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Conserved domains on  [gi|1227098282|gb|OXU22488.1|]
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hypothetical protein TSAR_006883 [Trichomalopsis sarcophagae]

Protein Classification

Tex family protein( domain architecture ID 13863307)

Tex (toxin expression) family protein is an RNA-binding transcriptional accessory protein; includes two functional domains, an N-terminal domain which may be a transcriptional factor, and a C-terminal S1 RNA-binding domain

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1305-1512 5.13e-97

SH2 domain;


:

Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 311.00  E-value: 5.13e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1305 KDNLVEEETKKVKQRQMYVTRVIIHPSFRNITYADAEKLMKTMPQGEAIIRPSSKGDDHLTVTWKVTDDVHQHIDVREEG 1384
Cdd:pfam14633    2 ADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLELD 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1385 KENKYSLGRSLWIGNEEFEDLDEILARHIDPMAASVRELMNFKsdYYVPhvmGMKDKAEEILKDLKSKNMNKIHYIISPS 1464
Cdd:pfam14633   82 KENEFSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHR--KFKD---GTKEEVEEWLREEKKANPKRSPYAFCLS 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1465 KNYPGKFLLSYLPRN--RCGHEFITVIPDGFRFRKNSFPRFSDLMGWFKK 1512
Cdd:pfam14633  157 HKHPGYFLLSFKANKnsRVHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
HHH_5 super family cl22429
Helix-hairpin-helix domain;
932-1035 1.81e-43

Helix-hairpin-helix domain;


The actual alignment was detected with superfamily member pfam14635:

Pssm-ID: 473956  Cd Length: 104  Bit Score: 153.47  E-value: 1.81e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  932 DEILCLKYHSLQDQLPKEDLLENINLEFVNRVNEVGVDINKTVQQPYSGNLLQYVCGLGARKGQHLIKMLKQTNQRLENR 1011
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80

                           90       100
                   ....*....|....*....|....
gi 1227098282 1012 TQLVTSCHMGPKVFINCAGFIKID 1035
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
RuvC-like super family cl21482
Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family ...
 774-928 4.01e-35

Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family consists of bacterial RuvC, fungal Cruciform cutting endonuclease 1 (CCE1), bacterial YqgF and monokaryotic chloroplast 1 protein (MOC1). RuvC, CCE1 and MOC1 are Holliday junction resolvases (HJRs), endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. CCE1 is a HJR specific for 4-way junctions; it is involved in the maintenance of mitochondrial DNA. Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


The actual alignment was detected with superfamily member pfam14639:

Pssm-ID: 473878  Cd Length: 150  Bit Score: 131.53  E-value: 4.01e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  774 KGLRVMGLAYVP-DFSIAAYACLIAPDGECTDYLKLphllkkknSYRDTDKIAKEADVLAIRNFLSTKKPHVVVIGGESR 852
Cdd:pfam14639    3 KIPRVLGVAFGSgRFDDAIICVLVNGEGEVTDFLKL--------AWREFDRENKAQFEETLKKFLLSKKPHVIGVSGENR 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1227098282  853 DALMIAEDVRECIATLVADEQFPSIGVEIMDNELAITYSNSNKGVSEFRDYPVELRQAISLARRLQDPLVEFSQLC 928
Cdd:pfam14639   75 DAQKFYEDVQRVLHELEQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
 301-410 4.38e-21

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: 89.93  E-value: 4.38e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  301 ATEKELAAEAQWIYNQAFERKTISIQDAHlneeakervkkgPQTVAKITTALDFIRNQHFEVPFISFYRKEYVL------ 374
Cdd:pfam14641    4 LTDEELEEEANWISNRLLVEKNDDFERLL------------EPFKEAVGNVLEFISKDNLEVPFIWQHRRDYLLhsekdg 71

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1227098282  375 -----PELNINDLWKVYKYDAKWCQLRQRKEALLVLFRKMK 410
Cdd:pfam14641   72 feighKLLNEDDLWRIVQLDIKFHSLIEKRNNLEKLYEKLG 112
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1224-1274 9.86e-11

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: 59.22  E-value: 9.86e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1227098282 1224 GIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDRFGV 1274
Cdd:pfam00575   18 GAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
HHH_9 super family cl40179
HHH domain;
1048-1125 4.90e-07

