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Conserved domains on  [gi|490519325|ref|WP_004384824|]
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MULTISPECIES: Holliday junction branch migration protein RuvA [Cronobacter]

Protein Classification

Holliday junction ATP-dependent DNA helicase RuvA( domain architecture ID 11478104)

Holliday junction ATP-dependent DNA helicase RuvA is involved in branch migration of heteroduplex DNA in homologous recombination by stimulating the ATPase activity of RuvB

CATH:  1.10.150.20
EC:  3.6.4.12
Gene Ontology:  GO:0009378|GO:0003677|GO:0016887|GO:0005524|GO:0006281|GO:0006310
SCOP:  4000746|4001893|4001026

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ruvA PRK00116
Holliday junction branch migration protein RuvA;
1-203 1.22e-100

Holliday junction branch migration protein RuvA;


:

Pssm-ID: 234645 [Multi-domain]  Cd Length: 192  Bit Score: 288.96  E-value: 1.22e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325   1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPETGKEAVVFTHFVVREDAQLLFGFNNKQERTLFRELIKVNG 80
Cdd:PRK00116   1 MIGYLKGKLVEKGPDYVVIEVNGVGYEVQVPMRTLYELPEVGEEVKLYTHLVVREDAILLYGFLTKEERELFRLLISVSG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325  81 VGPKLALAILSGMSAQQFVNAVEREEPAALVKLPGIGKKTAERLVVEMKDRFKGLHGDLFTPAADLVLTSPAspavddae 160
Cdd:PRK00116  81 VGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEA-------- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 490519325 161 aeaVAALVSLGYKPQEASRMVSKVAQADASSETLIREALRAAL 203
Cdd:PRK00116 153 ---VSALVALGYKPKEASKAVAKILKEAASVEELIREALKLLS 192
 
Name Accession Description Interval E-value
ruvA PRK00116
Holliday junction branch migration protein RuvA;
1-203 1.22e-100

Holliday junction branch migration protein RuvA;


Pssm-ID: 234645 [Multi-domain]  Cd Length: 192  Bit Score: 288.96  E-value: 1.22e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325   1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPETGKEAVVFTHFVVREDAQLLFGFNNKQERTLFRELIKVNG 80
Cdd:PRK00116   1 MIGYLKGKLVEKGPDYVVIEVNGVGYEVQVPMRTLYELPEVGEEVKLYTHLVVREDAILLYGFLTKEERELFRLLISVSG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325  81 VGPKLALAILSGMSAQQFVNAVEREEPAALVKLPGIGKKTAERLVVEMKDRFKGLHGDLFTPAADLVLTSPAspavddae 160
Cdd:PRK00116  81 VGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEA-------- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 490519325 161 aeaVAALVSLGYKPQEASRMVSKVAQADASSETLIREALRAAL 203
Cdd:PRK00116 153 ---VSALVALGYKPKEASKAVAKILKEAASVEELIREALKLLS 192
RuvA COG0632
Holliday junction resolvasome RuvABC DNA-binding subunit [Replication, recombination and ...
 1-200 5.06e-94

Holliday junction resolvasome RuvABC DNA-binding subunit [Replication, recombination and repair];


Pssm-ID: 440397 [Multi-domain]  Cd Length: 195  Bit Score: 272.40  E-value: 5.06e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325   1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPETGKEAVVFTHFVVREDAQLLFGFNNKQERTLFRELIKVNG 80
Cdd:COG0632    1 MIAYLRGTLVEKGPDYVVIDVGGVGYEVFVPLSTLSALPEVGEEVKLYTHLVVREDALTLYGFATEEERELFRLLISVSG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325  81 VGPKLALAILSGMSAQQFVNAVEREEPAALVKLPGIGKKTAERLVVEMKDRFKGLHGDLFTPAAdlvltspASPAVDDAE 160
Cdd:COG0632   81 VGPKLALAILSGLSPEELARAIASGDVKALTKVPGIGKKTAERIILELKDKLGKLALAAGAAAA-------AAAAASSAL 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 490519325 161 AEAVAALVSLGYKPQEASRMVSKVAQA--DASSETLIREALR 200
Cdd:COG0632  154 EEAVSALVALGYSPKEAEKAVAKVLKEgpDASVEELIRAALK 195
ruvA TIGR00084
Holliday junction DNA helicase, RuvA subunit; RuvA specifically binds Holliday junctions as a ...
 1-203 2.47e-79

