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Conserved domains on  [gi|821658135|gb|AKH60670|]
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DNA primase/helicase, partial [Salmonella phage SEN2]

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
RepA super family cl34641
RecA-family ATPase [Replication, recombination and repair];
24-149 6.66e-12

RecA-family ATPase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG3598:

Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 63.00  E-value: 6.66e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821658135  24 FKFYDDRLWLFGLTGTAKAERLIEIFTYARRRYGIQLFIIDSLMKCGIGD-DDYNGQKAFVDALCDFKNKTNSHIILVTH 102
Cdd:COG3598   80 FADLDGRLRLLSLAGDLDDTDDLEALERAIEEEGPDLVVIDPLARVFGGDeNDAEEMRAFLNPLDRLAERTGAAVLLVHH 159

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 821658135 103 SRKGDSEEKPTGkmDVKGSGAITDLTDNLFIIWRNK-ARERALQRVQA 149
Cdd:COG3598  160 TGKGGAGKDSGD--RARGSSALRGAARSVLVLSREKgEDLRVLTRAKS 205
 
Name Accession Description Interval E-value
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
24-149 6.66e-12

RecA-family ATPase [Replication, recombination and repair];


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 63.00  E-value: 6.66e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821658135  24 FKFYDDRLWLFGLTGTAKAERLIEIFTYARRRYGIQLFIIDSLMKCGIGD-DDYNGQKAFVDALCDFKNKTNSHIILVTH 102
Cdd:COG3598   80 FADLDGRLRLLSLAGDLDDTDDLEALERAIEEEGPDLVVIDPLARVFGGDeNDAEEMRAFLNPLDRLAERTGAAVLLVHH 159

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 821658135 103 SRKGDSEEKPTGkmDVKGSGAITDLTDNLFIIWRNK-ARERALQRVQA 149
Cdd:COG3598  160 TGKGGAGKDSGD--RARGSSALRGAARSVLVLSREKgEDLRVLTRAKS 205
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 40-185 1.00e-09

Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family includes the homo-hexameric replicative helicase RepA encoded by plasmid RSF1010. RSF1010 is found in most Gram-negative bacteria and some Gram-positive bacteria . The RepA protein of Plasmid RSF1010 is a 5'-3' DNA helicase which can utilize ATP, dATP, GTP and dGTP (and CTP and dCTP to a lesser extent).


Pssm-ID: 410870  Cd Length: 238  Bit Score: 55.85  E-value: 1.00e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821658135  40 AKAERLIEiftyarRRYGIQLFIIDSLMKCGIGDD--DYNGQKAFVDALCDFKNKTNSHIILVTHSRKGDSEEKPTGkmd 117
Cdd:cd01125   93 PELERIIE------ELEGVRLIIIDTLARVLHGGDenDAADMGAFVAGLDRIARETGAAVLLVHHTGKDAAGDSQQA--- 163

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 821658135 118 VKGSGAITDLTDNLFIIWRNKArERALQRVQAGEQINE-----KDQQLLAAPASVLMLEKQRNGEGWE--GGVPL 185
Cdd:cd01125  164 ARGSSALRGAADAEINLSKMDA-TEAEKVGLDKDLRRRfvrldVTKANYAAPGAVRWFKREEGAIALGepKGVLL 237
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 26-108 1.01e-06

AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.


Pssm-ID: 463892 [Multi-domain]  Cd Length: 193  Bit Score: 46.99  E-value: 1.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821658135   26 FYDDRLWLFGLTGTAKAERLIEIFTYARRRYGIQLFIIDSLMKCGIGDDDYNGQ-KAFVDALCDFKNKTNSHIILVTHSR 104
Cdd:pfam13481 110 VESLPLFFLDRGGPLLDADVDALEAALEEVEDPDLVVIDPLARALGGDENSNSDvGRLVKALDRLARRTGATVLLVHHVG 189


                  ....
gi 821658135  105 KGDS 108
Cdd:pfam13481 190 KDGA 193
 
Name Accession Description Interval E-value
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
24-149 6.66e-12

RecA-family ATPase [Replication, recombination and repair];


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 63.00  E-value: 6.66e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821658135  24 FKFYDDRLWLFGLTGTAKAERLIEIFTYARRRYGIQLFIIDSLMKCGIGD-DDYNGQKAFVDALCDFKNKTNSHIILVTH 102
Cdd:COG3598   80 FADLDGRLRLLSLAGDLDDTDDLEALERAIEEEGPDLVVIDPLARVFGGDeNDAEEMRAFLNPLDRLAERTGAAVLLVHH 159

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 821658135 103 SRKGDSEEKPTGkmDVKGSGAITDLTDNLFIIWRNK-ARERALQRVQA 149
Cdd:COG3598  160 TGKGGAGKDSGD--RARGSSALRGAARSVLVLSREKgEDLRVLTRAKS 205
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 40-185 1.00e-09

Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family includes the homo-hexameric replicative helicase RepA encoded by plasmid RSF1010. RSF1010 is found in most Gram-negative bacteria and some Gram-positive bacteria . The RepA protein of Plasmid RSF1010 is a 5'-3' DNA helicase which can utilize ATP, dATP, GTP and dGTP (and CTP and dCTP to a lesser extent).


