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Conserved domains on  [gi|1002295647|ref|XP_015611282|]
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uncharacterized protein [Oryza sativa Japonica Group]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AAA super family cl47477
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 114-242 1.43e-06

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.


The actual alignment was detected with superfamily member pfam00004:

Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 47.20  E-value: 1.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 114 LLHGP--CDKKAVVEGIGRTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESrDGPLLIFLDRFDELVPHNRCGSTVM 191
Cdd:pfam00004   2 LLYGPpgTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKK-LAPCVIFIDEIDALAGSRGSGGDSE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002295647 192 TDITTTQLKLLLDDPwVIFGHRITILVVSVRwINLICPTILSRIRTRFYCG 242
Cdd:pfam00004  81 SRRVVNQLLTELDGF-TSSNSKVIVIAATNR-PDKLDPALLGRFDRIIEFP 129
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 276-394 5.22e-05

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 cd19526:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 158  Bit Score: 43.19  E-value: 5.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 276 TNAILYGNTSLSKSDVTKLFAATQSFDSIVIDAMQVLKDFKNTGSKAVSDLFLRATARRPCIILIQQLDAIN-------- 347
Cdd:cd19526    28 SGILLYGPPGCGKTLLASAIASECGLNFISVKGPELLNKYIGASEQNVRDLFSRAQSAKPCILFFDEFDSIApkrghdst 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002295647 348 --NETLISLILHEMNNMD--RDLHVFASTRWWQLIHHMFLESRLFTRRVFC 394
Cdd:cd19526   108 gvTDRVVNQLLTQLDGVEglDGVYVLAATSRPDLIDPALLRPGRLDKLVYC 158
 
Name Accession Description Interval E-value
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 114-242 1.43e-06

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: 47.20  E-value: 1.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 114 LLHGP--CDKKAVVEGIGRTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESrDGPLLIFLDRFDELVPHNRCGSTVM 191
Cdd:pfam00004   2 LLYGPpgTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKK-LAPCVIFIDEIDALAGSRGSGGDSE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002295647 192 TDITTTQLKLLLDDPwVIFGHRITILVVSVRwINLICPTILSRIRTRFYCG 242
Cdd:pfam00004  81 SRRVVNQLLTELDGF-TSSNSKVIVIAATNR-PDKLDPALLGRFDRIIEFP 129
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 276-394 5.22e-05

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: 43.19  E-value: 5.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 276 TNAILYGNTSLSKSDVTKLFAATQSFDSIVIDAMQVLKDFKNTGSKAVSDLFLRATARRPCIILIQQLDAIN-------- 347
Cdd:cd19526    28 SGILLYGPPGCGKTLLASAIASECGLNFISVKGPELLNKYIGASEQNVRDLFSRAQSAKPCILFFDEFDSIApkrghdst 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002295647 348 --NETLISLILHEMNNMD--RDLHVFASTRWWQLIHHMFLESRLFTRRVFC 394
Cdd:cd19526   108 gvTDRVVNQLLTQLDGVEglDGVYVLAATSRPDLIDPALLRPGRLDKLVYC 158
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 98-206 1.27e-04

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: 42.39  E-value: 1.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647  98 YYTHLPHEATKGkmtFLLHGP--CDKKAVVEGIGRTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESrDGPLLIFLD 175
Cdd:cd19518    25 YFQHLGVEPPRG---VLLHGPpgCGKTMLANAIAGELKVPFLKISATEIVSGVSGESEEKIRELFDQAIS-NAPCIVFID 100

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1002295647 176 RFDELVPHNRCGSTVMTDITTTQLKLLLDDP 206
Cdd:cd19518   101 EIDAITPKRESAQREMERRIVSQLLTCMDEL 131
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 279-372 2.77e-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: 37.57  E-value: 2.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 279 ILYGNTSLSKSDVTKLFAATQSFDSIVIDAMQVLKDFKNTGSKAVSDLFLRATARRPCIILIQQLDAIN----------N 348
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAgsrgsggdseS 81

                          90       100
                  ....*....|....*....|....*..
gi 1002295647 349 ETLISLILHEMNNMDRD---LHVFAST 372
Cdd:pfam00004  82 RRVVNQLLTELDGFTSSnskVIVIAAT 108
 
Name Accession Description Interval E-value
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 114-242 1.43e-06