HHH domain;


The actual alignment was detected with superfamily member pfam17674:

Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 48.69  E-value: 4.90e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1227098282 1048 EVLDGSRVHPETYEWARKMAVDAleyddedanpAGALEEILESPERLKDLDLDAFAEElerqGFGNkcITLYDIRSEL 1125
Cdd:pfam17674    1 NPLDNTAIHPESYPLAEKILKDL----------GLDLKDLIGNSALLKKLDPKKLAEE----EVGL--PTLKDILEEL 62
Tex_N super family cl46305
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 362-623 2.83e-03

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


The actual alignment was detected with superfamily member pfam09371:

Pssm-ID: 480645  Cd Length: 183  Bit Score: 40.47  E-value: 2.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  362 VPFISFYRKEYV--LPELNINDLWKVYKYdakWCQLRQRKEALLvlfrkmkryqedfimkdpdaplpdnmRLIEEEDI-- 437
Cdd:pfam09371   25 VPFIARYRKEATggLDEVQLREIEERLEY---LRELEKRKETIL--------------------------KSIEEQGKlt 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  438 ----KQLENVQTTEELNDCYhhfmLYYsheipkmqeivrkqeKEKRRqeriqkrkqliaeaeengedpppedpfeedddn 513
Cdd:pfam09371   76 delkAAIEAADTLTELEDLY----LPY---------------KPKRR--------------------------------- 103

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  514 epeeTLKQavrtgpysICRRAGLESLAKRfglppeqyaknlseeyqIFeveqELNEPTAVAAEYV--GEKFQTADEVLKA 591
Cdd:pfam09371  104 ----TKAT--------IAREKGLEPLADA-----------------IL----AQPDPEEEAAKYInpEKGVADVEEALAG 150

                          250       260       270
                   ....*....|....*....|....*....|..
gi 1227098282  592 AQLMVAIQLAREPLVRESVRKMYKEKAKISVR 623
Cdd:pfam09371  151 ARDIIAERISEDAELRKKLRELLWREGVIVSK 182
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1305-1512 5.13e-97

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 311.00  E-value: 5.13e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1305 KDNLVEEETKKVKQRQMYVTRVIIHPSFRNITYADAEKLMKTMPQGEAIIRPSSKGDDHLTVTWKVTDDVHQHIDVREEG 1384
Cdd:pfam14633    2 ADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLELD 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1385 KENKYSLGRSLWIGNEEFEDLDEILARHIDPMAASVRELMNFKsdYYVPhvmGMKDKAEEILKDLKSKNMNKIHYIISPS 1464
Cdd:pfam14633   82 KENEFSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHR--KFKD---GTKEEVEEWLREEKKANPKRSPYAFCLS 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1465 KNYPGKFLLSYLPRN--RCGHEFITVIPDGFRFRKNSFPRFSDLMGWFKK 1512
Cdd:pfam14633  157 HKHPGYFLLSFKANKnsRVHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
HHH_7 pfam14635
Helix-hairpin-helix motif;
932-1035 1.81e-43

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 153.47  E-value: 1.81e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  932 DEILCLKYHSLQDQLPKEDLLENINLEFVNRVNEVGVDINKTVQQPYSGNLLQYVCGLGARKGQHLIKMLKQTNQRLENR 1011
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80

                           90       100
                   ....*....|....*....|....
gi 1227098282 1012 TQLVTSCHMGPKVFINCAGFIKID 1035
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 ...
 1329-1412 1.78e-42

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: 150.08  E-value: 1.78e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1329 HPSFRNITYADAEKLMKTMPQGEAIIRPSSKGDDHLTVTWKVTDDVHQHIDVREEGKENKYSLGRSLWIGNEEFEDLDEI 1408
Cdd:cd09918      2 HPLFKNVNYKQAEAYLKSKDVGEVVIRPSSKGVDHLTVTWKVADGVYQHIDIEELNKENPFSLGKELIIGGEEYEDLDEI 81


                   ....
gi 1227098282 1409 LARH 1412
Cdd:cd09918     82 IARF 85
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 774-928 4.01e-35

