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Conserved domains on  [gi|1954872940|gb|QQM89236|]
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UvrD-helicase domain-containing protein (plasmid) [Klebsiella variicola]

Protein Classification

DEAD/DEAH box helicase family protein( domain architecture ID 1000205)

DEAD/DEAH box helicase family protein such as a DEAD/DEAH box-containing ATP-dependent helicase, which catalyzes the unwinding of DNA or RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 55-101 3.37e-16

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd17932:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 189  Bit Score: 69.85  E-value: 3.37e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1954872940  55 HMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIYSFRAASAS 101
Cdd:cd17932   122 YILVDEYQDTNPLQYELLKLLAGDGKNLFVVGDDDQSIYGFRGADPE 168
 
Name Accession Description Interval E-value
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 55-101 3.37e-16

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 69.85  E-value: 3.37e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1954872940  55 HMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIYSFRAASAS 101
Cdd:cd17932   122 YILVDEYQDTNPLQYELLKLLAGDGKNLFVVGDDDQSIYGFRGADPE 168
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 18-98 2.46e-15

UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.


Pssm-ID: 395462 [Multi-domain]  Cd Length: 267  Bit Score: 68.81  E-value: 2.46e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954872940  18 RAYMSRCEETNDTDYN-IACREVVLGLRADKVR---RLNVTHMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIY 93
Cdd:pfam00580 170 QEYQERLKENNALDFDdLLLLTLELLRSDPELLeayRERFKYILVDEFQDTNPIQYRLLKLLAGGHENLFLVGDPDQSIY 249


                  ....*
gi 1954872940  94 SFRAA 98
Cdd:pfam00580 250 GFRGA 254
uvrD PRK11773
DNA-dependent helicase II; Provisional
 54-98 3.39e-15

DNA-dependent helicase II; Provisional


Pssm-ID: 236976 [Multi-domain]  Cd Length: 721  Bit Score: 69.51  E-value: 3.39e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1954872940  54 THMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIYSFRAA 98
Cdd:PRK11773  215 THILVDEFQDTNAIQYAWIRLLAGDTGKVMIVGDDDQSIYGWRGA 259
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
55-101 4.43e-15

Superfamily I DNA or RNA helicase [Replication, recombination and repair];


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 69.19  E-value: 4.43e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1954872940  55 HMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIYSFRAASAS 101
Cdd:COG0210   215 YILVDEYQDTNPAQYELLRLLAGDGRNLCVVGDDDQSIYGFRGADPE 261
recB TIGR00609
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ...
 58-98 1.75e-06

exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273172 [Multi-domain]  Cd Length: 1087  Bit Score: 44.73  E-value: 1.75e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1954872940   58 VDEFQDTDEVQlawlWE------HAAHGIKVTAVGDDDQSIYSFRAA 98
Cdd:TIGR00609  302 IDEFQDTDPQQ----YRifsklfIAQKETSLFLIGDPKQAIYSFRGA 344
 
Name Accession Description Interval E-value
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 55-101 3.37e-16

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 69.85  E-value: 3.37e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1954872940  55 HMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIYSFRAASAS 101
Cdd:cd17932   122 YILVDEYQDTNPLQYELLKLLAGDGKNLFVVGDDDQSIYGFRGADPE 168
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 18-98 2.46e-15

UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.


Pssm-ID: 395462 [Multi-domain]  Cd Length: 267  Bit Score: 68.81  E-value: 2.46e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954872940  18 RAYMSRCEETNDTDYN-IACREVVLGLRADKVR---RLNVTHMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIY 93
Cdd:pfam00580 170 QEYQERLKENNALDFDdLLLLTLELLRSDPELLeayRERFKYILVDEFQDTNPIQYRLLKLLAGGHENLFLVGDPDQSIY 249


                  ....*
gi 1954872940  94 SFRAA 98
Cdd:pfam00580 250 GFRGA 254
uvrD PRK11773
DNA-dependent helicase II; Provisional
 54-98 3.39e-15

DNA-dependent helicase II; Provisional


Pssm-ID: 236976 [Multi-domain]  Cd Length: 721  Bit Score: 69.51  E-value: 3.39e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1954872940  54 THMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIYSFRAA 98
Cdd:PRK11773  215 THILVDEFQDTNAIQYAWIRLLAGDTGKVMIVGDDDQSIYGWRGA 259
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
55-101 4.43e-15

Superfamily I DNA or RNA helicase [Replication, recombination and repair];


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 69.19  E-value: 4.43e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1954872940  55 HMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIYSFRAASAS 101
Cdd:COG0210   215 YILVDEYQDTNPAQYELLRLLAGDGRNLCVVGDDDQSIYGFRGADPE 261
RecB COG1074
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 55-98 5.55e-10

