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Conserved domains on  [gi|400189748|gb|EJO23823|]
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hypothetical protein HMPREF1148_2007 [Selenomonas sp. FOBRC6]

Protein Classification

PDDEXK family nuclease( domain architecture ID 1750065)

PDDEXK family nuclease similar to Halobacterium salinarum endonuclease NucS 1 that cleaves both 3' and 5' ssDNA extremities of branched DNA structures

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PDDEXK_nuclease-like super family cl40440
PDDEXK family nucleases; Superfamily of PDDEXK nucleases including very short patch repair ...
 3-158 7.08e-42

PDDEXK family nucleases; Superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


The actual alignment was detected with superfamily member cd22348:

Pssm-ID: 477358  Cd Length: 218  Bit Score: 138.73  E-value: 7.08e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748   3 FGYSSDAyDNGEKVLHSTLSADRFVSIADTgRSLKVVCGSEKISIIAEDGIEYAYWTRDQLKNAFEKKYKnKFVYAKAQS 82
Cdd:cd22348   69 YGYESDN-DPGRKALHVTLYTKEFNNIKGK-PGFKLNVTEDRIEIVHIHGKIVGTWDLETLRDSFERKLP-EVLLVKADS 145

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 400189748  83 RGKGASEEFRFVEAYEVAGFNYEAFVDLLEQGKIYIDLRIGQYhggvKNGRTHDHGTGFRIK-ESDQPLLFKINRRI 158
Cdd:cd22348  146 RGSGGDEEFWYNEAWVLSGFDFDRFLRLIREGIIKVDLRIGIY----PNGRKHDHGTGFRIVlESKLDLCFETRDRI 218
 
Name Accession Description Interval E-value
PDDEXK_nuclease cd22348
uncharacterized PDDEXK nuclease may function as a restriction endonuclease; This family ...
 3-158 7.08e-42

uncharacterized PDDEXK nuclease may function as a restriction endonuclease; This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411752  Cd Length: 218  Bit Score: 138.73  E-value: 7.08e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748   3 FGYSSDAyDNGEKVLHSTLSADRFVSIADTgRSLKVVCGSEKISIIAEDGIEYAYWTRDQLKNAFEKKYKnKFVYAKAQS 82
Cdd:cd22348   69 YGYESDN-DPGRKALHVTLYTKEFNNIKGK-PGFKLNVTEDRIEIVHIHGKIVGTWDLETLRDSFERKLP-EVLLVKADS 145

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 400189748  83 RGKGASEEFRFVEAYEVAGFNYEAFVDLLEQGKIYIDLRIGQYhggvKNGRTHDHGTGFRIK-ESDQPLLFKINRRI 158
Cdd:cd22348  146 RGSGGDEEFWYNEAWVLSGFDFDRFLRLIREGIIKVDLRIGIY----PNGRKHDHGTGFRIVlESKLDLCFETRDRI 218
MvaI_BcnI pfam15515
MvaI/BcnI restriction endonuclease family; This family of proteins includes the restriction ...
 3-152 3.40e-24

MvaI/BcnI restriction endonuclease family; This family of proteins includes the restriction endonucleases MvaI and BcnI. These enzymes both function as monomers. MvaI cleaves the sequence CC/WGG, where W is an A or a T nucleotide, leaving sticky ends. BcnI cleaves the sequence CC/SGG, where S is G or C, leaving sticky ends.


Pssm-ID: 434771  Cd Length: 225  Bit Score: 93.57  E-value: 3.40e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748    3 FGYSSDAYdNGEKVLHSTlsadRFVSIADTGRSLKVVCGSEKISI--IAEDGIEYAYWTRDQLKNAFEKKYKNKFvYAKA 80
Cdd:pfam15515  83 YGYPHKEA-GDEKSFRTT----IFTYPNARGFKLEVDRENTKLRIvfDKEKIDDEAYWGFDDLSKKLGKKHKNTF-YVKA 156

