transcription elongation factor SPT6-like isoform X2 [Branchiostoma floridae]
Protein Classification
DLD and SH2_Cterm_SPT6_like domain-containing protein( domain architecture ID 13863247)
protein containing domains YqgFc, DLD, SH2_Nterm_SPT6_like, and SH2_Cterm_SPT6_like
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| SH2_2 | pfam14633 | SH2 domain; |
1344-1548 | 4.27e-109 | |||||||||
SH2 domain; : Pssm-ID: 464227 [Multi-domain] Cd Length: 206 Bit Score: 345.67 E-value: 4.27e-109
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| RuvC-like super family | cl21482 | Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family ... |
811-965 | 5.08e-49 | |||||||||
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: 171.59 E-value: 5.08e-49
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| HHH_5 super family | cl22429 | Helix-hairpin-helix domain; |
969-1072 | 8.84e-45 | |||||||||
Helix-hairpin-helix domain; The actual alignment was detected with superfamily member pfam14635: Pssm-ID: 473956 Cd Length: 104 Bit Score: 157.32 E-value: 8.84e-45
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| Tex super family | cl34417 | Transcriptional accessory protein Tex/SPT6 [Transcription]; |
599-1163 | 5.47e-31 | |||||||||
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: 132.07 E-value: 5.47e-31
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| HTH_44 | pfam14641 | Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ... |
367-441 | 4.24e-25 | |||||||||
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: 101.49 E-value: 4.24e-25
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
1262-1316 | 6.64e-12 | |||||||||
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: 62.69 E-value: 6.64e-12
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| SPT6_acidic | pfam14632 | Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ... |
84-140 | 1.77e-04 | |||||||||
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: 42.08 E-value: 1.77e-04
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| PHA03247 super family | cl33720 | large tegument protein UL36; Provisional |
1552-1805 | 5.16e-04 | |||||||||
large tegument protein UL36; Provisional The actual alignment was detected with superfamily member PHA03247: Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 45.31 E-value: 5.16e-04
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| Name | Accession | Description | Interval | E-value | |||||||||
| SH2_2 | pfam14633 | SH2 domain; |
1344-1548 | 4.27e-109 | |||||||||
SH2 domain; Pssm-ID: 464227 [Multi-domain] Cd Length: 206 Bit Score: 345.67 E-value: 4.27e-109
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| YqgF | pfam14639 | Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ... |
811-965 | 5.08e-49 | |||||||||
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: 171.59 E-value: 5.08e-49
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| HHH_7 | pfam14635 | Helix-hairpin-helix motif; |
969-1072 | 8.84e-45 | |||||||||
Helix-hairpin-helix motif; Pssm-ID: 291309 Cd Length: 104 Bit Score: 157.32 E-value: 8.84e-45
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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 ... |
1367-1450 | 1.17e-44 | |||||||||
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: 156.24 E-value: 1.17e-44
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| Tex | COG2183 | Transcriptional accessory protein Tex/SPT6 [Transcription]; |
599-1163 | 5.47e-31 | |||||||||
Transcriptional accessory protein Tex/SPT6 [Transcription]; Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 132.07 E-value: 5.47e-31
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| HTH_44 | pfam14641 | Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ... |
367-441 | 4.24e-25 | |||||||||
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: 101.49 E-value: 4.24e-25
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| YqgFc | smart00732 | Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ... |
814-925 | 5.88e-12 | |||||||||
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: 63.74 E-value: 5.88e-12
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
1262-1316 | 6.64e-12 | |||||||||
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: 62.69 E-value: 6.64e-12
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
1262-1317 | 1.00e-10 | |||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 59.15 E-value: 1.00e-10
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| S1_like | cd00164 | S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
1259-1315 | 2.43e-09 | |||||||||
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: 55.08 E-value: 2.43e-09
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| rpsA | PRK07899 | 30S ribosomal protein S1; Reviewed |
1248-1333 | 4.97e-08 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 57.75 E-value: 4.97e-08
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| HHH_9 | pfam17674 | HHH domain; |
1086-1177 | 1.62e-07 | |||||||||
HHH domain; Pssm-ID: 465451 [Multi-domain] Cd Length: 70 Bit Score: 49.84 E-value: 1.62e-07
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
1262-1315 | 9.06e-05 | |||||||||
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 46.96 E-value: 9.06e-05
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| SPT6_acidic | pfam14632 | Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ... |
84-140 | 1.77e-04 | |||||||||
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: 42.08 E-value: 1.77e-04
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
1270-1317 | 4.77e-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: 44.72 E-value: 4.77e-04
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
1552-1805 | 5.16e-04 | |||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 45.31 E-value: 5.16e-04
