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Conserved domains on  [gi|528532851|dbj|BAN67209|]
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transcription elongation factor Spt6 [Schizosaccharomyces pombe]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1142-1353 7.45e-111

SH2 domain;


:

Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 347.21  E-value: 7.45e-111
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851  1142 EAEKRDTERMQAETQAEQRVARVIKHPLFKDLNASQAEAYLSKMQVGDLVIRPSSKGSDHIVVTWKVAEGSYQHIDVLEL 1221
Cdd:pfam14633    1 DADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLEL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851  1222 EKENEFTIGQKLLVKGrfekmtYQYSDLDELIVLHIKAIAKKIDEMCIHDKFRKGTQAETEKWLESYSEANPKRSCYAFC 1301
Cdd:pfam14633   81 DKENEFSLGKTLRIGG------EEYEDLDELIARHVQPMARKVEEMMNHRKFKDGTKEEVEEWLREEKKANPKRSPYAFC 154

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528532851  1302 FDHQHPGYFILCFKASVNSPVTAWPVKVIPNAFFLQGNVYGDMTALCNGFKL 1353
Cdd:pfam14633  155 LSHKHPGYFLLSFKANKNSRVHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 683-821 2.08e-67

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: 223.59  E-value: 2.08e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   683 RGTIPSVLAVSNGKGESSDAIICVFVDDVGEPTDSLKLA-DLRDLANQAMFAE----FVEKVKPDVIGVSGMSVSAHKIR 757
Cdd:pfam14639    1 QGKIPRVLGVAFGSGRFDDAIICVLVNGEGEVTDFLKLAwREFDRENKAQFEEtlkkFLLSKKPHVIGVSGENRDAQKFY 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   758 QHVQDSLTSHE------PVDLIMVNDEVARLYQNSTRAVDEFPTLPTISCYCVALARYVQNPLFEYAAMG 821
Cdd:pfam14639   81 EDVQRVLHELEqdsrlhTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
HHH_7 pfam14635
Helix-hairpin-helix motif;
822-925 2.56e-57

Helix-hairpin-helix motif;


:

Pssm-ID: 291309  Cd Length: 104  Bit Score: 192.76  E-value: 2.56e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   822 RDLMSLSFDPWQHLLPPDVLWKYLETALVDISSLVGIDINEAVTNKYEANILPYIAGLGPRKADYVLKKIAATGGRIDNR 901
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80

                           90       100
                   ....*....|....*....|....
gi 528532851   902 SDLISKQIMSRKVFINCSSFFIIP 925
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
 281-394 2.18e-46

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: 161.96  E-value: 2.18e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   281 NIDCSEDEFREQVAWIIDYLLKNRRDIDAELYEPFQTAVRYVVHFFIRDSLEVPFIWQHRRDYIVHNNRERNTI-TPLLS 359
Cdd:pfam14641    1 YIDLTDEELEEEANWISNRLLVEKNDDFERLLEPFKEAVGNVLEFISKDNLEVPFIWQHRRDYLLHSEKDGFEIgHKLLN 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 528532851   360 QNDLWNIFFLCTKFWSLHSKKQDILKLYSDLGIND 394
Cdd:pfam14641   81 EDDLWRIVQLDIKFHSLIEKRNNLEKLYEKLGIDD 115
SPT6_acidic pfam14632
Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ...
 53-133 2.70e-17

Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.


:

Pssm-ID: 464226  Cd Length: 89  Bit Score: 77.90  E-value: 2.70e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851    53 DSSE-ESATDEEAERQVREGFIVEDEEDEVPQEIRRKKKRKKH----AESTADQDMLDEEDLELVMENTG--QGSRFSKL 125
Cdd:pfam14632    1 DSSEeEDDDDEEEARKVREGFIVDDDEEEEEEEEDDEERRRRKkkrkRREEEEDDRLDEDDLDLIEENTGvkRRRSSSKF 80


                   ....*...
gi 528532851   126 RRLKRGRD 133
Cdd:pfam14632   81 KRLKRGHD 88
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1053-1116 1.45e-06

