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Conserved domains on  [gi|41179064|ref|NP_958421|]
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hypothetical protein ChreCp065 (chloroplast) [Chlamydomonas reinhardtii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPT1 super family cl34191
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 2295-2367 1.51e-07

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


The actual alignment was detected with superfamily member COG1222:

Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 56.17  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETICLP-----------NIHTSNiLNFTKNYEIFKSAKD 2363
Cdd:COG1222  199 TVNQLLAELDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPlpdeeareeilKIHLRD-MPLADDVDLDKLAKL 277


                 ....
gi 41179064 2364 TSNF 2367
Cdd:COG1222  278 TEGF 281
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 2009-2097 1.27e-06

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd19481:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 158  Bit Score: 50.74  E-value: 1.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2009 FNKQISKNILLVNP----KTtsnnlvdynvLLIQALAGETEMKIITDNAQRyaLVNRGFAIGIKLLREVFDAIALNTPCI 2084
Cdd:cd19481   21 YGLGLPKGILLYGPpgtgKT----------LLAKALAGELGLPLIVVKLSS--LLSKYVGESEKNLRKIFERARRLAPCI 88

                         90
                 ....*....|...
gi 41179064 2085 FLLEDIHAIGERR 2097
Cdd:cd19481   89 LFIDEIDAIGRKR 101
 
Name Accession Description Interval E-value
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 2295-2367 1.51e-07

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 56.17  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETICLP-----------NIHTSNiLNFTKNYEIFKSAKD 2363
Cdd:COG1222  199 TVNQLLAELDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPlpdeeareeilKIHLRD-MPLADDVDLDKLAKL 277


                 ....
gi 41179064 2364 TSNF 2367
Cdd:COG1222  278 TEGF 281
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 2295-2392 1.83e-07

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: 56.84  E-value: 1.83e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064   2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETICLPnihtsnILNFTKNYEIFKSAKDTSNFGKKIILN 2374
Cdd:TIGR01243  574 IVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVP------PPDEEARKEIFKIHTRSMPLAEDVDLE 647

                           90
                   ....*....|....*...
gi 41179064   2375 EMQNLTTTSTQRDMYLSC 2392
Cdd:TIGR01243  648 ELAEMTEGYTGADIEAVC 665
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 2299-2338 3.53e-07

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: 52.29  E-value: 3.53e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 41179064 2299 LLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:cd19481  117 LLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEVI 156
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 2009-2097 1.27e-06

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: 50.74  E-value: 1.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2009 FNKQISKNILLVNP----KTtsnnlvdynvLLIQALAGETEMKIITDNAQRyaLVNRGFAIGIKLLREVFDAIALNTPCI 2084
Cdd:cd19481   21 YGLGLPKGILLYGPpgtgKT----------LLAKALAGELGLPLIVVKLSS--LLSKYVGESEKNLRKIFERARRLAPCI 88

                         90
                 ....*....|...
gi 41179064 2085 FLLEDIHAIGERR 2097
Cdd:cd19481   89 LFIDEIDAIGRKR 101
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
2296-2343 2.52e-05

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 50.03  E-value: 2.52e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 41179064  2296 ITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETIC--LPNI 2343
Cdd:PRK10733  275 LNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVvgLPDV 324
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
2009-2117 1.14e-04

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 46.42  E-value: 1.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2009 FNKQISKNILLVNP----KTTsnnlvdynvlLIQALAGETEMKIITDNAQryALVNRGFAIGIKLLREVFDAIAlNTPCI 2084
Cdd:COG1223   30 FGLWPPRKILFYGPpgtgKTM----------LAEALAGELKLPLLTVRLD--SLIGSYLGETARNLRKLFDFAR-RAPCV 96

                         90       100       110
                 ....*....|....*....|....*....|...
gi 41179064 2085 FLLEDIHAIGERRpmlisdfggGMSDDNGSFKE 2117
Cdd:COG1223   97 IFFDEFDAIAKDR---------GDQNDVGEVKR 120
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 2017-2097 1.29e-04

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: 44.12  E-value: 1.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064   2017 ILLVNP----KTTsnnlvdynvlLIQALAGETEMKIITDNAqrYALVNRGFAIGIKLLREVFDAIALNTPCIFLLEDIHA 2092
Cdd:pfam00004    1 LLLYGPpgtgKTT----------LAKAVAKELGAPFIEISG--SELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDA 68


                   ....*
gi 41179064   2093 IGERR 2097
Cdd:pfam00004   69 LAGSR 73
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
2012-2107 1.02e-03