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: 131.53  E-value: 4.01e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  774 KGLRVMGLAYVP-DFSIAAYACLIAPDGECTDYLKLphllkkknSYRDTDKIAKEADVLAIRNFLSTKKPHVVVIGGESR 852
Cdd:pfam14639    3 KIPRVLGVAFGSgRFDDAIICVLVNGEGEVTDFLKL--------AWREFDRENKAQFEETLKKFLLSKKPHVIGVSGENR 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1227098282  853 DALMIAEDVRECIATLVADEQFPSIGVEIMDNELAITYSNSNKGVSEFRDYPVELRQAISLARRLQDPLVEFSQLC 928
Cdd:pfam14639   75 DAQKFYEDVQRVLHELEQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
890-1125 5.08e-24

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 109.73  E-value: 5.08e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  890 YSNSNKGVSEFRDYPVELRQAISLARRLQDPLVEFsqlcnaddeilcLK----------Y-HSL-QDQLPKEdlleninL 957
Cdd:COG2183    414 YSASELAREEFPDLDVTVRGAVSIARRLQDPLAEL------------VKidpksigvgqYqHDVnQKKLKRS-------L 474

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  958 EFV--NRVNEVGVDINkTVqqpySGNLLQYVCGLGARKGQHLIKMlKQTNQRLENRTQL--VTSchMGPKVFINCAGFIK 1033
Cdd:COG2183    475 DAVveDCVNAVGVDLN-TA----SAPLLSYVSGLNPTLAKNIVAY-RDENGAFKSRKELlkVPR--LGPKAFEQAAGFLR 546

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1034 IDTnslGDsteayvEVLDGSRVHPETYEWARKMAvDALEYDdedanpagaLEEILESPERLKDLDLDAFAEELerqgFGN 1113
Cdd:COG2183    547 IRD---GD------NPLDNSAVHPESYPVVEKIL-KDLGVS---------VKDLIGNKELLKKLDPEKYADEL----FGL 603

                          250
                   ....*....|..
gi 1227098282 1114 kcITLYDIRSEL 1125
Cdd:COG2183    604 --PTLRDILKEL 613
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
 301-410 4.38e-21

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: 89.93  E-value: 4.38e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  301 ATEKELAAEAQWIYNQAFERKTISIQDAHlneeakervkkgPQTVAKITTALDFIRNQHFEVPFISFYRKEYVL------ 374
Cdd:pfam14641    4 LTDEELEEEANWISNRLLVEKNDDFERLL------------EPFKEAVGNVLEFISKDNLEVPFIWQHRRDYLLhsekdg 71

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1227098282  375 -----PELNINDLWKVYKYDAKWCQLRQRKEALLVLFRKMK 410
Cdd:pfam14641   72 feighKLLNEDDLWRIVQLDIKFHSLIEKRNNLEKLYEKLG 112
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1224-1274 9.86e-11

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: 59.22  E-value: 9.86e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1227098282 1224 GIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDRFGV 1274
Cdd:pfam00575   18 GAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1224-1271 7.45e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 56.46  E-value: 7.45e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1227098282  1224 GIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDR 1271
Cdd:smart00316   17 GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEK 64
SH2 smart00252
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ...
 1332-1412 1.36e-09

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: 56.08  E-value: 1.36e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  1332 FRNITYADAEKLMKTMPQGEAIIRPSSKGDDHLTVTWKVTDDVHqHIDVREEgKENKYSLGrslwiGNEEFEDLDEILAR 1411
Cdd:smart00252    5 HGFISREEAEKLLKNEGDGDFLVRDSESSPGDYVLSVRVKGKVK-HYRIRRN-EDGKFYLE-----GGRKFPSLVELVEH 77


                    .
gi 1227098282  1412 H 1412
Cdd:smart00252   78 Y 78
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1224-1271 8.75e-08

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: 50.46  E-value: 8.75e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1227098282 1224 GIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDR 1271
Cdd:cd00164     12 GVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK 59
HHH_9 pfam17674
HHH domain;
1048-1125 4.90e-07