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: 46.99  E-value: 1.45e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528532851 1053 VPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFI-PPPQLLQVGQTVEGVIISLDEANFMVDLS 1116
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVkDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1142-1353 7.45e-111

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 347.21  E-value: 7.45e-111
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851  1142 EAEKRDTERMQAETQAEQRVARVIKHPLFKDLNASQAEAYLSKMQVGDLVIRPSSKGSDHIVVTWKVAEGSYQHIDVLEL 1221
Cdd:pfam14633    1 DADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLEL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851  1222 EKENEFTIGQKLLVKGrfekmtYQYSDLDELIVLHIKAIAKKIDEMCIHDKFRKGTQAETEKWLESYSEANPKRSCYAFC 1301
Cdd:pfam14633   81 DKENEFSLGKTLRIGG------EEYEDLDELIARHVQPMARKVEEMMNHRKFKDGTKEEVEEWLREEKKANPKRSPYAFC 154

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528532851  1302 FDHQHPGYFILCFKASVNSPVTAWPVKVIPNAFFLQGNVYGDMTALCNGFKL 1353
Cdd:pfam14633  155 LSHKHPGYFLLSFKANKNSRVHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 683-821 2.08e-67

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: 223.59  E-value: 2.08e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   683 RGTIPSVLAVSNGKGESSDAIICVFVDDVGEPTDSLKLA-DLRDLANQAMFAE----FVEKVKPDVIGVSGMSVSAHKIR 757
Cdd:pfam14639    1 QGKIPRVLGVAFGSGRFDDAIICVLVNGEGEVTDFLKLAwREFDRENKAQFEEtlkkFLLSKKPHVIGVSGENRDAQKFY 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   758 QHVQDSLTSHE------PVDLIMVNDEVARLYQNSTRAVDEFPTLPTISCYCVALARYVQNPLFEYAAMG 821
Cdd:pfam14639   81 EDVQRVLHELEqdsrlhTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
HHH_7 pfam14635
Helix-hairpin-helix motif;
822-925 2.56e-57

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 192.76  E-value: 2.56e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   822 RDLMSLSFDPWQHLLPPDVLWKYLETALVDISSLVGIDINEAVTNKYEANILPYIAGLGPRKADYVLKKIAATGGRIDNR 901
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80

                           90       100
                   ....*....|....*....|....
gi 528532851   902 SDLISKQIMSRKVFINCSSFFIIP 925
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
 281-394 2.18e-46

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: 161.96  E-value: 2.18e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   281 NIDCSEDEFREQVAWIIDYLLKNRRDIDAELYEPFQTAVRYVVHFFIRDSLEVPFIWQHRRDYIVHNNRERNTI-TPLLS 359
Cdd:pfam14641    1 YIDLTDEELEEEANWISNRLLVEKNDDFERLLEPFKEAVGNVLEFISKDNLEVPFIWQHRRDYLLHSEKDGFEIgHKLLN 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 528532851   360 QNDLWNIFFLCTKFWSLHSKKQDILKLYSDLGIND 394
Cdd:pfam14641   81 EDDLWRIVQLDIKFHSLIEKRNNLEKLYEKLGIDD 115
SH2_Cterm_SPT6_like cd09928
C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription ...
 1266-1355 4.11e-38

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: 137.36  E-value: 4.11e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851 1266 EMCIHDKFRKGTQAETEKWLESYSEANPKRSCYAFCFDHQHPGYFILCFKASvNSPVTAWPVKVIPNAFFLQGNVYGDMT 1345
Cdd:cd09928     1 EMLNHHKYFRGTKEEVEKLLKEEKKANPKRIPYAFCVSKKYPGKFLLSYLPA-NTRVRHEYVKVTPDGFRFRGQVFPSVD 79

                          90
                  ....*....|
gi 528532851 1346 ALCNGFKLLY 1355
Cdd:cd09928    80 SLLNWFKEHF 89
SPT6_acidic pfam14632
Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ...
 53-133 2.70e-17

Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.


