchMGPKVFMNCAGFLKIDTASlgdstdsyiEVLDGSRVHPETYEWARKMAvDALEYDesaed 1082
Cdd:COG2183  515 rdeNGAFKSRKELlkVPR--LGPKAFEQAAGFLRIRDGD---------NPLDNSAVHPESYPVVEKIL-KDLGVS----- 577
                        570       580       590       600
                 ....*....|....*....|....*....|....*....|....*...
gi 27597090 1083 anpagaLEEILENPERLKDLDLDAFAEELerqgYGDkhITLYDIRAEL 1130
Cdd:COG2183  578 ------VKDLIGNKELLKKLDPEKYADEL----FGL--PTLRDILKEL 613
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
347-422 2.53e-24

Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins.


Pssm-ID: 464230  Cd Length: 115  Bit Score: 99.17  E-value: 2.53e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    347 SFSRKGPSTIQKIKEALGFMRNQHFEVPFIAFYRKEYVE-----------PELHINDLWRVWQWDEKWTQLRIRKENLTR 415
Cdd:pfam14641   27 DFERLLEPFKEAVGNVLEFISKDNLEVPFIWQHRRDYLLhsekdgfeighKLLNEDDLWRIVQLDIKFHSLIEKRNNLEK 106

                   ....*..
gi 27597090    416 LFEKMQA 422
Cdd:pfam14641  107 LYEKLGI 113
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
779-894 1.34e-16

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 76.84  E-value: 1.34e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090     779 IRVLGIAFSsarDHPVFCALVNGEGEVTDFLRLPHFTKrrtawreeerekKAQDIETLKKFLLNKKPHVVTVAGENRDAQ 858
Cdd:smart00732    1 KRVLGLDPG---RKGIGVAVVDETGKLADPLEVIPRTN------------KEADAARLKKLIKKYQPDLIVIGLPLNMNG 65
                            90       100       110
                    ....*....|....*....|....*....|....*.
gi 27597090     859 MLIEDVKRIVHELDqgQQLSSIGVELVDNELAILYM 894
Cdd:smart00732   66 TASRETEEAFAELL--KERFNLPVVLVDERLATVYA 99
SH2 smart00252
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ...
1332-1421 7.64e-12

Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.


Pssm-ID: 214585 [Multi-domain]  Cd Length: 84  Bit Score: 62.63  E-value: 7.64e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    1332 HPSFH-NINFKQAEKMMETMDQGDVIIRPSSKGENHLTVTWKVSDGIYqHVDVREEgKENAFSLGATLWinseeFEDLDE 1410
Cdd:smart00252    1 QPWYHgFISREEAEKLLKNEGDGDFLVRDSESSPGDYVLSVRVKGKVK-HYRIRRN-EDGKFYLEGGRK-----FPSLVE 73
                            90
                    ....*....|.
gi 27597090    1411 IVARYVQPMAS 1421
Cdd:smart00252   74 LVEHYQKNSLG 84
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1227-1282 4.32e-09

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 54.53  E-value: 4.32e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 27597090    1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEKFSADLTCR 1282
Cdd:smart00316   17 GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
HHH_9 pfam17674
HHH domain;
1051-1131 1.84e-07

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 49.84  E-value: 1.84e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090   1051 EVLDGSRVHPETYEWARKMAVDAleydesaedanpAGALEEILENPERLKDLDLDAFAEElerqGYGDkhITLYDIRAEL 1130
Cdd:pfam17674    1 NPLDNTAIHPESYPLAEKILKDL------------GLDLKDLIGNSALLKKLDPKKLAEE----EVGL--PTLKDILEEL 62

                   .
gi 27597090   1131 S 1131
Cdd:pfam17674   63 A 63
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
1227-1274 3.31e-07

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 48.92  E-value: 3.31e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 27597090 1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEK 1274
Cdd:cd00164   12 GVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK 59
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
1227-1281 4.84e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 48.82  E-value: 4.84e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 27597090   1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEKFSADLTC 1281
Cdd:pfam00575   18 GAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
1227-1271 2.34e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 42.46  E-value: 2.34e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 27597090  1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKID 1271
Cdd:PRK06299  475 GAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID 519
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1308-1512 4.98e-98

