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Conserved domains on  [gi|899720991|gb|AKI82131|]
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polyprotein, partial [Sapovirus fur seal/ATROP02/BR/2012]

Protein Classification

RNA helicase domain-containing protein( domain architecture ID 10468696)

RNA helicase domain-containing protein may be involved in duplex unwinding during viral RNA replication

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 352-445 2.12e-28

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


:

Pssm-ID: 459992  Cd Length: 102  Bit Score: 109.62  E-value: 2.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 899720991  352 IIFTGPPGIGKTMLAQSIGK------GFGKISTFTL--ANDHHDAYTGNKVALWDEFDVDTKGLFVETMIGLVNTQPYPL 423
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARallkklGLPKDSVYSRnpDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                          90       100
                  ....*....|....*....|..
gi 899720991  424 NCDRVENKGKVFSSDIILCTSN 445
Cdd:pfam00910  81 PMAALEEKGTPFTSKFVIVTSN 102
SpoVK super family cl33891
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 328-371 1.79e-03

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG0464:

Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 41.82  E-value: 1.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 899720991 328 ELEQVAQGIRSTIQL--DTPRKPPVCIIFTGPPGIGKTMLAQSIGK 371
Cdd:COG0464  168 ELRELVALPLKRPELreEYGLPPPRGLLLYGPPGTGKTLLARALAG 213
 
Name Accession Description Interval E-value
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 352-445 2.12e-28

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 109.62  E-value: 2.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 899720991  352 IIFTGPPGIGKTMLAQSIGK------GFGKISTFTL--ANDHHDAYTGNKVALWDEFDVDTKGLFVETMIGLVNTQPYPL 423
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARallkklGLPKDSVYSRnpDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                          90       100
                  ....*....|....*....|..
gi 899720991  424 NCDRVENKGKVFSSDIILCTSN 445
Cdd:pfam00910  81 PMAALEEKGTPFTSKFVIVTSN 102
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 334-466 8.97e-06

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: 46.76  E-value: 8.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 899720991 334 QGIRSTIQLDTPRKPPVCIIFTGPPGIGKTMLAQSIGKGFGKISTFTLANDHHDAYTGNKVAlwdeFDVDTKGLFVETMI 413
Cdd:cd00009    4 EEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVA----ELFGHFLVRLLFEL 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 899720991 414 gLVNTQPYPLNCD------------------RVENKGKVFSSDIILCTSNFPTSVIPENPRAAAFYRRVTI 466
Cdd:cd00009   80 -AEKAKPGVLFIDeidslsrgaqnallrvleTLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVI 149
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 328-371 1.79e-03

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: 41.82  E-value: 1.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 899720991 328 ELEQVAQGIRSTIQL--DTPRKPPVCIIFTGPPGIGKTMLAQSIGK 371
Cdd:COG0464  168 ELRELVALPLKRPELreEYGLPPPRGLLLYGPPGTGKTLLARALAG 213
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 318-369 4.69e-03

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: 38.92  E-value: 4.69e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 899720991 318 LAGVIRTYLSELEQVAQGIR-STIQLDTPRKPPVCIIFTGPPGIGKTMLAQSI 369
Cdd:cd19518    2 IGGMDSTLKELCELLIHPILpPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAI 54
 
Name Accession Description Interval E-value
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 352-445 2.12e-28

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 109.62  E-value: 2.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 899720991  352 IIFTGPPGIGKTMLAQSIGK------GFGKISTFTL--ANDHHDAYTGNKVALWDEFDVDTKGLFVETMIGLVNTQPYPL 423
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARallkklGLPKDSVYSRnpDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                          90       100
                  ....*....|....*....|..
gi 899720991  424 NCDRVENKGKVFSSDIILCTSN 445
Cdd:pfam00910  81 PMAALEEKGTPFTSKFVIVTSN 102
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 334-466 8.97e-06

