ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial isoform X1 [Homo sapiens]
Protein Classification
Zn-ribbon and AAA domain-containing protein( domain architecture ID 11641334)
Zn-ribbon and AAA domain-containing protein
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| ClpX | COG1219 | ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ... |
172-591 | 0e+00 | |||||||
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein turnover, chaperones]; : Pssm-ID: 440832 [Multi-domain] Cd Length: 409 Bit Score: 559.67 E-value: 0e+00
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| Zn-ribbon super family | cl02609 | C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ... |
104-132 | 7.55e-03 | |||||||
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II. The actual alignment was detected with superfamily member cd00656: Pssm-ID: 445850 Cd Length: 45 Bit Score: 34.60 E-value: 7.55e-03
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| Name | Accession | Description | Interval | E-value | ||||||||
| ClpX | COG1219 | ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ... |
172-591 | 0e+00 | ||||||||
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440832 [Multi-domain] Cd Length: 409 Bit Score: 559.67 E-value: 0e+00
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| clpX | PRK05342 | ATP-dependent Clp protease ATP-binding subunit ClpX; |
172-594 | 0e+00 | ||||||||
ATP-dependent Clp protease ATP-binding subunit ClpX; Pssm-ID: 235422 [Multi-domain] Cd Length: 412 Bit Score: 553.61 E-value: 0e+00
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| RecA-like_ClpX | cd19497 | ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ... |
172-492 | 6.78e-144 | ||||||||
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent protease ClpXP. In ClpXP, ClpX ATPase serves to specifically recognize, unfold, and translocate protein substrates into the chamber of ClpP protease for degradation. This RecA-like_ClpX domain subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410905 [Multi-domain] Cd Length: 251 Bit Score: 417.00 E-value: 6.78e-144
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| clpX | TIGR00382 | endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ... |
102-586 | 4.13e-143 | ||||||||
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides] Pssm-ID: 273047 [Multi-domain] Cd Length: 413 Bit Score: 421.48 E-value: 4.13e-143
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| AAA_2 | pfam07724 | AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ... |
271-489 | 4.23e-32 | ||||||||
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Pssm-ID: 400187 [Multi-domain] Cd Length: 168 Bit Score: 121.92 E-value: 4.23e-32
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| ClpB_D2-small | smart01086 | C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ... |
495-589 | 4.48e-20 | ||||||||
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N at the N-terminus as well as AAA and AAA_2. Pssm-ID: 198154 [Multi-domain] Cd Length: 90 Bit Score: 84.80 E-value: 4.48e-20
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| Zn-ribbon | cd00656 | C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ... |
104-132 | 7.55e-03 | ||||||||
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II. Pssm-ID: 259791 Cd Length: 45 Bit Score: 34.60 E-value: 7.55e-03
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| RPB9 | COG1594 | DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ... |
104-132 | 7.99e-03 | ||||||||
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase Pssm-ID: 441202 [Multi-domain] Cd Length: 103 Bit Score: 36.46 E-value: 7.99e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| ClpX | COG1219 | ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ... |
172-591 | 0e+00 | |||||||||
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440832 [Multi-domain] Cd Length: 409 Bit Score: 559.67 E-value: 0e+00
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| clpX | PRK05342 | ATP-dependent Clp protease ATP-binding subunit ClpX; |
172-594 | 0e+00 | |||||||||
ATP-dependent Clp protease ATP-binding subunit ClpX; Pssm-ID: 235422 [Multi-domain] Cd Length: 412 Bit Score: 553.61 E-value: 0e+00
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| RecA-like_ClpX | cd19497 | ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ... |
172-492 | 6.78e-144 | |||||||||
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent protease ClpXP. In ClpXP, ClpX ATPase serves to specifically recognize, unfold, and translocate protein substrates into the chamber of ClpP protease for degradation. This RecA-like_ClpX domain subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410905 [Multi-domain] Cd Length: 251 Bit Score: 417.00 E-value: 6.78e-144