Holliday junction DNA helicase, RuvA subunit; RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129193 [Multi-domain]  Cd Length: 191  Bit Score: 234.96  E-value: 2.47e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325    1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPEtGKEAVVFTHFVVREDAQLLFGFNNKQERTLFRELIKVNG 80
Cdd:TIGR00084   1 MIGFLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAYELNL-EQKAQVFTHLVVREDAELLFGFNTLEERELFKELIKVNG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325   81 VGPKLALAILSGMSAQQFVNAVEREEPAALVKLPGIGKKTAERLVVEMKDRFKGLHG-DLFTPAADLvltspaspavdda 159
Cdd:TIGR00084  80 VGPKLALAILSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGKLKGNKNlEMFTPTEAA------------- 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 490519325  160 EAEAVAALVSLGYKPQEASRMVSKVAQ-ADASSETLIREALRAAL 203
Cdd:TIGR00084 147 RDELFEALVSLGYKPQEIQQALKKIKNkPDFAIEQDIEEALKQLL 191
RuvA_N pfam01330
RuvA N terminal domain; The N terminal domain of RuvA has an OB-fold structure. This domain ...
 1-62 3.19e-27

RuvA N terminal domain; The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts.


Pssm-ID: 460162 [Multi-domain]  Cd Length: 61  Bit Score: 97.88  E-value: 3.19e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490519325    1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPEtGKEAVVFTHFVVREDAQLLFG 62
Cdd:pfam01330   1 MIAYLKGTVVEKGPDYVVIDVGGVGYEVFISLSTLSKLAV-GEEVKLYTHLVVREDALTLYG 61
UBA_RuvA_C cd14332
C-terminal UBA-like domain of holliday junction ATP-dependent DNA helicase RuvA; RuvA, along ...
 167-200 2.35e-07

C-terminal UBA-like domain of holliday junction ATP-dependent DNA helicase RuvA; RuvA, along with RuvB and RuvC proteins, is involved in branch migration of heteroduplex DNA in homologous recombination that is a crucial process for maintaining genomic integrity and generating biological diversity in all living organisms. RuvA has a tetrameric architecture in which each subunit comprised of three distinct domains. This model corresponds to the C-terminal domain of RuvA which is distantly related to the ubiquitin-associated (UBA) domain. It plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB. Within the Holliday junction, the C-terminal domain makes no interaction with DNA.


Pssm-ID: 270517 [Multi-domain]  Cd Length: 45  Bit Score: 45.52  E-value: 2.35e-07
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490519325 167 LVSLGYKPQEASRMVSKVAQ--ADASSETLIREALR 200
Cdd:cd14332   10 LVALGYSRKEAEKAVKKVLAeaPGLSVEELIREALK 45
 
Name Accession Description Interval E-value
ruvA PRK00116
Holliday junction branch migration protein RuvA;
1-203 1.22e-100

Holliday junction branch migration protein RuvA;


Pssm-ID: 234645 [Multi-domain]  Cd Length: 192  Bit Score: 288.96  E-value: 1.22e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325   1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPETGKEAVVFTHFVVREDAQLLFGFNNKQERTLFRELIKVNG 80
Cdd:PRK00116   1 MIGYLKGKLVEKGPDYVVIEVNGVGYEVQVPMRTLYELPEVGEEVKLYTHLVVREDAILLYGFLTKEERELFRLLISVSG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325  81 VGPKLALAILSGMSAQQFVNAVEREEPAALVKLPGIGKKTAERLVVEMKDRFKGLHGDLFTPAADLVLTSPAspavddae 160
Cdd:PRK00116  81 VGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEA-------- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 490519325 161 aeaVAALVSLGYKPQEASRMVSKVAQADASSETLIREALRAAL 203
Cdd:PRK00116 153 ---VSALVALGYKPKEASKAVAKILKEAASVEELIREALKLLS 192
RuvA COG0632
Holliday junction resolvasome RuvABC DNA-binding subunit [Replication, recombination and ...
 1-200 5.06e-94

