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Conserved domains on  [gi|1332547700|gb|AUR88009|]
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putative packaging ATPase [Vibrio phage 1.107.A._10N.286.52.E10]

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
HerA super family cl33869
Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase ...
 3-37 6.22e-08

Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase domains [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0433:

Pssm-ID: 440202 [Multi-domain]  Cd Length: 388  Bit Score: 51.15  E-value: 6.22e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1332547700   3 HCAIVGMTESGKSSLARKMAVELQKSGIQIIVFDP 37
Cdd:COG0433    49 HILILGATGSGKSNTLQVLLEELSRAGVPVLVFDP 83
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 2-80 5.46e-03

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 cd00009:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 151  Bit Score: 35.58  E-value: 5.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332547700   2 PHCAIVGMTESGKSSLARKMAVELQKSGIQIIVFdplsdpewcNCLDLNNAFITDNENEFLNVYW------NSKNCAVFF 75
Cdd:cd00009    20 KNLLLYGPPGTGKTTLARAIANELFRPGAPFLYL---------NASDLLEGLVVAELFGHFLVRLlfelaeKAKPGVLFI 90


                  ....*
gi 1332547700  76 DEAGD 80
Cdd:cd00009    91 DEIDS 95
 
Name Accession Description Interval E-value
HerA COG0433
Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase ...
 3-37 6.22e-08

Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase domains [Replication, recombination and repair];


Pssm-ID: 440202 [Multi-domain]  Cd Length: 388  Bit Score: 51.15  E-value: 6.22e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1332547700   3 HCAIVGMTESGKSSLARKMAVELQKSGIQIIVFDP 37
Cdd:COG0433    49 HILILGATGSGKSNTLQVLLEELSRAGVPVLVFDP 83
DUF87 pfam01935
Helicase HerA, central domain; This entry represents the central domain found in archaeal ...
 3-67 1.02e-05

Helicase HerA, central domain; This entry represents the central domain found in archaeal proteins such as DNA double-strand break repair helicase HerA (EC:3.6.4.12). HerA is a helicase which is able to utilize either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus. This domain includes the the central RecA-like catalytic core and a flanking four-helix bundle. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.


Pssm-ID: 376671 [Multi-domain]  Cd Length: 220  Bit Score: 44.28  E-value: 1.02e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1332547700   3 HCAIVGMTESGKSSLARKMAVEL-QKSGIQIIVFDPLSDPEWCNC-LDLNNAFITDNENEFLNVYWN 67
Cdd:pfam01935  25 HFAILGSTGSGKSNTVAVLLEELlEKKGATVLIFDPHGEYGTLFRdLGAENVNVITPDPELKINPWL 91
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 3-37 1.05e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 37.74  E-value: 1.05e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1332547700    3 HCAIVGMTESGKSSLARKMAVELQKSGIQIIVFDP 37
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDG 38
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 2-80 5.46e-03

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: 35.58  E-value: 5.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332547700   2 PHCAIVGMTESGKSSLARKMAVELQKSGIQIIVFdplsdpewcNCLDLNNAFITDNENEFLNVYW------NSKNCAVFF 75
Cdd:cd00009    20 KNLLLYGPPGTGKTTLARAIANELFRPGAPFLYL---------NASDLLEGLVVAELFGHFLVRLlfelaeKAKPGVLFI 90


                  ....*
gi 1332547700  76 DEAGD 80
Cdd:cd00009    91 DEIDS 95
 
Name Accession Description Interval E-value
HerA COG0433
Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase ...
 3-37 6.22e-08

Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase domains [Replication, recombination and repair];


Pssm-ID: 440202 [Multi-domain]  Cd Length: 388  Bit Score: 51.15  E-value: 6.22e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1332547700   3 HCAIVGMTESGKSSLARKMAVELQKSGIQIIVFDP 37
Cdd:COG0433    49 HILILGATGSGKSNTLQVLLEELSRAGVPVLVFDP 83
DUF87 pfam01935
Helicase HerA, central domain; This entry represents the central domain found in archaeal ...
 3-67 1.02e-05

Helicase HerA, central domain; This entry represents the central domain found in archaeal proteins such as DNA double-strand break repair helicase HerA (EC:3.6.4.12). HerA is a helicase which is able to utilize either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus. This domain includes the the central RecA-like catalytic core and a flanking four-helix bundle. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.


Pssm-ID: 376671 [Multi-domain]  Cd Length: 220  Bit Score: 44.28  E-value: 1.02e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1332547700   3 HCAIVGMTESGKSSLARKMAVEL-QKSGIQIIVFDPLSDPEWCNC-LDLNNAFITDNENEFLNVYWN 67
Cdd:pfam01935  25 HFAILGSTGSGKSNTVAVLLEELlEKKGATVLIFDPHGEYGTLFRdLGAENVNVITPDPELKINPWL 91
VirB4 COG3451
Type IV secretory pathway, VirB4 component [Intracellular trafficking, secretion, and ...
 2-37 1.85e-05

Type IV secretory pathway, VirB4 component [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442674 [Multi-domain]  Cd Length: 546  Bit Score: 43.78  E-value: 1.85e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1332547700   2 PHCAIVGMTESGKSSLARKMAVELQKSGIQIIVFDP 37
Cdd:COG3451   205 GNTLILGPSGSGKSFLLKLLLLQLLRYGARIVIFDP 240
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 3-37 1.05e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 37.74  E-value: 1.05e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1332547700    3 HCAIVGMTESGKSSLARKMAVELQKSGIQIIVFDP 37
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDG 38
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 2-80 5.46e-03

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: 35.58  E-value: 5.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332547700   2 PHCAIVGMTESGKSSLARKMAVELQKSGIQIIVFdplsdpewcNCLDLNNAFITDNENEFLNVYW------NSKNCAVFF 75
Cdd:cd00009    20 KNLLLYGPPGTGKTTLARAIANELFRPGAPFLYL---------NASDLLEGLVVAELFGHFLVRLlfelaeKAKPGVLFI 90


                  ....*
gi 1332547700  76 DEAGD 80
Cdd:cd00009    91 DEIDS 95
 
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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