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 48.69  E-value: 4.90e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1227098282 1048 EVLDGSRVHPETYEWARKMAVDAleyddedanpAGALEEILESPERLKDLDLDAFAEElerqGFGNkcITLYDIRSEL 1125
Cdd:pfam17674    1 NPLDNTAIHPESYPLAEKILKDL----------GLDLKDLIGNSALLKKLDPKKLAEE----EVGL--PTLKDILEEL 62
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 1219-1271 7.02e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 53.89  E-value: 7.02e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1227098282 1219 PGKAT-----GIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDR 1271
Cdd:PRK07899   298 PGKVTklvpfGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLER 355
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 826-891 2.87e-05

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: 44.48  E-value: 2.87e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1227098282   826 KEADVLAIRNFLSTKKPHVVVIGGESRDALMIAEDVRECIATLVadEQFPSIGVEIMDNELAITYS 891
Cdd:smart00732   36 KEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETEEAFAELL--KERFNLPVVLVDERLATVYA 99
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1221-1270 1.45e-04

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 46.27  E-value: 1.45e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1221 KATGIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVD 1270
Cdd:TIGR00717  458 KDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKK 507
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 362-623 2.83e-03

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


Pssm-ID: 462777  Cd Length: 183  Bit Score: 40.47  E-value: 2.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  362 VPFISFYRKEYV--LPELNINDLWKVYKYdakWCQLRQRKEALLvlfrkmkryqedfimkdpdaplpdnmRLIEEEDI-- 437
Cdd:pfam09371   25 VPFIARYRKEATggLDEVQLREIEERLEY---LRELEKRKETIL--------------------------KSIEEQGKlt 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  438 ----KQLENVQTTEELNDCYhhfmLYYsheipkmqeivrkqeKEKRRqeriqkrkqliaeaeengedpppedpfeedddn 513
Cdd:pfam09371   76 delkAAIEAADTLTELEDLY----LPY---------------KPKRR--------------------------------- 103

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  514 epeeTLKQavrtgpysICRRAGLESLAKRfglppeqyaknlseeyqIFeveqELNEPTAVAAEYV--GEKFQTADEVLKA 591
Cdd:pfam09371  104 ----TKAT--------IAREKGLEPLADA-----------------IL----AQPDPEEEAAKYInpEKGVADVEEALAG 150

                          250       260       270
                   ....*....|....*....|....*....|..
gi 1227098282  592 AQLMVAIQLAREPLVRESVRKMYKEKAKISVR 623
Cdd:pfam09371  151 ARDIIAERISEDAELRKKLRELLWREGVIVSK 182
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1305-1512 5.13e-97

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 311.00  E-value: 5.13e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1305 KDNLVEEETKKVKQRQMYVTRVIIHPSFRNITYADAEKLMKTMPQGEAIIRPSSKGDDHLTVTWKVTDDVHQHIDVREEG 1384
Cdd:pfam14633    2 ADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLELD 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1385 KENKYSLGRSLWIGNEEFEDLDEILARHIDPMAASVRELMNFKsdYYVPhvmGMKDKAEEILKDLKSKNMNKIHYIISPS 1464
Cdd:pfam14633   82 KENEFSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHR--KFKD---GTKEEVEEWLREEKKANPKRSPYAFCLS 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1465 KNYPGKFLLSYLPRN--RCGHEFITVIPDGFRFRKNSFPRFSDLMGWFKK 1512
Cdd:pfam14633  157 HKHPGYFLLSFKANKnsRVHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
HHH_7 pfam14635
Helix-hairpin-helix motif;
932-1035 1.81e-43

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 153.47  E-value: 1.81e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  932 DEILCLKYHSLQDQLPKEDLLENINLEFVNRVNEVGVDINKTVQQPYSGNLLQYVCGLGARKGQHLIKMLKQTNQRLENR 1011
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80

                           90       100
                   ....*....|....*....|....
gi 1227098282 1012 TQLVTSCHMGPKVFINCAGFIKID 1035
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 ...
 1329-1412 1.78e-42

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: 150.08  E-value: 1.78e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1329 HPSFRNITYADAEKLMKTMPQGEAIIRPSSKGDDHLTVTWKVTDDVHQHIDVREEGKENKYSLGRSLWIGNEEFEDLDEI 1408
Cdd:cd09918      2 HPLFKNVNYKQAEAYLKSKDVGEVVIRPSSKGVDHLTVTWKVADGVYQHIDIEELNKENPFSLGKELIIGGEEYEDLDEI 81