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| clpX | TIGR00382 | endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ... |
102-586 | 4.13e-143 | |||||||||
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides] Pssm-ID: 273047 [Multi-domain] Cd Length: 413 Bit Score: 421.48 E-value: 4.13e-143
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| hslU | PRK05201 | ATP-dependent protease ATPase subunit HslU; |
172-583 | 1.30e-43 | |||||||||
ATP-dependent protease ATPase subunit HslU; Pssm-ID: 235364 [Multi-domain] Cd Length: 443 Bit Score: 161.78 E-value: 1.30e-43
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| HslU | COG1220 | ATP-dependent protease HslVU (ClpYQ), ATPase subunit HslU [Posttranslational modification, ... |
172-583 | 1.89e-39 | |||||||||
ATP-dependent protease HslVU (ClpYQ), ATPase subunit HslU [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440833 [Multi-domain] Cd Length: 454 Bit Score: 150.58 E-value: 1.89e-39
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| RecA-like_HslU | cd19498 | ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease ... |
172-410 | 1.86e-33 | |||||||||
ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease HslVU. In HslVU, HslU ATPase serves to unfold and translocate protein substrate, and the HslV protease degrades the unfolded proteins. This RecA-like_HslU subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410906 [Multi-domain] Cd Length: 183 Bit Score: 126.34 E-value: 1.86e-33
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| hslU | TIGR00390 | ATP-dependent protease HslVU, ATPase subunit; This model represents the ATPase subunit of ... |
172-583 | 2.21e-33 | |||||||||
ATP-dependent protease HslVU, ATPase subunit; This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment) is Ser in other members of the seed alignment. [Protein fate, Protein folding and stabilization] Pssm-ID: 273052 [Multi-domain] Cd Length: 441 Bit Score: 133.02 E-value: 2.21e-33
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| AAA_2 | pfam07724 | AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ... |
271-489 | 4.23e-32 | |||||||||
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Pssm-ID: 400187 [Multi-domain] Cd Length: 168 Bit Score: 121.92 E-value: 4.23e-32
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| ClpB_D2-small | smart01086 | C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ... |
495-589 | 4.48e-20 | |||||||||
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N at the N-terminus as well as AAA and AAA_2. Pssm-ID: 198154 [Multi-domain] Cd Length: 90 Bit Score: 84.80 E-value: 4.48e-20
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| AAA | cd00009 | The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ... |
272-418 | 3.01e-16 | |||||||||
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases. Pssm-ID: 99707 [Multi-domain] Cd Length: 151 Bit Score: 76.03 E-value: 3.01e-16
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| RecA-like_protease | cd19481 | proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ... |
272-376 | 4.00e-16 | |||||||||
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410889 [Multi-domain] Cd Length: 158 Bit Score: 76.17 E-value: 4.00e-16
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| AAA | pfam00004 | ATPase family associated with various cellular activities (AAA); AAA family proteins often ... |
275-376 | 3.32e-12 | |||||||||
ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Pssm-ID: 459627 [Multi-domain] Cd Length: 130 Bit Score: 63.77 E-value: 3.32e-12
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| SpoVK | COG0464 | AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ... |
275-376 | 2.47e-11 | |||||||||
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]; Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 65.70 E-value: 2.47e-11
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| ClpB_D2-small | pfam10431 | C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ... |
495-566 | 4.30e-10 | |||||||||
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, pfam00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerization, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilize the functional assembly. The domain is associated with two Clp_N, pfam02861, at the N-terminus as well as AAA, pfam00004 and AAA_2, pfam07724. Pssm-ID: 463090 [Multi-domain] Cd Length: 81 Bit Score: 56.26 E-value: 4.30e-10
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| AAA | smart00382 | ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
272-379 | 5.76e-09 | |||||||||