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| CTD | smart01104 | Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1618-1741 | 2.80e-03 | |||||||||
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif. Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 39.43 E-value: 2.80e-03
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| Pneumo_att_G | pfam05539 | Pneumovirinae attachment membrane glycoprotein G; |
1659-1811 | 3.05e-03 | |||||||||
Pneumovirinae attachment membrane glycoprotein G; Pssm-ID: 114270 [Multi-domain] Cd Length: 408 Bit Score: 41.96 E-value: 3.05e-03
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| SPT5 | COG5164 | Transcription elongation factor SPT5 [Transcription]; |
1618-1820 | 5.45e-03 | |||||||||
Transcription elongation factor SPT5 [Transcription]; Pssm-ID: 444063 [Multi-domain] Cd Length: 495 Bit Score: 41.55 E-value: 5.45e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| SH2_2 | pfam14633 | SH2 domain; |
1344-1548 | 4.27e-109 | |||||||||
SH2 domain; Pssm-ID: 464227 [Multi-domain] Cd Length: 206 Bit Score: 345.67 E-value: 4.27e-109
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| YqgF | pfam14639 | Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ... |
811-965 | 5.08e-49 | |||||||||
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: 171.59 E-value: 5.08e-49
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| HHH_7 | pfam14635 | Helix-hairpin-helix motif; |
969-1072 | 8.84e-45 | |||||||||
Helix-hairpin-helix motif; Pssm-ID: 291309 Cd Length: 104 Bit Score: 157.32 E-value: 8.84e-45
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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 ... |
1367-1450 | 1.17e-44 | |||||||||
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: 156.24 E-value: 1.17e-44
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| SH2_Cterm_SPT6_like | cd09928 | C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription ... |
1459-1550 | 9.31e-36 | |||||||||
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: 131.19 E-value: 9.31e-36
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| Tex | COG2183 | Transcriptional accessory protein Tex/SPT6 [Transcription]; |
599-1163 | 5.47e-31 | |||||||||
Transcriptional accessory protein Tex/SPT6 [Transcription]; Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 132.07 E-value: 5.47e-31
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| HTH_44 | pfam14641 | Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ... |
367-441 | 4.24e-25 | |||||||||
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: 101.49 E-value: 4.24e-25
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| YqgFc | smart00732 | Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ... |
814-925 | 5.88e-12 | |||||||||
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: 63.74 E-value: 5.88e-12
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
1262-1316 | 6.64e-12 | |||||||||
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: 62.69 E-value: 6.64e-12
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
1262-1317 | 1.00e-10 | |||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 59.15 E-value: 1.00e-10
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| S1_like | cd00164 | S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
1259-1315 | 2.43e-09 | |||||||||
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: 55.08 E-value: 2.43e-09
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| SH2 | cd00173 | Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they ... |
1368-1450 | 3.12e-09 | |||||||||
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: 55.15 E-value: 3.12e-09
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| rpsA | PRK07899 | 30S ribosomal protein S1; Reviewed |
1248-1333 | 4.97e-08 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 57.75 E-value: 4.97e-08
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| HHH_3 | pfam12836 | Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain. |
1002-1069 | 7.10e-08 | |||||||||
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain. Pssm-ID: 463723 [Multi-domain] Cd Length: 62 Bit Score: 50.94 E-value: 7.10e-08
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| HHH_9 | pfam17674 | HHH domain; |
1086-1177 | 1.62e-07 | |||||||||
HHH domain; Pssm-ID: 465451 [Multi-domain] Cd Length: 70 Bit Score: 49.84 E-value: 1.62e-07
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| S1_Tex | cd05685 | S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
1261-1315 | 1.41e-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: 44.53 E-value: 1.41e-05
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
1261-1315 | 2.00e-05 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 49.10 E-value: 2.00e-05
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| S1_RPS1_repeat_hs4 | cd05692 | S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
1262-1315 | 2.12e-05 | |||||||||
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: 44.20 E-value: 2.12e-05
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| SH2 | pfam00017 | SH2 domain; |
1370-1447 | 3.48e-05 | |||||||||
SH2 domain; Pssm-ID: 425423 [Multi-domain] Cd Length: 77 Bit Score: 43.74 E-value: 3.48e-05
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
1262-1323 | 4.33e-05 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 48.24 E-value: 4.33e-05
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
1262-1317 | 4.70e-05 | |||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 48.40 E-value: 4.70e-05
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
1262-1315 | 9.06e-05 | |||||||||
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 46.96 E-value: 9.06e-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 ... |
1262-1317 | 1.01e-04 | |||||||||
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: 42.21 E-value: 1.01e-04