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 314.09  E-value: 4.98e-98
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090   1308 ADHKQEEDMKRKQQRTTYIKRVIAHPSFHNINFKQAEKMMETMDQGDVIIRPSSKGENHLTVTWKVSDGIYQHVDVREEG 1387
Cdd:pfam14633    2 ADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLELD 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090   1388 KENAFSLGATLWINSEEFEDLDEIVARYVQPMASFARDLLNHKYYQDcsgGDRKKLEELLIKTKKEKPTFIPYFICACKE 1467
Cdd:pfam14633   82 KENEFSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFKD---GTKEEVEEWLREEKKANPKRSPYAFCLSHK 158
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 27597090   1468 LPGKFLLGYQPRGKPRI--EYVTVTPEGFRYRGQIFPTVNGLFRWFK 1512
Cdd:pfam14633  159 HPGYFLLSFKANKNSRVhhWYVKVTPDGFRLRGQQFPDVDALCNGFK 205
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
775-931 1.40e-77

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage


Pssm-ID: 258777  Cd Length: 150  Bit Score: 253.25  E-value: 1.40e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    775 QGKGIRVLGIAFSSAR-DHPVFCALVNGEGEVTDFLRLphftkrrtAWREEEREKKAQDIETLKKFLLNKKPHVVTVAGE 853
Cdd:pfam14639    1 QGKIPRVLGVAFGSGRfDDAIICVLVNGEGEVTDFLKL--------AWREFDRENKAQFEETLKKFLLSKKPHVIGVSGE 72
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27597090    854 NRDAQMLIEDVKRIVHELDQGQQLSSIGVELVDNELAILYMNSKKSEAEFRDYPPVLRQAVSLARRIQDPLIEFAQVC 931
Cdd:pfam14639   73 NRDAQKFYEDVQRVLHELEQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
HHH_7 pfam14635
Helix-hairpin-helix motif;
935-1038 9.06e-60

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 200.08  E-value: 9.06e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    935 EDILCLKFHPLQEHVVKEELLNALYCEFINRVNEVGVDVNRAIAHPYSQALIQYVCGLGPRKGTHLLKILKQNNTRLESR 1014
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80
                           90       100
                   ....*....|....*....|....
gi 27597090   1015 TQLVTMCHMGPKVFMNCAGFLKID 1038
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
SH2_Nterm_SPT6_like cd09918
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ...
1331-1415 1.76e-45

N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198174  Cd Length: 85  Bit Score: 158.55  E-value: 1.76e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090 1331 AHPSFHNINFKQAEKMMETMDQGDVIIRPSSKGENHLTVTWKVSDGIYQHVDVREEGKENAFSLGATLWINSEEFEDLDE 1410
Cdd:cd09918    1 RHPLFKNVNYKQAEAYLKSKDVGEVVIRPSSKGVDHLTVTWKVADGVYQHIDIEELNKENPFSLGKELIIGGEEYEDLDE 80

                 ....*
gi 27597090 1411 IVARY 1415
Cdd:cd09918   81 IIARF 85
SH2_Cterm_SPT6_like cd09928
C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription ...
1424-1515 1.27e-35

C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198182  Cd Length: 89  Bit Score: 130.81  E-value: 1.27e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090 1424 RDLLNHKYYQdcsgGDRKKLEELLIKTKKEKPTFIPYFICACKELPGKFLLGYQP-RGKPRIEYVTVTPEGFRYRGQIFP 1502
Cdd:cd09928    1 EMLNHHKYFR----GTKEEVEKLLKEEKKANPKRIPYAFCVSKKYPGKFLLSYLPaNTRVRHEYVKVTPDGFRFRGQVFP 76
                         90
                 ....*....|...
gi 27597090 1503 TVNGLFRWFKDHY 1515
Cdd:cd09928   77 SVDSLLNWFKEHF 89
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
564-1130 8.76e-34