Holliday junction resolvasome RuvABC DNA-binding subunit [Replication, recombination and repair];


Pssm-ID: 440397 [Multi-domain]  Cd Length: 195  Bit Score: 272.40  E-value: 5.06e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325   1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPETGKEAVVFTHFVVREDAQLLFGFNNKQERTLFRELIKVNG 80
Cdd:COG0632    1 MIAYLRGTLVEKGPDYVVIDVGGVGYEVFVPLSTLSALPEVGEEVKLYTHLVVREDALTLYGFATEEERELFRLLISVSG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325  81 VGPKLALAILSGMSAQQFVNAVEREEPAALVKLPGIGKKTAERLVVEMKDRFKGLHGDLFTPAAdlvltspASPAVDDAE 160
Cdd:COG0632   81 VGPKLALAILSGLSPEELARAIASGDVKALTKVPGIGKKTAERIILELKDKLGKLALAAGAAAA-------AAAAASSAL 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 490519325 161 AEAVAALVSLGYKPQEASRMVSKVAQA--DASSETLIREALR 200
Cdd:COG0632  154 EEAVSALVALGYSPKEAEKAVAKVLKEgpDASVEELIRAALK 195
ruvA TIGR00084
Holliday junction DNA helicase, RuvA subunit; RuvA specifically binds Holliday junctions as a ...
 1-203 2.47e-79

Holliday junction DNA helicase, RuvA subunit; RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129193 [Multi-domain]  Cd Length: 191  Bit Score: 234.96  E-value: 2.47e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325    1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPEtGKEAVVFTHFVVREDAQLLFGFNNKQERTLFRELIKVNG 80
Cdd:TIGR00084   1 MIGFLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAYELNL-EQKAQVFTHLVVREDAELLFGFNTLEERELFKELIKVNG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325   81 VGPKLALAILSGMSAQQFVNAVEREEPAALVKLPGIGKKTAERLVVEMKDRFKGLHG-DLFTPAADLvltspaspavdda 159
Cdd:TIGR00084  80 VGPKLALAILSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGKLKGNKNlEMFTPTEAA------------- 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 490519325  160 EAEAVAALVSLGYKPQEASRMVSKVAQ-ADASSETLIREALRAAL 203
Cdd:TIGR00084 147 RDELFEALVSLGYKPQEIQQALKKIKNkPDFAIEQDIEEALKQLL 191
RuvA_N pfam01330
RuvA N terminal domain; The N terminal domain of RuvA has an OB-fold structure. This domain ...
 1-62 3.19e-27

RuvA N terminal domain; The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts.


Pssm-ID: 460162 [Multi-domain]  Cd Length: 61  Bit Score: 97.88  E-value: 3.19e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490519325    1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPEtGKEAVVFTHFVVREDAQLLFG 62
Cdd:pfam01330   1 MIAYLKGTVVEKGPDYVVIDVGGVGYEVFISLSTLSKLAV-GEEVKLYTHLVVREDALTLYG 61
ruvA PRK14600
Holliday junction branch migration protein RuvA;
1-200 5.69e-23

Holliday junction branch migration protein RuvA;