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| S1_RPS1_repeat_ec3 | cd05688 | S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
1270-1315 | 1.13e-04 | |||||||||
S1_RPS1_repeat_ec3: 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 3 (ec3) 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: 240193 [Multi-domain] Cd Length: 68 Bit Score: 41.85 E-value: 1.13e-04
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
1261-1315 | 1.18e-04 | |||||||||
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 46.58 E-value: 1.18e-04
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| SPT6_acidic | pfam14632 | Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ... |
84-140 | 1.77e-04 | |||||||||
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: 42.08 E-value: 1.77e-04
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
1262-1343 | 2.19e-04 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 45.64 E-value: 2.19e-04
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
1270-1317 | 4.77e-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: 44.72 E-value: 4.77e-04
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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 ... |
1259-1314 | 5.03e-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: 40.30 E-value: 5.03e-04
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
1552-1805 | 5.16e-04 | |||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 45.31 E-value: 5.16e-04
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| Tex_N | pfam09371 | Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ... |
605-658 | 8.10e-04 | |||||||||
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: 42.39 E-value: 8.10e-04
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
1262-1315 | 8.76e-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: 43.95 E-value: 8.76e-04
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| S1_RPS1_repeat_ec2_hs2 | cd04465 | S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
1269-1317 | 1.39e-03 | |||||||||
S1_RPS1_repeat_ec2_hs2: 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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Pssm-ID: 239911 [Multi-domain] Cd Length: 67 Bit Score: 38.98 E-value: 1.39e-03
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
1262-1315 | 1.57e-03 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 43.23 E-value: 1.57e-03
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
1551-1806 | 1.71e-03 | |||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 43.39 E-value: 1.71e-03
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| CTD | smart01104 | Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1618-1741 | 2.80e-03 | |||||||||
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif. Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 39.43 E-value: 2.80e-03
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| Pneumo_att_G | pfam05539 | Pneumovirinae attachment membrane glycoprotein G; |
1659-1811 | 3.05e-03 | |||||||||
Pneumovirinae attachment membrane glycoprotein G; Pssm-ID: 114270 [Multi-domain] Cd Length: 408 Bit Score: 41.96 E-value: 3.05e-03
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
1262-1315 | 4.97e-03 | |||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 41.86 E-value: 4.97e-03
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| S1_RPS1_repeat_ec5 | cd05690 | S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
1262-1314 | 5.06e-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: 37.47 E-value: 5.06e-03
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| SPT5 | COG5164 | Transcription elongation factor SPT5 [Transcription]; |
1618-1820 | 5.45e-03 | |||||||||
Transcription elongation factor SPT5 [Transcription]; Pssm-ID: 444063 [Multi-domain] Cd Length: 495 Bit Score: 41.55 E-value: 5.45e-03
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| CTD | smart01104 | Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1662-1798 | 6.53e-03 | |||||||||
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif. Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 38.66 E-value: 6.53e-03
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| S1_IF2_alpha | cd04452 | S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ... |
1262-1317 | 6.65e-03 | |||||||||
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein. Pssm-ID: 239899 [Multi-domain] Cd Length: 76 Bit Score: 37.18 E-value: 6.65e-03
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
1553-1811 | 6.80e-03 | |||||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 41.59 E-value: 6.80e-03
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| S1_RPS1_repeat_ec6 | cd05691 | S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
1259-1320 | 7.58e-03 | |||||||||
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: 36.86 E-value: 7.58e-03
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| DUF5585 | pfam17823 | Family of unknown function (DUF5585); This is a family of unknown function found in chordata. |
1557-1820 | 7.71e-03 | |||||||||
Family of unknown function (DUF5585); This is a family of unknown function found in chordata. Pssm-ID: 465521 [Multi-domain] Cd Length: 506 Bit Score: 41.10 E-value: 7.71e-03
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
1551-1827 | 7.71e-03 | |||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 41.46 E-value: 7.71e-03
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
1260-1317 | 8.01e-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: 40.87 E-value: 8.01e-03
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| PRK10263 | PRK10263 | DNA translocase FtsK; Provisional |
1658-1810 | 8.56e-03 | |||||||||
DNA translocase FtsK; Provisional Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 41.22 E-value: 8.56e-03
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