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: 47.20  E-value: 1.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 114 LLHGP--CDKKAVVEGIGRTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESrDGPLLIFLDRFDELVPHNRCGSTVM 191
Cdd:pfam00004   2 LLYGPpgTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKK-LAPCVIFIDEIDALAGSRGSGGDSE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002295647 192 TDITTTQLKLLLDDPwVIFGHRITILVVSVRwINLICPTILSRIRTRFYCG 242
Cdd:pfam00004  81 SRRVVNQLLTELDGF-TSSNSKVIVIAATNR-PDKLDPALLGRFDRIIEFP 129
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 276-394 5.22e-05

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: 43.19  E-value: 5.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 276 TNAILYGNTSLSKSDVTKLFAATQSFDSIVIDAMQVLKDFKNTGSKAVSDLFLRATARRPCIILIQQLDAIN-------- 347
Cdd:cd19526    28 SGILLYGPPGCGKTLLASAIASECGLNFISVKGPELLNKYIGASEQNVRDLFSRAQSAKPCILFFDEFDSIApkrghdst 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002295647 348 --NETLISLILHEMNNMD--RDLHVFASTRWWQLIHHMFLESRLFTRRVFC 394
Cdd:cd19526   108 gvTDRVVNQLLTQLDGVEglDGVYVLAATSRPDLIDPALLRPGRLDKLVYC 158
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 98-206 1.27e-04

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: 42.39  E-value: 1.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647  98 YYTHLPHEATKGkmtFLLHGP--CDKKAVVEGIGRTLGLPVASVDASSLIKDFPSDSVSQINTCIQRPESrDGPLLIFLD 175
Cdd:cd19518    25 YFQHLGVEPPRG---VLLHGPpgCGKTMLANAIAGELKVPFLKISATEIVSGVSGESEEKIRELFDQAIS-NAPCIVFID 100

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1002295647 176 RFDELVPHNRCGSTVMTDITTTQLKLLLDDP 206
Cdd:cd19518   101 EIDAITPKRESAQREMERRIVSQLLTCMDEL 131
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 279-373 5.75e-04

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: 40.34  E-value: 5.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 279 ILYGNTSLSKSDVTKLFAATQSFDSIVIDAMQVLKDFKNTGSKAVSDLFLRATARRPCIILIQQLDAI------NNET-- 350
Cdd:cd19511    31 LLYGPPGCGKTLLAKALASEAGLNFISVKGPELFSKYVGESERAVREIFQKARQAAPCIIFFDEIDSLaprrgqSDSSgv 110

                          90       100
                  ....*....|....*....|....*....
gi 1002295647 351 ---LISLILHEMNNMDRDLHVF---ASTR 373
Cdd:cd19511   111 tdrVVSQLLTELDGIESLKGVVviaATNR 139
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 279-372 2.77e-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: 37.57  E-value: 2.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 279 ILYGNTSLSKSDVTKLFAATQSFDSIVIDAMQVLKDFKNTGSKAVSDLFLRATARRPCIILIQQLDAIN----------N 348
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAgsrgsggdseS 81

                          90       100
                  ....*....|....*....|....*..
gi 1002295647 349 ETLISLILHEMNNMDRD---LHVFAST 372
Cdd:pfam00004  82 RRVVNQLLTELDGFTSSnskVIVIAAT 108
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 276-369 5.94e-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: 37.47  E-value: 5.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 276 TNAILYGNTSLSKSDVTKLFAATQSFDSIVIDAMQVLKDFKNTGSKAVSDLFLRATARRPCIILIQQLDAI--------- 346
Cdd:cd19530    31 TGVLLYGPPGCGKTLLAKAVANESGANFISVKGPELLNKYVGESERAVRQVFQRARASAPCVIFFDEVDALvpkrgdggs 110

                          90       100
                  ....*....|....*....|....
gi 1002295647 347 -NNETLISLILHEMNNMDRDLHVF 369
Cdd:cd19530   111 wASERVVNQLLTEMDGLEERSNVF 134
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 277-346 7.47e-03

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: 36.88  E-value: 7.47e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002295647 277 NAILYGNTSLSKSDVTKLFAATQSFDSIVIDAMQVLKDFKNTGSKAVSDLFLRATARRPCIILIQQLDAI 346
Cdd:cd19481    28 GILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKYVGESEKNLRKIFERARRLAPCILFIDEIDAI 97
 
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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