                   ....
gi 1227098282 1409 LARH 1412
Cdd:cd09918     82 IARF 85
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 774-928 4.01e-35

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: 131.53  E-value: 4.01e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  774 KGLRVMGLAYVP-DFSIAAYACLIAPDGECTDYLKLphllkkknSYRDTDKIAKEADVLAIRNFLSTKKPHVVVIGGESR 852
Cdd:pfam14639    3 KIPRVLGVAFGSgRFDDAIICVLVNGEGEVTDFLKL--------AWREFDRENKAQFEETLKKFLLSKKPHVIGVSGENR 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1227098282  853 DALMIAEDVRECIATLVADEQFPSIGVEIMDNELAITYSNSNKGVSEFRDYPVELRQAISLARRLQDPLVEFSQLC 928
Cdd:pfam14639   75 DAQKFYEDVQRVLHELEQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
SH2_Cterm_SPT6_like cd09928
C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription ...
 1436-1514 1.08e-27

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: 108.08  E-value: 1.08e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1436 MGMKDKAEEILKDLKSKNMNKIHYIISPSKNYPGKFLLSYLP-RNRCGHEFITVIPDGFRFRKNSFPRFSDLMGWFKKHY 1514
Cdd:cd09928     10 RGTKEEVEKLLKEEKKANPKRIPYAFCVSKKYPGKFLLSYLPaNTRVRHEYVKVTPDGFRFRGQVFPSVDSLLNWFKEHF 89
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
890-1125 5.08e-24

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 109.73  E-value: 5.08e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  890 YSNSNKGVSEFRDYPVELRQAISLARRLQDPLVEFsqlcnaddeilcLK----------Y-HSL-QDQLPKEdlleninL 957
Cdd:COG2183    414 YSASELAREEFPDLDVTVRGAVSIARRLQDPLAEL------------VKidpksigvgqYqHDVnQKKLKRS-------L 474

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  958 EFV--NRVNEVGVDINkTVqqpySGNLLQYVCGLGARKGQHLIKMlKQTNQRLENRTQL--VTSchMGPKVFINCAGFIK 1033
Cdd:COG2183    475 DAVveDCVNAVGVDLN-TA----SAPLLSYVSGLNPTLAKNIVAY-RDENGAFKSRKELlkVPR--LGPKAFEQAAGFLR 546

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1034 IDTnslGDsteayvEVLDGSRVHPETYEWARKMAvDALEYDdedanpagaLEEILESPERLKDLDLDAFAEELerqgFGN 1113
Cdd:COG2183    547 IRD---GD------NPLDNSAVHPESYPVVEKIL-KDLGVS---------VKDLIGNKELLKKLDPEKYADEL----FGL 603

                          250
                   ....*....|..
gi 1227098282 1114 kcITLYDIRSEL 1125
Cdd:COG2183    604 --PTLRDILKEL 613
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
 301-410 4.38e-21

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: 89.93  E-value: 4.38e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  301 ATEKELAAEAQWIYNQAFERKTISIQDAHlneeakervkkgPQTVAKITTALDFIRNQHFEVPFISFYRKEYVL------ 374
Cdd:pfam14641    4 LTDEELEEEANWISNRLLVEKNDDFERLL------------EPFKEAVGNVLEFISKDNLEVPFIWQHRRDYLLhsekdg 71

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1227098282  375 -----PELNINDLWKVYKYDAKWCQLRQRKEALLVLFRKMK 410
Cdd:pfam14641   72 feighKLLNEDDLWRIVQLDIKFHSLIEKRNNLEKLYEKLG 112
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1224-1274 9.86e-11

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: 59.22  E-value: 9.86e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1227098282 1224 GIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDRFGV 1274
Cdd:pfam00575   18 GAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1224-1271 7.45e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 56.46  E-value: 7.45e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1227098282  1224 GIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDR 1271
Cdd:smart00316   17 GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEK 64
SH2 smart00252
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ...
 1332-1412 1.36e-09

