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Conserved domains on  [gi|1494593464|gb|AYN07255|]
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REP, partial [Goat blood associated circularviruslike virus]

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 ...
 115-163 4.73e-14

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: 65.70  E-value: 4.73e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1494593464 115 IWLYGPAGCGKSTWAKALGDHLGGWYEKAQN---------KWWDGYEGEKVVILDDLD 163
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDsvysrnpddDFWDGYTGQPVVIIDDFG 58
SpoVK super family cl33891
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 71-138 1.09e-05

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: 45.67  E-value: 1.09e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1494593464  71 ILNTPMKQLVDEgviSIKDVSAYQRGIAAYKLleKPGvkskcRGIWLYGPAGCGKSTWAKALGDHLGG 138
Cdd:COG0464   160 GGLEEVKEELRE---LVALPLKRPELREEYGL--PPP-----RGLLLYGPPGTGKTLLARALAGELGL 217
 
Name Accession Description Interval E-value
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 115-163 4.73e-14

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: 65.70  E-value: 4.73e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1494593464 115 IWLYGPAGCGKSTWAKALGDHLGGWYEKAQN---------KWWDGYEGEKVVILDDLD 163
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDsvysrnpddDFWDGYTGQPVVIIDDFG 58
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 71-138 1.09e-05

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: 45.67  E-value: 1.09e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1494593464  71 ILNTPMKQLVDEgviSIKDVSAYQRGIAAYKLleKPGvkskcRGIWLYGPAGCGKSTWAKALGDHLGG 138
Cdd:COG0464   160 GGLEEVKEELRE---LVALPLKRPELREEYGL--PPP-----RGLLLYGPPGTGKTLLARALAGELGL 217
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 113-137 1.18e-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: 41.11  E-value: 1.18e-04
                          10        20
                  ....*....|....*....|....*
gi 1494593464 113 RGIWLYGPAGCGKSTWAKALGDHLG 137
Cdd:cd19481    27 KGILLYGPPGTGKTLLAKALAGELG 51
Cmk COG0283
Cytidylate kinase [Nucleotide transport and metabolism];
119-137 2.55e-03

Cytidylate kinase [Nucleotide transport and metabolism];


Pssm-ID: 440052 [Multi-domain]  Cd Length: 220  Bit Score: 38.08  E-value: 2.55e-03
                          10
                  ....*....|....*....
gi 1494593464 119 GPAGCGKSTWAKALGDHLG 137
Cdd:COG0283     7 GPAGSGKSTVAKALAKRLG 25
PRK05541 PRK05541
adenylylsulfate kinase; Provisional
 115-160 7.59e-03

adenylylsulfate kinase; Provisional


Pssm-ID: 235498  Cd Length: 176  Bit Score: 36.19  E-value: 7.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1494593464 115 IWLYGPAGCGKSTWAKALgdhlggwYEKAQNKwwdgyeGEKVVILD 160
Cdd:PRK05541   10 IWITGLAGSGKTTIAKAL-------YERLKLK------YSNVIYLD 42
 
Name Accession Description Interval E-value
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 115-163 4.73e-14

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: 65.70  E-value: 4.73e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1494593464 115 IWLYGPAGCGKSTWAKALGDHLGGWYEKAQN---------KWWDGYEGEKVVILDDLD 163
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDsvysrnpddDFWDGYTGQPVVIIDDFG 58
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 71-138 1.09e-05

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: 45.67  E-value: 1.09e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1494593464  71 ILNTPMKQLVDEgviSIKDVSAYQRGIAAYKLleKPGvkskcRGIWLYGPAGCGKSTWAKALGDHLGG 138
Cdd:COG0464   160 GGLEEVKEELRE---LVALPLKRPELREEYGL--PPP-----RGLLLYGPPGTGKTLLARALAGELGL 217
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 113-137 1.18e-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: 41.11  E-value: 1.18e-04
                          10        20
                  ....*....|....*....|....*
gi 1494593464 113 RGIWLYGPAGCGKSTWAKALGDHLG 137
Cdd:cd19481    27 KGILLYGPPGTGKTLLAKALAGELG 51
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 113-132 1.47e-03

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: 38.03  E-value: 1.47e-03
                          10        20
                  ....*....|....*....|
gi 1494593464 113 RGIWLYGPAGCGKSTWAKAL 132
Cdd:cd19511    28 KGVLLYGPPGCGKTLLAKAL 47
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 102-138 1.68e-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: 38.24  E-value: 1.68e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1494593464 102 LLEKPGVKsKCRGIWLYGPAGCGKSTWAKALGDHLGG 138
Cdd:cd19504    26 IVEQLGCK-HVKGILLYGPPGTGKTLMARQIGKMLNA 61
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 101-157 1.81e-03

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: 37.79  E-value: 1.81e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1494593464 101 KLLEKPgvkskcRGIWLYGPAGCGKSTWAKALGDHLGGWYEKAQ-----NKWWDgyEGEKVV 157
Cdd:cd19520    30 RLLQPP------KGVLLYGPPGCGKTMLAKATAKEAGARFINLQvssltDKWYG--ESQKLV 83
CMPK cd02020
Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine ...
 119-137 1.94e-03

Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.


Pssm-ID: 238978 [Multi-domain]  Cd Length: 147  Bit Score: 37.47  E-value: 1.94e-03
                          10
                  ....*....|....*....
gi 1494593464 119 GPAGCGKSTWAKALGDHLG 137
Cdd:cd02020     6 GPAGSGKSTVAKLLAKKLG 24
Cmk COG0283
Cytidylate kinase [Nucleotide transport and metabolism];
119-137 2.55e-03

Cytidylate kinase [Nucleotide transport and metabolism];


Pssm-ID: 440052 [Multi-domain]  Cd Length: 220  Bit Score: 38.08  E-value: 2.55e-03
                          10
                  ....*....|....*....
gi 1494593464 119 GPAGCGKSTWAKALGDHLG 137
Cdd:COG0283     7 GPAGSGKSTVAKALAKRLG 25
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
86-164 2.56e-03

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 37.94  E-value: 2.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1494593464  86 SIKDVSAYQRgiaAYKLLEKPGvKSKCRGIWLYGPAGCGKSTWAKAL-----------------GDHLGgwyEKAQN--K 146
Cdd:COG1223    13 KLKLIIKELR---RRENLRKFG-LWPPRKILFYGPPGTGKTMLAEALagelklplltvrldsliGSYLG---ETARNlrK 85

                          90
                  ....*....|....*....
gi 1494593464 147 WWDGYEGEK-VVILDDLDT 164
Cdd:COG1223    86 LFDFARRAPcVIFFDEFDA 104
PRK05541 PRK05541
adenylylsulfate kinase; Provisional
 115-160 7.59e-03

adenylylsulfate kinase; Provisional


Pssm-ID: 235498  Cd Length: 176  Bit Score: 36.19  E-value: 7.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1494593464 115 IWLYGPAGCGKSTWAKALgdhlggwYEKAQNKwwdgyeGEKVVILD 160
Cdd:PRK05541   10 IWITGLAGSGKTTIAKAL-------YERLKLK------YSNVIYLD 42
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 113-137 7.79e-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: 36.23  E-value: 7.79e-03
                          10        20
                  ....*....|....*....|....*
gi 1494593464 113 RGIWLYGPAGCGKSTWAKALGDHLG 137
Cdd:cd19518    35 RGVLLHGPPGCGKTMLANAIAGELK 59
 
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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