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: 46.76  E-value: 8.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 899720991 334 QGIRSTIQLDTPRKPPVCIIFTGPPGIGKTMLAQSIGKGFGKISTFTLANDHHDAYTGNKVAlwdeFDVDTKGLFVETMI 413
Cdd:cd00009    4 EEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVA----ELFGHFLVRLLFEL 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 899720991 414 gLVNTQPYPLNCD------------------RVENKGKVFSSDIILCTSNFPTSVIPENPRAAAFYRRVTI 466
Cdd:cd00009   80 -AEKAKPGVLFIDeidslsrgaqnallrvleTLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVI 149
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 328-453 1.40e-04

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: 43.43  E-value: 1.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 899720991 328 ELEQVAQGIRSTIQLDT-PRKPPVCIIFTGPPGIGKTMLAQSIG----------KGFGKIS------------TFTLAND 384
Cdd:cd19481    4 SLREAVEAPRRGSRLRRyGLGLPKGILLYGPPGTGKTLLAKALAgelglplivvKLSSLLSkyvgeseknlrkIFERARR 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 899720991 385 HHDAytgnkVALWDEFDV-----DTKGLFVETMIGLvntqPYPLNC-DRVENKGKVfssdIILCTSNFPTSVIPE 453
Cdd:cd19481   84 LAPC-----ILFIDEIDAigrkrDSSGESGELRRVL----NQLLTElDGVNSRSKV----LVIAATNRPDLLDPA 145
TsaE pfam02367
Threonylcarbamoyl adenosine biosynthesis protein TsaE; This family of proteins is involved in ...
 347-402 7.76e-04

Threonylcarbamoyl adenosine biosynthesis protein TsaE; This family of proteins is involved in the synthesis of threonylcarbamoyl adenosine (t(6)A).


Pssm-ID: 460540  Cd Length: 127  Bit Score: 40.49  E-value: 7.76e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 899720991  347 KPPVCIIFTGPPGIGKTMLAQSIGKGFG---KIS--TFTLANdhhdAYTGNKVALWdEFDV 402
Cdd:pfam02367  19 KPGDVILLSGDLGAGKTTFTRGLARGLGvtgPVTspTFTLVN----EYEGGGLPLY-HFDL 74
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 328-371 1.79e-03

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: 41.82  E-value: 1.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 899720991 328 ELEQVAQGIRSTIQL--DTPRKPPVCIIFTGPPGIGKTMLAQSIGK 371
Cdd:COG0464  168 ELRELVALPLKRPELreEYGLPPPRGLLLYGPPGTGKTLLARALAG 213
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 318-369 4.69e-03

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: 38.92  E-value: 4.69e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 899720991 318 LAGVIRTYLSELEQVAQGIR-STIQLDTPRKPPVCIIFTGPPGIGKTMLAQSI 369
Cdd:cd19518    2 IGGMDSTLKELCELLIHPILpPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAI 54
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
328-369 6.90e-03

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 39.48  E-value: 6.90e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 899720991 328 ELEQVAQGIRSTIQLDTPRK----PPVCIIFTGPPGIGKTMLAQSI 369
Cdd:COG1223   10 AKKKLKLIIKELRRRENLRKfglwPPRKILFYGPPGTGKTMLAEAL 55
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 347-369 7.56e-03

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: 38.43  E-value: 7.56e-03
                         10        20
                 ....*....|....*....|...
gi 899720991 347 KPPVCIIFTGPPGIGKTMLAQSI 369
Cdd:cd19503   32 KPPRGVLLHGPPGTGKTLLARAV 54
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 352-375 9.11e-03

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: 38.31  E-value: 9.11e-03
                         10        20
                 ....*....|....*....|....
gi 899720991 352 IIFTGPPGIGKTMLAQSIGKGFGK 375
Cdd:cd19500   40 LCLVGPPGVGKTSLGKSIARALGR 63
 
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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