3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440692 [Multi-domain]  Cd Length: 866  Bit Score: 54.58  E-value: 5.55e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1954872940  55 HMIVDEFQDTDEVQ---LAWLW-EHAAHGIKVTAVGDDDQSIYSFRAA 98
Cdd:COG1074   287 HILVDEFQDTSPLQweiLRRLAgEALADGRTLFLVGDPKQSIYRFRGA 334
AAA_19 pfam13245
AAA domain;
41-96 1.06e-07

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 46.44  E-value: 1.06e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1954872940  41 LGLRADKVRRLNVTHMIVDEFQDTDeVQLAW-LWEHAAHGIKVTAVGDDDQSIYSFR 96
Cdd:pfam13245  81 GGFLRDEEEPLDGDLLIVDEFSMVD-LPLAYrLLKALPDGAQLLLVGDPDQLPSVGP 136
PRK13909 PRK13909
RecB-like helicase;
50-101 6.01e-07

RecB-like helicase;


Pssm-ID: 237554 [Multi-domain]  Cd Length: 910  Bit Score: 45.73  E-value: 6.01e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954872940  50 RL--NVTHMIVDEFQDTDEVQ---LAWLWEHAAHGIKVTA------VGDDDQSIYSFRAASAS 101
Cdd:PRK13909  324 RLdsKISHILIDEFQDTSVLQykiLLPLIDEIKSGEGQKKfrsffyVGDVKQSIYRFRGGKKE 386
PRK10919 PRK10919
ATP-dependent DNA helicase Rep; Provisional
 53-98 1.11e-06

ATP-dependent DNA helicase Rep; Provisional


Pssm-ID: 182838 [Multi-domain]  Cd Length: 672  Bit Score: 45.22  E-value: 1.11e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1954872940  53 VTHMIVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIYSFRAA 98
Cdd:PRK10919  208 IRYLLVDEYQDTNTSQYELVKLLVGSRARFTVVGDDDQSIYSWRGA 253
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 48-98 1.68e-06

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 43.24  E-value: 1.68e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1954872940  48 VRRLNVTHmiVDEFQDTDEVQLAWLWEHAAHGIKVTAVGDDDQSIYSFRAA 98
Cdd:cd17914    44 AAQLDNIL--VDEAAQILEPETSRLIDLALDQGRVILVGDHDQLGPVWRGA 92
recB TIGR00609
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ...
 58-98 1.75e-06

exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273172 [Multi-domain]  Cd Length: 1087  Bit Score: 44.73  E-value: 1.75e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1954872940   58 VDEFQDTDEVQlawlWE------HAAHGIKVTAVGDDDQSIYSFRAA 98
Cdd:TIGR00609  302 IDEFQDTDPQQ----YRifsklfIAQKETSLFLIGDPKQAIYSFRGA 344
addA_Gpos TIGR02785
helicase-exonuclease AddAB, AddA subunit, Firmicutes type; AddAB, also called RexAB, ...
 57-98 5.82e-05

helicase-exonuclease AddAB, AddA subunit, Firmicutes type; AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274299 [Multi-domain]  Cd Length: 1230  Bit Score: 40.46  E-value: 5.82e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1954872940   57 IVDEFQDTDEVQ---LAWLWEHAAHGIKVTAVGDDDQSIYSFRAA 98
Cdd:TIGR02785  393 LVDEYQDTNLVQesiLQLVKRGPEEEGNLFMVGDVKQSIYRFRQA 437
addA_alphas TIGR02784
double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, ...
 55-98 2.33e-04

double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274298 [Multi-domain]  Cd Length: 1135  Bit Score: 38.52  E-value: 2.33e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1954872940   55 HMIVDEFQDTDEVQlawlWE---------HAAHGIK------VTAVGDDDQSIYSFRAA 98
Cdd:TIGR02784  393 HILVDEAQDTSPEQ----WDiiqalaeefFSGEGARsgvertIFAVGDEKQSIYSFQGA 447
helD PRK11054
DNA helicase IV; Provisional
 55-98 5.32e-04

DNA helicase IV; Provisional


Pssm-ID: 182930 [Multi-domain]  Cd Length: 684  Bit Score: 37.62  E-value: 5.32e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1954872940  55 HMIVDEFQDTDEVQLAWLwehAA-----HGIKVTAVGDDDQSIYSFRAA 98
Cdd:PRK11054  433 HILVDEFQDISPQRAALL---AAlrkqnSQTTLFAVGDDWQAIYRFSGA 478
recB PRK10876
exonuclease V subunit beta; Provisional
 56-98 5.36e-03

exonuclease V subunit beta; Provisional


Pssm-ID: 236784 [Multi-domain]  Cd Length: 1181  Bit Score: 34.56  E-value: 5.36e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1954872940   56 MIvDEFQDTDEVQLAwLWEHAAHGIKVTA---VGDDDQSIYSFRAA 98
Cdd:PRK10876   382 MI-DEFQDTDPQQYR-IFRRIYRHQPETAlllIGDPKQAIYAFRGA 425
 
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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