Pssm-ID: 410870  Cd Length: 238  Bit Score: 55.85  E-value: 1.00e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821658135  40 AKAERLIEiftyarRRYGIQLFIIDSLMKCGIGDD--DYNGQKAFVDALCDFKNKTNSHIILVTHSRKGDSEEKPTGkmd 117
Cdd:cd01125   93 PELERIIE------ELEGVRLIIIDTLARVLHGGDenDAADMGAFVAGLDRIARETGAAVLLVHHTGKDAAGDSQQA--- 163

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 821658135 118 VKGSGAITDLTDNLFIIWRNKArERALQRVQAGEQINE-----KDQQLLAAPASVLMLEKQRNGEGWE--GGVPL 185
Cdd:cd01125  164 ARGSSALRGAADAEINLSKMDA-TEAEKVGLDKDLRRRfvrldVTKANYAAPGAVRWFKREEGAIALGepKGVLL 237
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 23-146 4.47e-09

RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the RecA-like domain of the Gp4D fragment of the Gene4 helicase-primase (Gp4) from bacteriophage T7. Gp4D (residues 241-566) is the minimal fragment of the Gp4 that forms hexameric rings, it contains the helicase domain and the linker connecting the helicase and primase domains. Helicases are ring-shaped oligomeric enzymes that unwind DNA at the replication fork; they couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. This family belongs to the RecA-like NTPase superfamily 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: 410891 [Multi-domain]  Cd Length: 231  Bit Score: 54.11  E-value: 4.47e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821658135  23 AFKFYDDRLWLFGLTGTAKAERLIEIFTYARRRYGIQLFIIDSLMKCGIGDDDYNGQKA---FVDALCDFKNKTNSHIIL 99
Cdd:cd19483   74 DNELGSGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKEldeIMTELAALVKELGVTIIL 153

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 821658135 100 VTHSRKGD-----SEEKPTGKMDVKGSGAITDLTDNLFIIWRNKARERALQR 146
Cdd:cd19483  154 VSHLRRPGggkghEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPVER 205
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 26-108 1.01e-06

AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.


Pssm-ID: 463892 [Multi-domain]  Cd Length: 193  Bit Score: 46.99  E-value: 1.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821658135   26 FYDDRLWLFGLTGTAKAERLIEIFTYARRRYGIQLFIIDSLMKCGIGDDDYNGQ-KAFVDALCDFKNKTNSHIILVTHSR 104
Cdd:pfam13481 110 VESLPLFFLDRGGPLLDADVDALEAALEEVEDPDLVVIDPLARALGGDENSNSDvGRLVKALDRLARRTGATVLLVHHVG 189


                  ....
gi 821658135  105 KGDS 108
Cdd:pfam13481 190 KDGA 193
Twinkle_C cd01122
C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid ...
 38-145 3.94e-05

C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid localization, also known as C10orf2, PEO1, SCA8, ATXN8, IOSCA, PEOA3 or SANDO) is a homohexameric DNA helicases which unwinds short stretches of double-stranded DNA in the 5' to 3' direction and, along with mitochondrial single-stranded DNA binding protein and mtDNA polymerase gamma, is thought to play a key role in mtDNA replication. Mutations in the human gene cause infantile onset spinocerebellar ataxia (IOSCA) and progressive external ophthalmoplegia (PEO) and are also associated with several mitochondrial depletion syndromes. This group also contains viral GP4-like and related bacterial helicases.


Pssm-ID: 410867  Cd Length: 266  Bit Score: 43.00  E-value: 3.94e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 821658135  38 GTAKAERLIEIFTYARRRYGIQLFIIDSL--MKCG--IGDDDYNGQKAFVDALCDFKNKTNSHIILVTHSRKGDsEEKPT 113
Cdd:cd01122  125 GSTDIDEVLDAMEHAVYVYDIQHIVIDNLqfMMGTqaSGSDRFELQDLIIGKFRRFATNNNVHITLVIHPRKED-DDNEL 203

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 821658135 114 GKMDVKGSGAITDLTDNLFIIWRNKA----RERALQ 145
Cdd:cd01122  204 TTSSIFGSAKATQEADNVLILQDKRLisgeGKKFLQ 239
 
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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