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 140.93  E-value: 8.76e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  564 AEPLELAKDYVCS--QFPTPEAVLEGARYMVALQIAREPLVRQVLRQTFQERAKLnITPTKKGRKDVD---EAHYAYSfk 638
Cdd:COG2183  135 GDPEAEAAKYINEekGVADVEAALDGARDILAERISEDAELRGKLRELLWKEGVL-VSKVKKGKEEEGakfRDYFDYS-- 211
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  639 ylknKPVKELRDDQFLKICLAEDEGLLTTDISIDlkgvegygnDQTYFEEIKQFYyrdeFSHQVQEWNRQRTMAIERALQ 718
Cdd:COG2183  212 ----EPLKKIPSHRILALNRGEKEGVLKVKLEPD---------EEEAEAYIARRF----IKDQGRPADEWLKEAVRDAYK 274
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  719 QFLYVQMAKELKNKLLAEAKEYVIKACSRKLYNWLRVAPYrpdqqveedddfmdenqgKGIRVLGIafssarDhPVF--- 795
Cdd:COG2183  275 RLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPA------------------GGKVVLGL------D-PGFrtg 329
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  796 --CALVNGEGEVTD----FlrlPHftkrrtawreEEREKKAQDIETLKKFLlnKKPHVVTVAGEN----RDAQMLIEDVK 865
Cdd:COG2183  330 ckVAVVDETGKLLDtatiY---PH----------PPQNKWEEAAKTLAALI--KKYKVELIAIGNgtasRETEQFVAELI 394
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  866 RivhelDQGQQLSSIGVelvdNEL-AILYMNSKKSEAEFRDYPPVLRQAVSLARRIQDPLIEFaqVcssdedilclKFHP 944
Cdd:COG2183  395 K-----ELDLKVQYVIV----SEAgASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAEL--V----------KIDP 453
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090  945 -------LQeHVVKEELLN-AL-----YCefinrVNEVGVDVNRAiahpySQALIQYVCGLGPRkgthllkiLKQN---- 1007
Cdd:COG2183  454 ksigvgqYQ-HDVNQKKLKrSLdavveDC-----VNAVGVDLNTA-----SAPLLSYVSGLNPT--------LAKNivay 514
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090 1008 ---NTRLESRTQL--VTMchMGPKVFMNCAGFLKIDTASlgdstdsyiEVLDGSRVHPETYEWARKMAvDALEYDesaed 1082
Cdd:COG2183  515 rdeNGAFKSRKELlkVPR--LGPKAFEQAAGFLRIRDGD---------NPLDNSAVHPESYPVVEKIL-KDLGVS----- 577
                        570       580       590       600
                 ....*....|....*....|....*....|....*....|....*...
gi 27597090 1083 anpagaLEEILENPERLKDLDLDAFAEELerqgYGDkhITLYDIRAEL 1130
Cdd:COG2183  578 ------VKDLIGNKELLKKLDPEKYADEL----FGL--PTLRDILKEL 613
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
347-422 2.53e-24

Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins.


Pssm-ID: 464230  Cd Length: 115  Bit Score: 99.17  E-value: 2.53e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    347 SFSRKGPSTIQKIKEALGFMRNQHFEVPFIAFYRKEYVE-----------PELHINDLWRVWQWDEKWTQLRIRKENLTR 415
Cdd:pfam14641   27 DFERLLEPFKEAVGNVLEFISKDNLEVPFIWQHRRDYLLhsekdgfeighKLLNEDDLWRIVQLDIKFHSLIEKRNNLEK 106

                   ....*..
gi 27597090    416 LFEKMQA 422
Cdd:pfam14641  107 LYEKLGI 113
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
779-894 1.34e-16

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 76.84  E-value: 1.34e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090     779 IRVLGIAFSsarDHPVFCALVNGEGEVTDFLRLPHFTKrrtawreeerekKAQDIETLKKFLLNKKPHVVTVAGENRDAQ 858
Cdd:smart00732    1 KRVLGLDPG---RKGIGVAVVDETGKLADPLEVIPRTN------------KEADAARLKKLIKKYQPDLIVIGLPLNMNG 65
                            90       100       110
                    ....*....|....*....|....*....|....*.
gi 27597090     859 MLIEDVKRIVHELDqgQQLSSIGVELVDNELAILYM 894
Cdd:smart00732   66 TASRETEEAFAELL--KERFNLPVVLVDERLATVYA 99
SH2 smart00252
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ...
1332-1421 7.64e-12

Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.