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 44.64  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064  2012 QISKNILLVNPKTTSNNLvdynvlLIQALAGETEMKIITDNAQRYalVNRGFAIGIKLLREVFDAIALNTPCIFLLEDIH 2091
Cdd:PRK10733  183 KIPKGVLMVGPPGTGKTL------LAKAIAGEAKVPFFTISGSDF--VEMFVGVGASRVRDMFEQAKKAAPCIIFIDEID 254

                          90
                  ....*....|....*.
gi 41179064  2092 AIGERRPmliSDFGGG 2107
Cdd:PRK10733  255 AVGRQRG---AGLGGG 267
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 2299-2341 7.63e-03

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: 39.11  E-value: 7.63e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 41179064   2299 LLVIIDSVRSNKG-FVVFATTDIPHVLDPALRrpGRLDETICLP 2341
Cdd:pfam00004   88 LLTELDGFTSSNSkVIVIAATNRPDKLDPALL--GRFDRIIEFP 129
 
Name Accession Description Interval E-value
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 2295-2367 1.51e-07

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 56.17  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETICLP-----------NIHTSNiLNFTKNYEIFKSAKD 2363
Cdd:COG1222  199 TVNQLLAELDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPlpdeeareeilKIHLRD-MPLADDVDLDKLAKL 277


                 ....
gi 41179064 2364 TSNF 2367
Cdd:COG1222  278 TEGF 281
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 2295-2392 1.83e-07

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: 56.84  E-value: 1.83e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064   2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETICLPnihtsnILNFTKNYEIFKSAKDTSNFGKKIILN 2374
Cdd:TIGR01243  574 IVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVP------PPDEEARKEIFKIHTRSMPLAEDVDLE 647

                           90
                   ....*....|....*...
gi 41179064   2375 EMQNLTTTSTQRDMYLSC 2392
Cdd:TIGR01243  648 ELAEMTEGYTGADIEAVC 665
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 2299-2338 3.53e-07

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: 52.29  E-value: 3.53e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 41179064 2299 LLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:cd19481  117 LLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEVI 156
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 2295-2340 9.21e-07

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: 51.14  E-value: 9.21e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETICL 2340
Cdd:cd19503  120 VVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRRPGRFDREVEI 165
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 2009-2097 1.27e-06

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: 50.74  E-value: 1.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2009 FNKQISKNILLVNP----KTtsnnlvdynvLLIQALAGETEMKIITDNAQRyaLVNRGFAIGIKLLREVFDAIALNTPCI 2084
Cdd:cd19481   21 YGLGLPKGILLYGPpgtgKT----------LLAKALAGELGLPLIVVKLSS--LLSKYVGESEKNLRKIFERARRLAPCI 88

                         90
                 ....*....|...
gi 41179064 2085 FLLEDIHAIGERR 2097
Cdd:cd19481   89 LFIDEIDAIGRKR 101
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 2299-2338 1.95e-06

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: 50.31  E-value: 1.95e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 41179064 2299 LLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:cd19501  130 LLVEMDGFESNTGVIVIAATNRPDVLDPALLRPGRFDRQV 169
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 2296-2338 2.23e-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: 47.28  E-value: 2.23e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 41179064 2296 ITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:cd19511  115 VSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDKLI 157
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
2296-2343 2.52e-05

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 50.03  E-value: 2.52e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 41179064  2296 ITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETIC--LPNI 2343
Cdd:PRK10733  275 LNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVvgLPDV 324
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 2290-2340 5.01e-05

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: 46.24  E-value: 5.01e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 41179064 2290 SAKLDM----ITDLLVIIDSV----RSNKGFVVFATTDIPHVLDPALRRPGRLDETICL 2340
Cdd:cd19518  111 SAQREMerriVSQLLTCMDELnnekTAGGPVLVIGATNRPDSLDPALRRAGRFDREICL 169
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 2295-2338 5.31e-05

second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP in 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 second 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_r2-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: 410936 [Multi-domain]  Cd Length: 161  Bit Score: 45.96  E-value: 5.31e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:cd19528  116 VINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQLI 159
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 2295-2338 5.53e-05

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: 46.28  E-value: 5.53e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:cd19519  120 IVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREI 163
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
2009-2117 1.14e-04

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 46.42  E-value: 1.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2009 FNKQISKNILLVNP----KTTsnnlvdynvlLIQALAGETEMKIITDNAQryALVNRGFAIGIKLLREVFDAIAlNTPCI 2084
Cdd:COG1223   30 FGLWPPRKILFYGPpgtgKTM----------LAEALAGELKLPLLTVRLD--SLIGSYLGETARNLRKLFDFAR-RAPCV 96

                         90       100       110
                 ....*....|....*....|....*....|...
gi 41179064 2085 FLLEDIHAIGERRpmlisdfggGMSDDNGSFKE 2117
Cdd:COG1223   97 IFFDEFDAIAKDR---------GDQNDVGEVKR 120
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 2017-2097 1.29e-04