Pssm-ID: 173064 [Multi-domain]  Cd Length: 186  Bit Score: 90.96  E-value: 5.69e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325   1 MIGRLRGIVLEKQPPLVLLEAGGVGYEVHMPMTCFYELPETGKEAVVFTHFVVREDAQLLFGFNNKQERTLFRELIKVNG 80
Cdd:PRK14600   1 MIGSLSGIVEEVRSDYIILNVGNVGYIVYLSAKVLSTCKIGDNIKLYIETYVNRDNVTQLYGFLNREEQDCLRMLVKVSG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490519325  81 VGPKLALAILSGMSAQQFVNAVEREEPAALvKLPGIGKKTAERLVVEMKDRFKGL--HGDLFTPAADLVLTSpaspavdd 158
Cdd:PRK14600  81 VNYKTAMSILSKLTPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQYKVSKLeiNETNFIIINDDALAA-------- 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 490519325 159 aeaeavaaLVSLGYKPQEASRMVSKVaQADASSETLIREALR 200
Cdd:PRK14600 152 --------LISLGYEKTKAFNAIQKI-KPNLSTQDIIRKALK 184
HHH_5 pfam14520
Helix-hairpin-helix domain;
72-130 5.22e-14

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 63.66  E-value: 5.22e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 490519325   72 FRELIKVNGVGPKLALAILSGMSAQqfVNAVEREEPAALVKLPGIGKKTAERLVVEMKD 130
Cdd:pfam14520   1 FEELLSISGIGPKTALALLSAGIGT--VEDLAEADVDELAEIPGIGEKTAQRIILELRD 57
RuvA_C pfam07499
RuvA, C-terminal domain; Homologous recombination is a crucial process in all living organizms. ...
 167-201 3.25e-08

RuvA, C-terminal domain; Homologous recombination is a crucial process in all living organizms. In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB. Within the Holliday junction, the C-terminal domain makes no interaction with DNA.


Pssm-ID: 462183 [Multi-domain]  Cd Length: 47  Bit Score: 48.24  E-value: 3.25e-08
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 490519325  167 LVSLGYKPQEASRMVSKVAQA-DASSETLIREALRA 201
Cdd:pfam07499  10 LVALGYKEKEAEKAVSKVLANpGLSVEELIRAALKL 45
UBA_RuvA_C cd14332
C-terminal UBA-like domain of holliday junction ATP-dependent DNA helicase RuvA; RuvA, along ...
 167-200 2.35e-07

C-terminal UBA-like domain of holliday junction ATP-dependent DNA helicase RuvA; RuvA, along with RuvB and RuvC proteins, is involved in branch migration of heteroduplex DNA in homologous recombination that is a crucial process for maintaining genomic integrity and generating biological diversity in all living organisms. RuvA has a tetrameric architecture in which each subunit comprised of three distinct domains. This model corresponds to the C-terminal domain of RuvA which is distantly related to the ubiquitin-associated (UBA) domain. It plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB. Within the Holliday junction, the C-terminal domain makes no interaction with DNA.


Pssm-ID: 270517 [Multi-domain]  Cd Length: 45  Bit Score: 45.52  E-value: 2.35e-07
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490519325 167 LVSLGYKPQEASRMVSKVAQ--ADASSETLIREALR 200
Cdd:cd14332   10 LVALGYSRKEAEKAVKKVLAeaPGLSVEELIREALK 45
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 74-124 9.62e-05

DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 39.46  E-value: 9.62e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 490519325  74 ELIKVNGVGPKLALAILSgmsaqqfvnavEREE------PAALVKLPGIGKKTAERL 124
Cdd:COG1555   22 ELQTLPGIGPKLAQRIVE-----------YREKngpfksVEDLLEVKGIGPKTLEKL 67
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
80-123 8.30e-03

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 35.92  E-value: 8.30e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 490519325  80 GVGPKLALAILS--GmSAQQFVNAvereEPAALVKLPGIGKKTAER 123
Cdd:COG1948  162 GIGPKLARRLLEhfG-SVEAVFNA----SEEELMKVEGIGEKTAER 202
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
109-125 9.39e-03

Recombinational DNA repair protein RecR [Replication, recombination and repair];


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 35.78  E-value: 9.39e-03
                         10
                 ....*....|....*..
gi 490519325 109 ALVKLPGIGKKTAERLV 125
Cdd:COG0353   12 ALSKLPGIGPKSAQRLA 28
 
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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