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 400189748   81 QSRGKGASEEFRFVEAYEVAGFNYEAFVDLLEQGKIYIDlrIGQYHGGvKNGRTHDHGTGFRIKESDQPLLF 152
Cdd:pfam15515 157 DSKKENGKEYFRYNKILHTKNPSFEKFLNLLEQGKITVD--FGLIKRY-PDGKVHDHGTKFRIKPSNLPLLY 225
 
Name Accession Description Interval E-value
PDDEXK_nuclease cd22348
uncharacterized PDDEXK nuclease may function as a restriction endonuclease; This family ...
 3-158 7.08e-42

uncharacterized PDDEXK nuclease may function as a restriction endonuclease; This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411752  Cd Length: 218  Bit Score: 138.73  E-value: 7.08e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748   3 FGYSSDAyDNGEKVLHSTLSADRFVSIADTgRSLKVVCGSEKISIIAEDGIEYAYWTRDQLKNAFEKKYKnKFVYAKAQS 82
Cdd:cd22348   69 YGYESDN-DPGRKALHVTLYTKEFNNIKGK-PGFKLNVTEDRIEIVHIHGKIVGTWDLETLRDSFERKLP-EVLLVKADS 145

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 400189748  83 RGKGASEEFRFVEAYEVAGFNYEAFVDLLEQGKIYIDLRIGQYhggvKNGRTHDHGTGFRIK-ESDQPLLFKINRRI 158
Cdd:cd22348  146 RGSGGDEEFWYNEAWVLSGFDFDRFLRLIREGIIKVDLRIGIY----PNGRKHDHGTGFRIVlESKLDLCFETRDRI 218
NciI-like cd22339
Restriction endonuclease NciI and similar endonucleases; NciI is a type II restriction ...
 55-155 4.28e-39

Restriction endonuclease NciI and similar endonucleases; NciI is a type II restriction endonuclease that recognizes and cleaves the sequence CC|SGG (S stands for C or G, | denotes the cleavage site). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411743  Cd Length: 170  Bit Score: 130.35  E-value: 4.28e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748  55 YAYWTRDQLKNAFEKKYKNKFVYAKAQSRGKGASEEFRFVEAYEVAGFNYEAFVDLLEQGKIYIDLRIGQYhggvkngrt 134
Cdd:cd22339   79 QPYWGFDDLKHKFGKKLKNCFYVVAATKKENGGNEEFHYNEAYLLSGFSFEKFLNLLEDGIIYVDFDARTG--------- 149

                         90       100
                 ....*....|....*....|.
gi 400189748 135 HDHGTGFRIKESDQPLLFKIN 155
Cdd:cd22339  150 HNHGTKFRIRQNKLPELYEKV 170
BcnI-like cd22310
Restriction endonuclease BcnI and similar endonucleases; Restriction endonuclease BcnI cleaves ...
 3-158 5.20e-33

Restriction endonuclease BcnI and similar endonucleases; Restriction endonuclease BcnI cleaves duplex DNA containing the sequence 5'-CC|SGG-3' (S stands for C or G, | designates a cleavage position) to generate staggered products with single nucleotide 5'-overhangs. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411714  Cd Length: 229  Bit Score: 116.58  E-value: 5.20e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748   3 FGYSSDAydNGEKVLHSTLSADRFVSiadTGRSLKVVcgSEKISIIAEDGIEYAYWTRDQLKNAFEKKYkNKFVYAKAQS 82
Cdd:cd22310   85 YGYEDEN--GRRKALYTTISGKRSNN---QGLKLEVD--DDIISLIHKKGTILAYWDLEDLVKKFKSKL-PRLLFVLADT 156

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 400189748  83 RGKGASEEFRFVEAYEVAGFNYEAFVDLLEQGKIYIDLRIGQYhggvKNGRTHDHGTGFRIKESDQPLLFKINRRI 158
Cdd:cd22310  157 RGEDGIEEFHFNEAYLLENPSFENFIKAIKSGEVVIDLRMHQK----PSGAVRDHGTAFRIKEKKLPLLFEEKERL 228
PDDEXK_nuclease cd22344
uncharacterized PDDEXK nuclease may function as a restriction endonuclease; This family ...
 11-153 1.69e-29

uncharacterized PDDEXK nuclease may function as a restriction endonuclease; This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411748  Cd Length: 220  Bit Score: 107.33  E-value: 1.69e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748  11 DNGEKVLHSTLSADRfvsiadTGRSLKVVCGSEKISIIAEDGIEYAYWTRDQLKNAFEKKYKNkFVYAKAQSRGKGASEE 90
Cdd:cd22344   89 KDGRLGLYYTVSSKP------NSQGLFLEVDEDKISLRHIDGIIIAYWQLEDLADRFKKKIPA-LILVSADTEERDGDEY 161