Pssm-ID: 464226  Cd Length: 89  Bit Score: 77.90  E-value: 2.70e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851    53 DSSE-ESATDEEAERQVREGFIVEDEEDEVPQEIRRKKKRKKH----AESTADQDMLDEEDLELVMENTG--QGSRFSKL 125
Cdd:pfam14632    1 DSSEeEDDDDEEEARKVREGFIVDDDEEEEEEEEDDEERRRRKkkrkRREEEEDDRLDEDDLDLIEENTGvkRRRSSSKF 80


                   ....*...
gi 528532851   126 RRLKRGRD 133
Cdd:pfam14632   81 KRLKRGHD 88
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1053-1116 1.45e-06

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: 46.99  E-value: 1.45e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528532851 1053 VPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFI-PPPQLLQVGQTVEGVIISLDEANFMVDLS 1116
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVkDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1050-1118 9.08e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 50.16  E-value: 9.08e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851 1050 DAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIP-PPQLLQVGQTVEGVIISLDEANFMVDLSLR 1118
Cdd:PRK06299  461 GSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEdATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1048-1118 2.05e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.05e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528532851   1048 QADAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIPPPQ-LLQVGQTVEGVIISLDEANFMVDLSLR 1118
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1047-1117 7.96e-05

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: 42.27  E-value: 7.96e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528532851  1047 LQADAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIP-PPQLLQVGQTVEGVIISLDEANFMVDLSL 1117
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEdPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
SH2 smart00252
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ...
 1170-1258 2.74e-04

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: 41.06  E-value: 2.74e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   1170 FKDLNASQAEAYLSKMQVGDLVIRPSSKGSDHIVVTWKVaEGSYQHIDVLELEkENEFTIGQKllvkgrfekmtYQYSDL 1249
Cdd:smart00252    5 HGFISREEAEKLLKNEGDGDFLVRDSESSPGDYVLSVRV-KGKVKHYRIRRNE-DGKFYLEGG-----------RKFPSL 71


                    ....*....
gi 528532851   1250 DELIVLHIK 1258
Cdd:smart00252   72 VELVEHYQK 80
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1042-1118 5.06e-03

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: 41.26  E-value: 5.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851  1042 ENP-----EELQADAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIPP-PQLLQVGQTVEGVIISLDEANFMVDL 1115
Cdd:TIGR00717  434 ENPwekfaAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDkTDEIKVGDEVEAKVVDIDKKNRKVSL 513


                   ...
gi 528532851  1116 SLR 1118
Cdd:TIGR00717  514 SVK 516
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1142-1353 7.45e-111

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 347.21  E-value: 7.45e-111
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851  1142 EAEKRDTERMQAETQAEQRVARVIKHPLFKDLNASQAEAYLSKMQVGDLVIRPSSKGSDHIVVTWKVAEGSYQHIDVLEL 1221
Cdd:pfam14633    1 DADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLEL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851  1222 EKENEFTIGQKLLVKGrfekmtYQYSDLDELIVLHIKAIAKKIDEMCIHDKFRKGTQAETEKWLESYSEANPKRSCYAFC 1301
Cdd:pfam14633   81 DKENEFSLGKTLRIGG------EEYEDLDELIARHVQPMARKVEEMMNHRKFKDGTKEEVEEWLREEKKANPKRSPYAFC 154

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528532851  1302 FDHQHPGYFILCFKASVNSPVTAWPVKVIPNAFFLQGNVYGDMTALCNGFKL 1353
Cdd:pfam14633  155 LSHKHPGYFLLSFKANKNSRVHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 683-821 2.08e-67

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: 223.59  E-value: 2.08e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   683 RGTIPSVLAVSNGKGESSDAIICVFVDDVGEPTDSLKLA-DLRDLANQAMFAE----FVEKVKPDVIGVSGMSVSAHKIR 757
Cdd:pfam14639    1 QGKIPRVLGVAFGSGRFDDAIICVLVNGEGEVTDFLKLAwREFDRENKAQFEEtlkkFLLSKKPHVIGVSGENRDAQKFY 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   758 QHVQDSLTSHE------PVDLIMVNDEVARLYQNSTRAVDEFPTLPTISCYCVALARYVQNPLFEYAAMG 821
Cdd:pfam14639   81 EDVQRVLHELEqdsrlhTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQVC 150
HHH_7 pfam14635
Helix-hairpin-helix motif;
822-925 2.56e-57