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: 56.08  E-value: 1.36e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  1332 FRNITYADAEKLMKTMPQGEAIIRPSSKGDDHLTVTWKVTDDVHqHIDVREEgKENKYSLGrslwiGNEEFEDLDEILAR 1411
Cdd:smart00252    5 HGFISREEAEKLLKNEGDGDFLVRDSESSPGDYVLSVRVKGKVK-HYRIRRN-EDGKFYLE-----GGRKFPSLVELVEH 77


                    .
gi 1227098282  1412 H 1412
Cdd:smart00252   78 Y 78
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1224-1271 8.75e-08

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: 50.46  E-value: 8.75e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1227098282 1224 GIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDR 1271
Cdd:cd00164     12 GVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK 59
HHH_9 pfam17674
HHH domain;
1048-1125 4.90e-07

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 48.69  E-value: 4.90e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1227098282 1048 EVLDGSRVHPETYEWARKMAVDAleyddedanpAGALEEILESPERLKDLDLDAFAEElerqGFGNkcITLYDIRSEL 1125
Cdd:pfam17674    1 NPLDNTAIHPESYPLAEKILKDL----------GLDLKDLIGNSALLKKLDPKKLAEE----EVGL--PTLKDILEEL 62
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 1219-1271 7.02e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 53.89  E-value: 7.02e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1227098282 1219 PGKAT-----GIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDR 1271
Cdd:PRK07899   298 PGKVTklvpfGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLER 355
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 965-1032 8.09e-07

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 47.48  E-value: 8.09e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1227098282  965 EVGVDINKTvqqpySGNLLQYVCGLGARKGQHLIKMlKQTNQRLENRTQLVTSCHMGPKVFINCAGFI 1032
Cdd:pfam12836    1 AVGVDINTA-----SAELLSRVPGLGPKLAKNIVEY-REENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
SH2 pfam00017
SH2 domain;
1332-1408 1.04e-06

SH2 domain;


Pssm-ID: 425423 [Multi-domain]  Cd Length: 77  Bit Score: 47.98  E-value: 1.04e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1227098282 1332 FRNITYADAEK-LMKTMPQGEAIIRPSSKGDDHLTVTWKvTDDVHQHIDVREEGKENKYSLGRslwignEEFEDLDEI 1408
Cdd:pfam00017    3 HGKISRQEAERlLLNGKPDGTFLVRESESTPGGYTLSVR-DDGKVKHYKIQSTDNGGYYISGG------VKFSSLAEL 73
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 1230-1271 2.75e-05

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: 43.38  E-value: 2.75e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1227098282 1230 DNGI--SGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDR 1271
Cdd:cd05685     19 DIGVkqDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEER 62
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 826-891 2.87e-05

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: 44.48  E-value: 2.87e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1227098282   826 KEADVLAIRNFLSTKKPHVVVIGGESRDALMIAEDVRECIATLVadEQFPSIGVEIMDNELAITYS 891
Cdd:smart00732   36 KEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETEEAFAELL--KERFNLPVVLVDERLATVYA 99
SH2 cd00173
Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they ...
 1332-1412 3.11e-05

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: 43.60  E-value: 3.11e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1332 FRNITYADAEKLMKTMPQGEAIIRPSSKGDDHLTVTWKVTDDVHQHIDVREEGKENKYSLGRSLWigneeFEDLDEILAR 1411
Cdd:cd00173      4 HGSISREEAERLLRGKPDGTFLVRESSSEPGDYVLSVRSGDGKVKHYLIERNEGGYYLLGGSGRT-----FPSLPELVEH 78


                   .
gi 1227098282 1412 H 1412
Cdd:cd00173     79 Y 79
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1221-1270 1.45e-04

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 46.27  E-value: 1.45e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1227098282 1221 KATGIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVD 1270
Cdd:TIGR00717  458 KDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKK 507
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1221-1271 2.46e-04

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: 41.07  E-value: 2.46e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1227098282 1221 KATGIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIEVDR 1271
Cdd:cd05697     12 RPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPER 62
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 890-918 3.69e-04

Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes.