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 55.07 E-value: 5.76e-09
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| RecA-like_CDC48_NLV2_r1-like | cd19503 | first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ... |
275-376 | 8.54e-09 | |||||||||
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410911 [Multi-domain] Cd Length: 165 Bit Score: 54.99 E-value: 8.54e-09
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| RPT1 | COG1222 | ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ... |
275-351 | 2.26e-07 | |||||||||
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440835 [Multi-domain] Cd Length: 326 Bit Score: 53.09 E-value: 2.26e-07
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| AAA_5 | pfam07728 | AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ... |
274-418 | 6.23e-07 | |||||||||
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Pssm-ID: 400191 [Multi-domain] Cd Length: 135 Bit Score: 48.83 E-value: 6.23e-07
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| ClpA | COG0542 | ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ... |
431-578 | 8.38e-07 | |||||||||
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440308 [Multi-domain] Cd Length: 836 Bit Score: 52.39 E-value: 8.38e-07
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| RecA-like_PAN_like | cd19502 | proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ... |
275-374 | 1.51e-06 | |||||||||
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410910 [Multi-domain] Cd Length: 171 Bit Score: 48.49 E-value: 1.51e-06
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| RecA-like_NVL_r1-like | cd19518 | first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ... |
275-351 | 1.69e-06 | |||||||||
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410926 [Multi-domain] Cd Length: 169 Bit Score: 48.55 E-value: 1.69e-06
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| RecA-like_VPS4-like | cd19509 | ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ... |
275-351 | 1.73e-06 | |||||||||
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This subfamily includes the ATPase domains of vacuolar protein sorting-associated protein 4 (VPS4), ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase), Katanin p60 ATPase-containing subunit A1 (KTNA1), Spastin, and Fidgetin-Like 1 (FIGL-1). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410917 [Multi-domain] Cd Length: 163 Bit Score: 48.12 E-value: 1.73e-06
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| hflB | PRK10733 | ATP-dependent zinc metalloprotease FtsH; |
275-354 | 5.43e-06 | |||||||||
ATP-dependent zinc metalloprotease FtsH; Pssm-ID: 182683 [Multi-domain] Cd Length: 644 Bit Score: 49.65 E-value: 5.43e-06
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| RecA-like_FtsH | cd19501 | ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ... |
275-350 | 1.10e-05 | |||||||||
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410909 [Multi-domain] Cd Length: 171 Bit Score: 46.07 E-value: 1.10e-05
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| RecA-like_CDC48_r2-like | cd19511 | second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ... |
275-351 | 3.69e-05 | |||||||||
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains; This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410919 [Multi-domain] Cd Length: 159 Bit Score: 44.20 E-value: 3.69e-05
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| RecA-like_ATAD1 | cd19520 | ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ... |
275-347 | 4.77e-05 | |||||||||
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase) is an ATPase that plays a critical role in regulating the surface expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, thereby regulating synaptic plasticity, learning and memory. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410928 [Multi-domain] Cd Length: 166 Bit Score: 44.34 E-value: 4.77e-05
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| RecA-like_spastin | cd19524 | ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ... |
275-349 | 8.04e-05 | |||||||||
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in microtubule dynamics; it specifically recognizes and cuts microtubules that are polyglutamylated. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410932 [Multi-domain] Cd Length: 164 Bit Score: 43.30 E-value: 8.04e-05
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| RecA-like_Lon | cd19500 | lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ... |
255-415 | 9.29e-05 | |||||||||