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: 44.12  E-value: 1.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064   2017 ILLVNP----KTTsnnlvdynvlLIQALAGETEMKIITDNAqrYALVNRGFAIGIKLLREVFDAIALNTPCIFLLEDIHA 2092
Cdd:pfam00004    1 LLLYGPpgtgKTT----------LAKAVAKELGAPFIEISG--SELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDA 68


                   ....*
gi 41179064   2093 IGERR 2097
Cdd:pfam00004   69 LAGSR 73
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 2009-2097 1.48e-04

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 46.54  E-value: 1.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2009 FNKQISKNILLVNP----KTtsnnlvdynvLLIQALAGETEMKIITDNAQryALVNRGFAIGIKLLREVFDAIALNTPCI 2084
Cdd:COG1222  107 YGIEPPKGVLLYGPpgtgKT----------LLAKAVAGELGAPFIRVRGS--ELVSKYIGEGARNVREVFELAREKAPSI 174

                         90
                 ....*....|...
gi 41179064 2085 FLLEDIHAIGERR 2097
Cdd:COG1222  175 IFIDEIDAIAARR 187
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 2295-2338 2.22e-04

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 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. PEX-1 is required for stability of PEX5. 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: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 44.34  E-value: 2.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:cd19526  113 VVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDKLV 156
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 2295-2338 2.58e-04

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: 44.02  E-value: 2.58e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:cd19529  114 VVNQLLTELDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDRLI 157
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 2295-2338 8.65e-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: 44.90  E-value: 8.65e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 41179064   2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:TIGR01243  298 VVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREI 341
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
2012-2107 1.02e-03

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 44.64  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064  2012 QISKNILLVNPKTTSNNLvdynvlLIQALAGETEMKIITDNAQRYalVNRGFAIGIKLLREVFDAIALNTPCIFLLEDIH 2091
Cdd:PRK10733  183 KIPKGVLMVGPPGTGKTL------LAKAIAGEAKVPFFTISGSDF--VEMFVGVGASRVRDMFEQAKKAAPCIIFIDEID 254

                          90
                  ....*....|....*.
gi 41179064  2092 AIGERRPmliSDFGGG 2107
Cdd:PRK10733  255 AVGRQRG---AGLGGG 267
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 2299-2335 1.45e-03

Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. 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: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 41.57  E-value: 1.45e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 41179064 2299 LLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLD 2335
Cdd:cd19510  112 LLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVD 148
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 2295-2338 2.73e-03

second 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: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 40.93  E-value: 2.73e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLDETI 2338
Cdd:cd19530  116 VVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRLDKTL 159
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 2295-2335 3.12e-03

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 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: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 40.96  E-value: 3.12e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 41179064 2295 MITDLLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLD 2335
Cdd:cd19517  125 IVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRRPGRFD 165
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
2299-2335 4.23e-03

ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 42.72  E-value: 4.23e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 41179064 2299 LLVIIDSVRSNKGFVVFATTDIPHVLDPALRRPGRLD 2335
Cdd:COG0465  268 LLVEMDGFEGNEGVIVIAATNRPDVLDPALLRPGRFD 304
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 2015-2112 6.61e-03

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: 40.01  E-value: 6.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179064 2015 KNILLVNPKTTSNNLvdynvlLIQALAGETEMKIITDNAQRyaLVNRGFAIGIKLLREVFDAIALNTPCIFLLEDIHAIG 2094
Cdd:cd19502   38 KGVLLYGPPGTGKTL------LAKAVANHTDATFIRVVGSE--LVQKYIGEGARLVRELFEMAREKAPSIIFIDEIDAIG 109

                         90
                 ....*....|....*...
gi 41179064 2095 ERRpmlisdFGGGMSDDN 2112
Cdd:cd19502  110 AKR------FDSGTGGDR 121
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 2299-2341 7.63e-03

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: 39.11  E-value: 7.63e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 41179064   2299 LLVIIDSVRSNKG-FVVFATTDIPHVLDPALRrpGRLDETICLP 2341
Cdd:pfam00004   88 LLTELDGFTSSNSkVIVIAATNRPDKLDPALL--GRFDRIIEFP 129
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 2313-2363 8.82e-03

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 41.30  E-value: 8.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41179064  2313 VVFATTDIpHVLDPALRRPGRLDETICLPN-----------IHTSNI-LNFTKNYEIFKSAKD 2363
Cdd:PTZ00361  325 VIMATNRI-ESLDPALIRPGRIDRKIEFPNpdektkrrifeIHTSKMtLAEDVDLEEFIMAKD 386
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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