Pssm-ID: 465314  Cd Length: 125  Bit Score: 42.00  E-value: 3.69e-04
                           10        20
                   ....*....|....*....|....*....
gi 1227098282  890 YSNSNKGVSEFRDYPVELRQAISLARRLQ 918
Cdd:pfam16921   97 YSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1220-1268 5.07e-04

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 39.96  E-value: 5.07e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1227098282 1220 GKATGIR-----LRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIE 1268
Cdd:cd05692      6 GTVTRLKpfgafVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1229-1270 1.09e-03

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 43.78  E-value: 1.09e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1227098282 1229 LDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIikIEVD 1270
Cdd:PRK00087   582 LEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKI--LEVD 621
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1221-1265 1.53e-03

S1_Rrp5_repeat_hs11_sc8: 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 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 38.73  E-value: 1.53e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1227098282 1221 KATGIRLRLDNGISGFIHIKNLSD--KHVTNPEDRVRIGNRIHCRII 1265
Cdd:cd05702     12 KPTQLNVQLADNVHGRIHVSEVFDewPDGKNPLSKFKIGQKIKARVI 58
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1221-1268 2.78e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 42.46  E-value: 2.78e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1227098282 1221 KATGIRLRLDNGISGFIHIKNLSDKHVTNPEDRVRIGNRIHCRIIKIE 1268
Cdd:PRK06299   472 KDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID 519
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 362-623 2.83e-03

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


Pssm-ID: 462777  Cd Length: 183  Bit Score: 40.47  E-value: 2.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  362 VPFISFYRKEYV--LPELNINDLWKVYKYdakWCQLRQRKEALLvlfrkmkryqedfimkdpdaplpdnmRLIEEEDI-- 437
Cdd:pfam09371   25 VPFIARYRKEATggLDEVQLREIEERLEY---LRELEKRKETIL--------------------------KSIEEQGKlt 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  438 ----KQLENVQTTEELNDCYhhfmLYYsheipkmqeivrkqeKEKRRqeriqkrkqliaeaeengedpppedpfeedddn 513
Cdd:pfam09371   76 delkAAIEAADTLTELEDLY----LPY---------------KPKRR--------------------------------- 103

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1227098282  514 epeeTLKQavrtgpysICRRAGLESLAKRfglppeqyaknlseeyqIFeveqELNEPTAVAAEYV--GEKFQTADEVLKA 591
Cdd:pfam09371  104 ----TKAT--------IAREKGLEPLADA-----------------IL----AQPDPEEEAAKYInpEKGVADVEEALAG 150

                          250       260       270
                   ....*....|....*....|....*....|..
gi 1227098282  592 AQLMVAIQLAREPLVRESVRKMYKEKAKISVR 623
Cdd:pfam09371  151 ARDIIAERISEDAELRKKLRELLWREGVIVSK 182
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1224-1271 2.96e-03

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 37.86  E-value: 2.96e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1227098282 1224 GIRLRLDNGISGFIHIKNLS-DKHVTNPEDRVRIGNRIHCRIIKIEVDR 1271
Cdd:cd05690     15 GIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVER 63
SH2 cd00173
Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they ...
 1439-1506 4.70e-03

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: 37.44  E-value: 4.70e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1227098282 1439 KDKAEEILKDLK--SknmnkihYIISPSKNYPGKFLLSYL-PRNRCGHEFITVIPDGFRFRKNSFPRFSDL 1506
Cdd:cd00173      9 REEAERLLRGKPdgT-------FLVRESSSEPGDYVLSVRsGDGKVKHYLIERNEGGYYLLGGSGRTFPSL 72
SH2_SOCS7 cd10388
Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) proteins; SH2 ...
 1334-1392 7.57e-03

Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) proteins; SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. Members (SOCS4-SOCS7) were identified by their conserved SOCS box, an adapter motif of 3 helices that associates substrate binding domains, such as the SOCS SH2 domain, ankryin, and WD40 with ubiquitin ligase components. These show limited cytokine induction. 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: 198251  Cd Length: 101  Bit Score: 37.72  E-value: 7.57e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1227098282 1334 NITYADAEKLMKTMPQGEAIIRPSSkgDDH--LTVTWKVTDDVHQhidVREEGKENKYSLG 1392
Cdd:cd10388     16 PMSWEDAEKVLSNKPDGSFLVRDSS--DDRyiFSLSFRSQGSVHH---TRIEQYQGTFSLG 71
 
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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