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an evolutionarily conserved ATP-dependent serine protease, present in bacteria and eukaryotic mitochondria and peroxisomes, which mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Lon protease is both an ATP-dependent peptidase and a protein-activated ATPase. This RecA-like Lon domain subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410908 [Multi-domain] Cd Length: 182 Bit Score: 43.70 E-value: 9.29e-05
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| PRK13342 | PRK13342 | recombination factor protein RarA; Reviewed |
273-379 | 2.46e-04 | |||||||||
recombination factor protein RarA; Reviewed Pssm-ID: 237355 [Multi-domain] Cd Length: 413 Bit Score: 43.92 E-value: 2.46e-04
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| RecA-like_CDC48_r1-like | cd19519 | first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ... |
275-349 | 2.87e-04 | |||||||||
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410927 [Multi-domain] Cd Length: 166 Bit Score: 42.04 E-value: 2.87e-04
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| CDC48 | TIGR01243 | AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ... |
275-400 | 2.91e-04 | |||||||||
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Pssm-ID: 273521 [Multi-domain] Cd Length: 733 Bit Score: 44.13 E-value: 2.91e-04
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| RecA-like_ClpB_Hsp104-like | cd19499 | Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ... |
276-348 | 5.63e-04 | |||||||||
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and eukaryotic Heat shock protein 104 (Hsp104) are ATP-dependent molecular chaperones and essential proteins of the heat-shock response. ClpB/Hsp104 ATPases, in concert with the DnaK/Hsp70 chaperone system, disaggregate and reactivate aggregated proteins. This RecA-like_ClpB_Hsp104_like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410907 [Multi-domain] Cd Length: 178 Bit Score: 41.01 E-value: 5.63e-04
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| RecA-like_KTNA1 | cd19522 | Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ... |
275-354 | 7.99e-04 | |||||||||
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410930 [Multi-domain] Cd Length: 170 Bit Score: 40.74 E-value: 7.99e-04
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| RecA-like_Figl-1 | cd19525 | ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ... |
275-351 | 9.70e-04 | |||||||||
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; it may be involved in DNA double-strand break repair via homologous recombination. Caenorhabditis elegans FIGL-1 is a nuclear protein and controls the mitotic progression in the germ line and mouse FIGL-1 may be involved in the control of male meiosis. human FIGL-1 has been shown to be a centrosome protein involved in ciliogenesis perhaps as a microtubule-severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410933 [Multi-domain] Cd Length: 186 Bit Score: 40.74 E-value: 9.70e-04
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| RecA-like_NSF-SEC18_r1-like | cd19504 | first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ... |
275-397 | 1.05e-03 | |||||||||
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; N-ethylmaleimide-sensitive factor (NSF) and Saccharomyces cerevisiae Vesicular-fusion protein Sec18, key factors for eukaryotic trafficking, are ATPases and SNARE disassembly chaperones. NSF/Sec18 activate or prime SNAREs, the terminal catalysts of membrane fusion. Sec18/NSF associates with SNARE complexes through binding Sec17/alpha-SNAP. Sec18 has an N-terminal cap domain and two nucleotide-binding domains (D1 and D2) which form the two rings of the hexameric complex. The hydrolysis of ATP by D1 generates most of the energy necessary to disassemble inactive SNARE bundles, while the D2 ring binds ATP to stabilize the homohexamer. This subfamily includes the first (D1) ATPase domain of NSF/Sec18, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410912 [Multi-domain] Cd Length: 177 Bit Score: 40.55 E-value: 1.05e-03
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| MoxR | COG0714 | MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ... |
275-348 | 1.42e-03 | |||||||||
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis Pssm-ID: 440478 [Multi-domain] Cd Length: 292 Bit Score: 40.92 E-value: 1.42e-03
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| MCM8 | cd17759 | DNA helicase Mcm8; Mcm8 plays an important role homologous recombination repair. It forms a ... |
271-382 | 1.48e-03 | |||||||||
DNA helicase Mcm8; Mcm8 plays an important role homologous recombination repair. It forms a complex with Mcm9 that is required for homologous recombination (HR) repair induced by DNA interstrand crosslinks (ICLs). Pssm-ID: 350665 [Multi-domain] Cd Length: 289 Bit Score: 40.98 E-value: 1.48e-03
