|
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
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| 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
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| 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
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| 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
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