Pssm-ID: 214585 [Multi-domain]  Cd Length: 84  Bit Score: 62.63  E-value: 7.64e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    1332 HPSFH-NINFKQAEKMMETMDQGDVIIRPSSKGENHLTVTWKVSDGIYqHVDVREEgKENAFSLGATLWinseeFEDLDE 1410
Cdd:smart00252    1 QPWYHgFISREEAEKLLKNEGDGDFLVRDSESSPGDYVLSVRVKGKVK-HYRIRRN-EDGKFYLEGGRK-----FPSLVE 73
                            90
                    ....*....|.
gi 27597090    1411 IVARYVQPMAS 1421
Cdd:smart00252   74 LVEHYQKNSLG 84
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1227-1282 4.32e-09

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 54.53  E-value: 4.32e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 27597090    1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEKFSADLTCR 1282
Cdd:smart00316   17 GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
968-1035 1.23e-08

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 52.87  E-value: 1.23e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090    968 EVGVDVNRAiahpySQALIQYVCGLGPRKGThllKILK--QNNTRLESRTQLVTMCHMGPKVFMNCAGFL 1035
Cdd:pfam12836    1 AVGVDINTA-----SAELLSRVPGLGPKLAK---NIVEyrEENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
HHH_9 pfam17674
HHH domain;
1051-1131 1.84e-07

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 49.84  E-value: 1.84e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090   1051 EVLDGSRVHPETYEWARKMAVDAleydesaedanpAGALEEILENPERLKDLDLDAFAEElerqGYGDkhITLYDIRAEL 1130
Cdd:pfam17674    1 NPLDNTAIHPESYPLAEKILKDL------------GLDLKDLIGNSALLKKLDPKKLAEE----EVGL--PTLKDILEEL 62

                   .
gi 27597090   1131 S 1131
Cdd:pfam17674   63 A 63
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
1227-1274 3.31e-07

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 48.92  E-value: 3.31e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 27597090 1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEK 1274
Cdd:cd00164   12 GVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK 59
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
1227-1281 4.84e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 48.82  E-value: 4.84e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 27597090   1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEKFSADLTC 1281
Cdd:pfam00575   18 GAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
SH2 cd00173
Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they ...
1333-1415 6.89e-07

Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1), Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others.


Pssm-ID: 198173 [Multi-domain]  Cd Length: 79  Bit Score: 48.61  E-value: 6.89e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090 1333 PSFH-NINFKQAEKMMETMDQGDVIIRPSSKGENHLTVTWKVSDGIYQHVDVREEGKENAFSLGATLWinseeFEDLDEI 1411
Cdd:cd00173    1 PWFHgSISREEAERLLRGKPDGTFLVRESSSEPGDYVLSVRSGDGKVKHYLIERNEGGYYLLGGSGRT-----FPSLPEL 75

                 ....
gi 27597090 1412 VARY 1415
Cdd:cd00173   76 VEHY 79
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
1224-1274 3.38e-05

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 43.38  E-value: 3.38e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 27597090 1224 QAIGVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEK 1274
Cdd:cd05697   12 RPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPER 62
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1234-1282 7.46e-05

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 42.60  E-value: 7.46e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 27597090 1234 NGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEKFSADLTCR 1282
Cdd:cd05698   22 NNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
1227-1274 1.80e-04

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 41.80  E-value: 1.80e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 27597090 1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEK 1274
Cdd:cd04461   29 GVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEK 76
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
1226-1274 7.44e-04

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 39.52  E-value: 7.44e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 27597090 1226 IGVKTrldngvTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKIDIEK 1274
Cdd:cd05685   20 IGVKQ------DGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEER 62
SH2 pfam00017
SH2 domain;
1335-1415 1.13e-03

SH2 domain;


Pssm-ID: 425423 [Multi-domain]  Cd Length: 77  Bit Score: 39.12  E-value: 1.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27597090   1335 FH-NINFKQAEKM-METMDQGDVIIRPSSKGENHLTVTWKVSDGIyQHVDVREEGKENAFSLGAtlwinsEEFEDLDEIV 1412
Cdd:pfam00017    2 YHgKISRQEAERLlLNGKPDGTFLVRESESTPGGYTLSVRDDGKV-KHYKIQSTDNGGYYISGG------VKFSSLAELV 74

                   ...
gi 27597090   1413 ARY 1415
Cdd:pfam00017   75 EHY 77
rpsA PRK06299
30S ribosomal protein S1; Reviewed
1227-1271 2.34e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 42.46  E-value: 2.34e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 27597090  1227 GVKTRLDNGVTGFIPTKFLSDKVVKRPEERVKVGMTVHCRIMKID 1271
Cdd:PRK06299  475 GAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID 519
 
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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