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| RecA-like_PEX6_r2 | cd19527 | second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ... |
271-349 | 1.58e-03 | |||||||||
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410935 [Multi-domain] Cd Length: 160 Bit Score: 39.42 E-value: 1.58e-03
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
270-353 | 1.65e-03 | |||||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 39.53 E-value: 1.65e-03
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| CDC6 | COG1474 | Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair]; |
273-354 | 2.59e-03 | |||||||||
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair]; Pssm-ID: 441083 [Multi-domain] Cd Length: 389 Bit Score: 40.60 E-value: 2.59e-03
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| aroK | PRK00131 | shikimate kinase; Reviewed |
270-300 | 3.11e-03 | |||||||||
shikimate kinase; Reviewed Pssm-ID: 234654 [Multi-domain] Cd Length: 175 Bit Score: 39.02 E-value: 3.11e-03
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| RecA-like_ATAD3-like | cd19512 | ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ... |
274-347 | 3.27e-03 | |||||||||
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase domains; ATPase AAA-domain protein 3 (ATAD3) is a ubiquitously expressed mitochondrial protein involved in mitochondrial dynamics, DNA-nucleoid structural organization, cholesterol transport and steroidogenesis. The ATAD3 gene family in human comprises three paralog genes: ATAD3A, ATAD3B and ATAD3C. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410920 [Multi-domain] Cd Length: 150 Bit Score: 38.66 E-value: 3.27e-03
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| NACHT | pfam05729 | NACHT domain; This NTPase domain is found in apoptosis proteins as well as those involved in ... |
275-378 | 3.52e-03 | |||||||||
NACHT domain; This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931. Pssm-ID: 428606 [Multi-domain] Cd Length: 166 Bit Score: 38.83 E-value: 3.52e-03
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| RecA-like_VCP_r2 | cd19529 | second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ... |
275-376 | 3.75e-03 | |||||||||
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ATPase domains; The Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), is an archaeal homolog of the ubiquitous Cdc48/p97. It is a protein unfoldase that functions in concert with the 20S proteasome by unfolding proteasome substrates and passing them on for degradation. VAT forms a homohexamer, each monomer contains two tandem ATPase domains, referred to as D1 and D2, and an N-terminal domain. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Pssm-ID: 410937 [Multi-domain] Cd Length: 159 Bit Score: 38.63 E-value: 3.75e-03
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| PTZ00361 | PTZ00361 | 26 proteosome regulatory subunit 4-like protein; Provisional |
275-374 | 4.67e-03 | |||||||||
26 proteosome regulatory subunit 4-like protein; Provisional Pssm-ID: 185575 [Multi-domain] Cd Length: 438 Bit Score: 39.75 E-value: 4.67e-03
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| PRK03992 | PRK03992 | proteasome-activating nucleotidase; Provisional |
273-351 | 5.68e-03 | |||||||||
proteasome-activating nucleotidase; Provisional Pssm-ID: 179699 [Multi-domain] Cd Length: 389 Bit Score: 39.43 E-value: 5.68e-03
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| CDC48 | TIGR01243 | AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ... |
275-376 | 5.69e-03 | |||||||||
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Pssm-ID: 273521 [Multi-domain] Cd Length: 733 Bit Score: 39.89 E-value: 5.69e-03
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| Zn-ribbon | cd00656 | C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ... |
104-132 | 7.55e-03 | |||||||||
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II. Pssm-ID: 259791 Cd Length: 45 Bit Score: 34.60 E-value: 7.55e-03
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| RPB9 | COG1594 | DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ... |
104-132 | 7.99e-03 | |||||||||
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase Pssm-ID: 441202 [Multi-domain] Cd Length: 103 Bit Score: 36.46 E-value: 7.99e-03
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| YifB | COG0606 | Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational ... |
274-292 | 9.83e-03 | |||||||||
Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440371 [Multi-domain] Cd Length: 502 Bit Score: 38.87 E-value: 9.83e-03
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