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Conserved domains on  [gi|1491220469|gb|RLG97403|]
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hypothetical protein DRO27_00105 [Candidatus Bathyarchaeota archaeon]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RuvC-like super family cl21482
Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family ...
 5-161 6.24e-13

Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family consists of bacterial RuvC, fungal Cruciform cutting endonuclease 1 (CCE1), bacterial YqgF and monokaryotic chloroplast 1 protein (MOC1). RuvC, CCE1 and MOC1 are Holliday junction resolvases (HJRs), endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. CCE1 is a HJR specific for 4-way junctions; it is involved in the maintenance of mitochondrial DNA. Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


The actual alignment was detected with superfamily member PRK00039:

Pssm-ID: 473878  Cd Length: 164  Bit Score: 63.21  E-value: 6.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469   5 ETIVFGLDPGVGR--FGCVGMHNKKV--LSYATFKSKGKpyTSMPnfLRVTQLAHQVVAWMKAqtngYKYVTIVIETPIY 80
Cdd:PRK00039    1 MMRILGIDPGLRRtgYGVIEVEGRRLsyVASGVIRTPSD--LDLP--ERLKQIYDGLSELIDE----YQPDEVAIEEVFF 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469  81 NKNAKAfelqwrlfqqVLTFAQH----MMAP-NEILEVSNGT---VKKAMTGSGRAEKI---DMVcASVFDGPEFEK-DD 148
Cdd:PRK00039   73 NKNPQS----------ALKLGQArgvaILAAaQRGLPVAEYTplqVKKAVVGYGRADKEqvqHMV-KRLLNLPEIPKpDD 141

                         170
                  ....*....|...
gi 1491220469 149 AealADAQGVALC 161
Cdd:PRK00039  142 A---ADALAIAIC 151
 
Name Accession Description Interval E-value
ruvC PRK00039
Holliday junction resolvase; Reviewed
 5-161 6.24e-13

Holliday junction resolvase; Reviewed


Pssm-ID: 234587  Cd Length: 164  Bit Score: 63.21  E-value: 6.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469   5 ETIVFGLDPGVGR--FGCVGMHNKKV--LSYATFKSKGKpyTSMPnfLRVTQLAHQVVAWMKAqtngYKYVTIVIETPIY 80
Cdd:PRK00039    1 MMRILGIDPGLRRtgYGVIEVEGRRLsyVASGVIRTPSD--LDLP--ERLKQIYDGLSELIDE----YQPDEVAIEEVFF 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469  81 NKNAKAfelqwrlfqqVLTFAQH----MMAP-NEILEVSNGT---VKKAMTGSGRAEKI---DMVcASVFDGPEFEK-DD 148
Cdd:PRK00039   73 NKNPQS----------ALKLGQArgvaILAAaQRGLPVAEYTplqVKKAVVGYGRADKEqvqHMV-KRLLNLPEIPKpDD 141

                         170
                  ....*....|...
gi 1491220469 149 AealADAQGVALC 161
Cdd:PRK00039  142 A---ADALAIAIC 151
RuvC COG0817
Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and ...
 8-161 3.97e-12

Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and repair];


Pssm-ID: 440579  Cd Length: 152  Bit Score: 60.86  E-value: 3.97e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469   8 VFGLDPGVGR--FGCVGMHNKKV--LSYATFKSKGKpyTSMPnfLRVTQLAHQVVAWMKAqtngYKYVTIVIETPIYNKN 83
Cdd:COG0817     1 ILGIDPGLRRtgYGVIEVDGNRLrlVASGVIRTPPK--LPLP--ERLLEIYEGLTELIEE----YKPDEVAIEEVFFNKN 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469  84 AKAfelqwrlfqqVLTFAQH----MMAPNE----ILEVSNGTVKKAMTGSGRAEK---IDMVCAsVFDGPEFEK-DDAea 151
Cdd:COG0817    73 PKS----------ALKLGQArgvaLLAAAQrglpVAEYTPLQVKKAVTGYGRADKeqvQAMVKR-LLGLDEIPKpDDA-- 139

                         170
                  ....*....|
gi 1491220469 152 lADAQGVALC 161
Cdd:COG0817   140 -ADALAIAIC 148
RuvC cd16962
Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC ...
 8-161 9.93e-10

Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC is also called Holliday junction resolvase RuvC. It is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is thought to bind either on the open, DNA exposed face of a single RuvA tetramer, or to replace one of the two tetramers. Binding is proposed to be mediated by an unstructured loop on RuvC, which becomes structured on binding RuvA. RuvC can be bound to the complex in either orientation, therefore resolving Holliday junctions in either a horizontal or vertical manner. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the Escherichia coli HJR. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438562  Cd Length: 152  Bit Score: 54.36  E-value: 9.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469   8 VFGLDPGVGRFG----CVGMHNKKVLSYATFKSKGKpytsMPNFLRVTQLAHQVVAWMKAqtngYKYVTIVIETPIYNKN 83
Cdd:cd16962     1 ILGIDPGLRRTGygviEVEGNKLRLLDYGVIRTPSK----LSLPERLKEIYDGLSELIEK----YKPDEVAIEKLFFNKN 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469  84 AK-AFELQwrlfqQV-----LTFAQHMMapnEILEVSNGTVKKAMTGSGRAEKID---MVCASVFDGPEFEKDDAealAD 154
Cdd:cd16962    73 PKsALKLG-----QArgvilLAAAQAGL---PVVEYTPRQVKQAVTGYGRADKEQvqyMVKRLLGLKEIPKPDDA---AD 141


                  ....*..
gi 1491220469 155 AQGVALC 161
Cdd:cd16962   142 ALAIALC 148
 
Name Accession Description Interval E-value
ruvC PRK00039
Holliday junction resolvase; Reviewed
 5-161 6.24e-13

Holliday junction resolvase; Reviewed


Pssm-ID: 234587  Cd Length: 164  Bit Score: 63.21  E-value: 6.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469   5 ETIVFGLDPGVGR--FGCVGMHNKKV--LSYATFKSKGKpyTSMPnfLRVTQLAHQVVAWMKAqtngYKYVTIVIETPIY 80
Cdd:PRK00039    1 MMRILGIDPGLRRtgYGVIEVEGRRLsyVASGVIRTPSD--LDLP--ERLKQIYDGLSELIDE----YQPDEVAIEEVFF 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469  81 NKNAKAfelqwrlfqqVLTFAQH----MMAP-NEILEVSNGT---VKKAMTGSGRAEKI---DMVcASVFDGPEFEK-DD 148
Cdd:PRK00039   73 NKNPQS----------ALKLGQArgvaILAAaQRGLPVAEYTplqVKKAVVGYGRADKEqvqHMV-KRLLNLPEIPKpDD 141

                         170
                  ....*....|...
gi 1491220469 149 AealADAQGVALC 161
Cdd:PRK00039  142 A---ADALAIAIC 151
RuvC COG0817
Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and ...
 8-161 3.97e-12

Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and repair];


Pssm-ID: 440579  Cd Length: 152  Bit Score: 60.86  E-value: 3.97e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469   8 VFGLDPGVGR--FGCVGMHNKKV--LSYATFKSKGKpyTSMPnfLRVTQLAHQVVAWMKAqtngYKYVTIVIETPIYNKN 83
Cdd:COG0817     1 ILGIDPGLRRtgYGVIEVDGNRLrlVASGVIRTPPK--LPLP--ERLLEIYEGLTELIEE----YKPDEVAIEEVFFNKN 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469  84 AKAfelqwrlfqqVLTFAQH----MMAPNE----ILEVSNGTVKKAMTGSGRAEK---IDMVCAsVFDGPEFEK-DDAea 151
Cdd:COG0817    73 PKS----------ALKLGQArgvaLLAAAQrglpVAEYTPLQVKKAVTGYGRADKeqvQAMVKR-LLGLDEIPKpDDA-- 139

                         170
                  ....*....|
gi 1491220469 152 lADAQGVALC 161
Cdd:COG0817   140 -ADALAIAIC 148
RuvC cd16962
Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC ...
 8-161 9.93e-10

Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC is also called Holliday junction resolvase RuvC. It is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is thought to bind either on the open, DNA exposed face of a single RuvA tetramer, or to replace one of the two tetramers. Binding is proposed to be mediated by an unstructured loop on RuvC, which becomes structured on binding RuvA. RuvC can be bound to the complex in either orientation, therefore resolving Holliday junctions in either a horizontal or vertical manner. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the Escherichia coli HJR. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438562  Cd Length: 152  Bit Score: 54.36  E-value: 9.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469   8 VFGLDPGVGRFG----CVGMHNKKVLSYATFKSKGKpytsMPNFLRVTQLAHQVVAWMKAqtngYKYVTIVIETPIYNKN 83
Cdd:cd16962     1 ILGIDPGLRRTGygviEVEGNKLRLLDYGVIRTPSK----LSLPERLKEIYDGLSELIEK----YKPDEVAIEKLFFNKN 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491220469  84 AK-AFELQwrlfqQV-----LTFAQHMMapnEILEVSNGTVKKAMTGSGRAEKID---MVCASVFDGPEFEKDDAealAD 154
Cdd:cd16962    73 PKsALKLG-----QArgvilLAAAQAGL---PVVEYTPRQVKQAVTGYGRADKEQvqyMVKRLLGLKEIPKPDDA---AD 141


                  ....*..
gi 1491220469 155 AQGVALC 161
Cdd:cd16962   142 ALAIALC 148
 
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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