transcription elongation factor SPT6 isoform X1 [Rattus norvegicus]
Protein Classification
DLD and SH2_Nterm_SPT6_like domain-containing protein( domain architecture ID 13390031)
protein containing domains DLD, S1_like, SH2_Nterm_SPT6_like, and SH2_Cterm_SPT6_like
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| SH2_2 | pfam14633 | SH2 domain; |
1307-1511 | 5.86e-98 | |||||||||
SH2 domain; : Pssm-ID: 464227 [Multi-domain] Cd Length: 206 Bit Score: 313.70 E-value: 5.86e-98
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| YqgF | pfam14639 | Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ... |
774-930 | 5.80e-77 | |||||||||
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage : Pssm-ID: 258777 Cd Length: 150 Bit Score: 251.32 E-value: 5.80e-77
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| HHH_7 | pfam14635 | Helix-hairpin-helix motif; |
934-1037 | 9.06e-60 | |||||||||
Helix-hairpin-helix motif; : Pssm-ID: 291309 Cd Length: 104 Bit Score: 200.08 E-value: 9.06e-60
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| Tex super family | cl34417 | Transcriptional accessory protein Tex/SPT6 [Transcription]; |
563-1129 | 5.15e-34 | |||||||||
Transcriptional accessory protein Tex/SPT6 [Transcription]; The actual alignment was detected with superfamily member COG2183: Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 141.32 E-value: 5.15e-34
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| HTH_44 | pfam14641 | Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ... |
346-421 | 2.73e-24 | |||||||||
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins. : Pssm-ID: 464230 Cd Length: 115 Bit Score: 99.17 E-value: 2.73e-24
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
1226-1281 | 4.54e-09 | |||||||||
Ribosomal protein S1-like RNA-binding domain; : Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 54.53 E-value: 4.54e-09
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| Name | Accession | Description | Interval | E-value | |||||||||
| SH2_2 | pfam14633 | SH2 domain; |
1307-1511 | 5.86e-98 | |||||||||
SH2 domain; Pssm-ID: 464227 [Multi-domain] Cd Length: 206 Bit Score: 313.70 E-value: 5.86e-98
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| YqgF | pfam14639 | Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ... |
774-930 | 5.80e-77 | |||||||||
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage Pssm-ID: 258777 Cd Length: 150 Bit Score: 251.32 E-value: 5.80e-77
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| HHH_7 | pfam14635 | Helix-hairpin-helix motif; |
934-1037 | 9.06e-60 | |||||||||
Helix-hairpin-helix motif; Pssm-ID: 291309 Cd Length: 104 Bit Score: 200.08 E-value: 9.06e-60
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| SH2_Nterm_SPT6_like | cd09918 | N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ... |
1330-1414 | 1.63e-45 | |||||||||
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. Pssm-ID: 198174 Cd Length: 85 Bit Score: 158.55 E-value: 1.63e-45
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| Tex | COG2183 | Transcriptional accessory protein Tex/SPT6 [Transcription]; |
563-1129 | 5.15e-34 | |||||||||
Transcriptional accessory protein Tex/SPT6 [Transcription]; Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 141.32 E-value: 5.15e-34
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| HTH_44 | pfam14641 | Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ... |
346-421 | 2.73e-24 | |||||||||
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins. Pssm-ID: 464230 Cd Length: 115 Bit Score: 99.17 E-value: 2.73e-24
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| YqgFc | smart00732 | Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ... |
778-893 | 3.01e-16 | |||||||||
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions. Pssm-ID: 128971 Cd Length: 99 Bit Score: 75.68 E-value: 3.01e-16
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| SH2 | smart00252 | Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ... |
1331-1420 | 7.49e-12 | |||||||||
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae. Pssm-ID: 214585 [Multi-domain] Cd Length: 84 Bit Score: 62.63 E-value: 7.49e-12
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
1226-1281 | 4.54e-09 | |||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 54.53 E-value: 4.54e-09
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| HHH_9 | pfam17674 | HHH domain; |
1050-1130 | 1.89e-07 | |||||||||
HHH domain; Pssm-ID: 465451 [Multi-domain] Cd Length: 70 Bit Score: 49.84 E-value: 1.89e-07
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| S1_like | cd00164 | S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
1226-1273 | 3.41e-07 | |||||||||
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold. Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 48.92 E-value: 3.41e-07
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
1226-1280 | 5.03e-07 | |||||||||
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Pssm-ID: 425760 [Multi-domain] Cd Length: 72 Bit Score: 48.82 E-value: 5.03e-07
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
1226-1270 | 2.30e-03 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 42.46 E-value: 2.30e-03
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
1224-1270 | 9.88e-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: 40.49 E-value: 9.88e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| SH2_2 | pfam14633 | SH2 domain; |
1307-1511 | 5.86e-98 | |||||||||
SH2 domain; Pssm-ID: 464227 [Multi-domain] Cd Length: 206 Bit Score: 313.70 E-value: 5.86e-98