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 192.76  E-value: 2.56e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   822 RDLMSLSFDPWQHLLPPDVLWKYLETALVDISSLVGIDINEAVTNKYEANILPYIAGLGPRKADYVLKKIAATGGRIDNR 901
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80

                           90       100
                   ....*....|....*....|....
gi 528532851   902 SDLISKQIMSRKVFINCSSFFIIP 925
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
 281-394 2.18e-46

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: 161.96  E-value: 2.18e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   281 NIDCSEDEFREQVAWIIDYLLKNRRDIDAELYEPFQTAVRYVVHFFIRDSLEVPFIWQHRRDYIVHNNRERNTI-TPLLS 359
Cdd:pfam14641    1 YIDLTDEELEEEANWISNRLLVEKNDDFERLLEPFKEAVGNVLEFISKDNLEVPFIWQHRRDYLLHSEKDGFEIgHKLLN 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 528532851   360 QNDLWNIFFLCTKFWSLHSKKQDILKLYSDLGIND 394
Cdd:pfam14641   81 EDDLWRIVQLDIKFHSLIEKRNNLEKLYEKLGIDD 115
SH2_Cterm_SPT6_like cd09928
C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription ...
 1266-1355 4.11e-38

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: 137.36  E-value: 4.11e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851 1266 EMCIHDKFRKGTQAETEKWLESYSEANPKRSCYAFCFDHQHPGYFILCFKASvNSPVTAWPVKVIPNAFFLQGNVYGDMT 1345
Cdd:cd09928     1 EMLNHHKYFRGTKEEVEKLLKEEKKANPKRIPYAFCVSKKYPGKFLLSYLPA-NTRVRHEYVKVTPDGFRFRGQVFPSVD 79

                          90
                  ....*....|
gi 528532851 1346 ALCNGFKLLY 1355
Cdd:cd09928    80 SLLNWFKEHF 89
SH2_Nterm_SPT6_like cd09918
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ...
 1166-1256 9.69e-37

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: 133.52  E-value: 9.69e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851 1166 KHPLFKDLNASQAEAYLSKMQVGDLVIRPSSKGSDHIVVTWKVAEGSYQHIDVLELEKENEFTIGQKLLVKGrfekmtYQ 1245
Cdd:cd09918     1 RHPLFKNVNYKQAEAYLKSKDVGEVVIRPSSKGVDHLTVTWKVADGVYQHIDIEELNKENPFSLGKELIIGG------EE 74

                          90
                  ....*....|.
gi 528532851 1246 YSDLDELIVLH 1256
Cdd:cd09918    75 YEDLDEIIARF 85
SPT6_acidic pfam14632
Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ...
 53-133 2.70e-17

Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.


Pssm-ID: 464226  Cd Length: 89  Bit Score: 77.90  E-value: 2.70e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851    53 DSSE-ESATDEEAERQVREGFIVEDEEDEVPQEIRRKKKRKKH----AESTADQDMLDEEDLELVMENTG--QGSRFSKL 125
Cdd:pfam14632    1 DSSEeEDDDDEEEARKVREGFIVDDDEEEEEEEEDDEERRRRKkkrkRREEEEDDRLDEDDLDLIEENTGvkRRRSSSKF 80


                   ....*...
gi 528532851   126 RRLKRGRD 133
Cdd:pfam14632   81 KRLKRGHD 88
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1053-1116 1.45e-06

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: 46.99  E-value: 1.45e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528532851 1053 VPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFI-PPPQLLQVGQTVEGVIISLDEANFMVDLS 1116
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVkDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1050-1118 1.61e-06