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| YqgF | pfam14639 | Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ... |
774-930 | 5.80e-77 | |||||||||
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage Pssm-ID: 258777 Cd Length: 150 Bit Score: 251.32 E-value: 5.80e-77
|
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| HHH_7 | pfam14635 | Helix-hairpin-helix motif; |
934-1037 | 9.06e-60 | |||||||||
Helix-hairpin-helix motif; Pssm-ID: 291309 Cd Length: 104 Bit Score: 200.08 E-value: 9.06e-60
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| SH2_Nterm_SPT6_like | cd09918 | N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ... |
1330-1414 | 1.63e-45 | |||||||||
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. Pssm-ID: 198174 Cd Length: 85 Bit Score: 158.55 E-value: 1.63e-45
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| SH2_Cterm_SPT6_like | cd09928 | C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription ... |
1423-1514 | 1.37e-35 | |||||||||
C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. Pssm-ID: 198182 Cd Length: 89 Bit Score: 130.42 E-value: 1.37e-35
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| Tex | COG2183 | Transcriptional accessory protein Tex/SPT6 [Transcription]; |
563-1129 | 5.15e-34 | |||||||||
Transcriptional accessory protein Tex/SPT6 [Transcription]; Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 141.32 E-value: 5.15e-34
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| HTH_44 | pfam14641 | Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ... |
346-421 | 2.73e-24 | |||||||||
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins. Pssm-ID: 464230 Cd Length: 115 Bit Score: 99.17 E-value: 2.73e-24
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| YqgFc | smart00732 | Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ... |
778-893 | 3.01e-16 | |||||||||
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions. Pssm-ID: 128971 Cd Length: 99 Bit Score: 75.68 E-value: 3.01e-16
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| SH2 | smart00252 | Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ... |
1331-1420 | 7.49e-12 | |||||||||
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae. Pssm-ID: 214585 [Multi-domain] Cd Length: 84 Bit Score: 62.63 E-value: 7.49e-12
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
1226-1281 | 4.54e-09 | |||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 54.53 E-value: 4.54e-09
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| HHH_3 | pfam12836 | Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain. |
967-1034 | 1.23e-08 | |||||||||
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain. Pssm-ID: 463723 [Multi-domain] Cd Length: 62 Bit Score: 52.87 E-value: 1.23e-08
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| HHH_9 | pfam17674 | HHH domain; |
1050-1130 | 1.89e-07 | |||||||||
HHH domain; Pssm-ID: 465451 [Multi-domain] Cd Length: 70 Bit Score: 49.84 E-value: 1.89e-07
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| S1_like | cd00164 | S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
1226-1273 | 3.41e-07 | |||||||||
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold. Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 48.92 E-value: 3.41e-07
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
1226-1280 | 5.03e-07 | |||||||||
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Pssm-ID: 425760 [Multi-domain] Cd Length: 72 Bit Score: 48.82 E-value: 5.03e-07
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| SH2 | cd00173 | Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they ... |
1332-1414 | 6.89e-07 | |||||||||
Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1), Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others. Pssm-ID: 198173 [Multi-domain] Cd Length: 79 Bit Score: 48.61 E-value: 6.89e-07
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| S1_Rrp5_repeat_hs5 | cd05697 | S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ... |
1223-1273 | 3.38e-05 | |||||||||
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240202 [Multi-domain] Cd Length: 69 Bit Score: 43.38 E-value: 3.38e-05
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| S1_Rrp5_repeat_hs6_sc5 | cd05698 | S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
1233-1281 | 7.45e-05 | |||||||||
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240203 [Multi-domain] Cd Length: 70 Bit Score: 42.60 E-value: 7.45e-05
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| S1_Rrp5_repeat_hs8_sc7 | cd04461 | S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ... |
1226-1273 | 1.80e-04 | |||||||||
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 239908 [Multi-domain] Cd Length: 83 Bit Score: 41.80 E-value: 1.80e-04
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| S1_Tex | cd05685 | S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
1225-1273 | 7.43e-04 | |||||||||
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea. Pssm-ID: 240190 [Multi-domain] Cd Length: 68 Bit Score: 39.52 E-value: 7.43e-04
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| SH2 | pfam00017 | SH2 domain; |
1334-1414 | 1.02e-03 | |||||||||
SH2 domain; Pssm-ID: 425423 [Multi-domain] Cd Length: 77 Bit Score: 39.51 E-value: 1.02e-03
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
1226-1270 | 2.30e-03 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 42.46 E-value: 2.30e-03
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
1224-1270 | 9.88e-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: 40.49 E-value: 9.88e-03
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