S1_RPS1_repeat_ec6: 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 6 (ec6) 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: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 46.88  E-value: 1.61e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851 1050 DAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIPP-PQLLQVGQTVEGVIISLDEANFMVDLSLR 1118
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDaTERFKVGDEVEAKITNVDRKNRKISLSIK 70
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1050-1118 9.08e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 50.16  E-value: 9.08e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851 1050 DAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIP-PPQLLQVGQTVEGVIISLDEANFMVDLSLR 1118
Cdd:PRK06299  461 GSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEdATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1048-1118 2.05e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.05e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528532851   1048 QADAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIPPPQ-LLQVGQTVEGVIISLDEANFMVDLSLR 1118
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
SH2 cd00173
Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they ...
 1172-1253 7.76e-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: 42.44  E-value: 7.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851 1172 DLNASQAEAYLSKMQVGDLVIRPSSKGSDHIVVTWKVAEGSYQHIDVLELEKENEFTIGQKLlvkgrfekmtyQYSDLDE 1251
Cdd:cd00173     6 SISREEAERLLRGKPDGTFLVRESSSEPGDYVLSVRSGDGKVKHYLIERNEGGYYLLGGSGR-----------TFPSLPE 74


                  ..
gi 528532851 1252 LI 1253
Cdd:cd00173    75 LV 76
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1047-1117 7.96e-05

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: 42.27  E-value: 7.96e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528532851  1047 LQADAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIP-PPQLLQVGQTVEGVIISLDEANFMVDLSL 1117
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEdPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
SH2 smart00252
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ...
 1170-1258 2.74e-04

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: 41.06  E-value: 2.74e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851   1170 FKDLNASQAEAYLSKMQVGDLVIRPSSKGSDHIVVTWKVaEGSYQHIDVLELEkENEFTIGQKllvkgrfekmtYQYSDL 1249
Cdd:smart00252    5 HGFISREEAEKLLKNEGDGDFLVRDSESSPGDYVLSVRV-KGKVKHYRIRRNE-DGKFYLEGG-----------RKFPSL 71


                    ....*....
gi 528532851   1250 DELIVLHIK 1258
Cdd:smart00252   72 VELVEHYQK 80
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1045-1118 1.47e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 43.01  E-value: 1.47e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528532851 1045 EELQADAIVPVNVRRVTNRFVAVKLDcGIDGNIKADEVS-DDFIPPPQLLQVGQTVEGVIISLDEANFMVDLSLR 1118
Cdd:PRK00087  473 NSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEISwGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLK 546
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1044-1118 4.02e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 41.47  E-value: 4.02e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528532851 1044 PEELQADAIVPVNVRRVtNRFVA-VKLDCGIDGNIKADEVSDDFIPPPQ-LLQVGQTVEGVIISLDEANFMVDLSLR 1118
Cdd:PRK00087  557 EEKYPVGSIVLGKVVRI-APFGAfVELEPGVDGLVHISQISWKRIDKPEdVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1042-1118 5.06e-03

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: 41.26  E-value: 5.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851  1042 ENP-----EELQADAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIPP-PQLLQVGQTVEGVIISLDEANFMVDL 1115
Cdd:TIGR00717  434 ENPwekfaAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDkTDEIKVGDEVEAKVVDIDKKNRKVSL 513


                   ...
gi 528532851  1116 SLR 1118
Cdd:TIGR00717  514 SVK 516
SH2 pfam00017
SH2 domain;
1170-1256 5.26e-03

SH2 domain;


Pssm-ID: 425423 [Multi-domain]  Cd Length: 77  Bit Score: 37.20  E-value: 5.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528532851  1170 FKDLNASQAEAYL-SKMQVGDLVIRPSSKGSDHIVVTWKvAEGSYQHIDVLELEKENEFTIGQKllvkgrfekmtyQYSD 1248
Cdd:pfam00017    3 HGKISRQEAERLLlNGKPDGTFLVRESESTPGGYTLSVR-DDGKVKHYKIQSTDNGGYYISGGV------------KFSS 69


                   ....*...
gi 528532851  1249 LDELIVLH 1256
Cdd:pfam00017   70 LAELVEHY 77
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1045-1117 7.62e-03

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: 36.80  E-value: 7.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 528532851 1045 EELQADAIVPVNVRRVTNRFVAVKLDCGIDGNIKADEVSDDFIPPPQ-LLQVGQTVEGVIISLDEANFMVDLSL 1117
Cdd:cd04461    10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSfGFKKGQSVTAKVTSVDEEKQRFLLSL 83
 
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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