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 400189748  91 FRFVEAYEVAGFNYEAFVDLLEQGKIYIDLRIGQYhggvKNGRTHDHGTGFRIKESDQPLLFK 153
Cdd:cd22344  162 FHYYEAYLLKGTSPELFRNQIKNDNILVDLRLHDK----GNGKARNHGTGFRIYEKKLPLLFK 220
MvaI_BcnI pfam15515
MvaI/BcnI restriction endonuclease family; This family of proteins includes the restriction ...
 3-152 3.40e-24

MvaI/BcnI restriction endonuclease family; This family of proteins includes the restriction endonucleases MvaI and BcnI. These enzymes both function as monomers. MvaI cleaves the sequence CC/WGG, where W is an A or a T nucleotide, leaving sticky ends. BcnI cleaves the sequence CC/SGG, where S is G or C, leaving sticky ends.


Pssm-ID: 434771  Cd Length: 225  Bit Score: 93.57  E-value: 3.40e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748    3 FGYSSDAYdNGEKVLHSTlsadRFVSIADTGRSLKVVCGSEKISI--IAEDGIEYAYWTRDQLKNAFEKKYKNKFvYAKA 80
Cdd:pfam15515  83 YGYPHKEA-GDEKSFRTT----IFTYPNARGFKLEVDRENTKLRIvfDKEKIDDEAYWGFDDLSKKLGKKHKNTF-YVKA 156

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 400189748   81 QSRGKGASEEFRFVEAYEVAGFNYEAFVDLLEQGKIYIDlrIGQYHGGvKNGRTHDHGTGFRIKESDQPLLF 152
Cdd:pfam15515 157 DSKKENGKEYFRYNKILHTKNPSFEKFLNLLEQGKITVD--FGLIKRY-PDGKVHDHGTKFRIKPSNLPLLY 225
MvaI-like cd22337
Restriction Endonuclease MvaI and similar endonucleases; Restriction endonuclease MvaI ...
 11-154 1.03e-22

Restriction Endonuclease MvaI and similar endonucleases; Restriction endonuclease MvaI recognizes the sequence CC|WGG (W stands for A or T, '|' designates the cleavage site) and generates products with single nucleotide 5'-overhangs; it belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411741  Cd Length: 239  Bit Score: 90.09  E-value: 1.03e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748  11 DNGEKVLHSTLSADRFVSIADTGRSLKVVCGSEKISIIAEDG-------IEYAYWTRDQLKNAFEKKYKnKFVYAKAQSR 83
Cdd:cd22337   89 EFNNKTLHTTVKSKINFNKYSLSYFFKIEVDRKEKRLIIRVFdkdleliDDSVYWSFDDLENQLEKKLK-TLAIISAESK 167

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 400189748  84 GKGASEEFRFVEAYEVAGFNYEAFVDLLEQGKIYIDLRIGQYHGGVKNGRTHDHGTGFRIKESDQPLLFKI 154
Cdd:cd22337  168 KINGKKYYKYNSIEIYTGLNIDSLLEAIENGKIKVDFRIGAYKSGKNKGKTHDHGTGFRINEEDLLKYYEV 238
PDDEXK_nuclease cd22347
uncharacterized PDDEXK nuclease may function as a restriction endonuclease; This family ...
 2-123 3.88e-17

uncharacterized PDDEXK nuclease may function as a restriction endonuclease; This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411751  Cd Length: 203  Bit Score: 74.57  E-value: 3.88e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 400189748   2 TFGYSSDayDNGEKVLHSTLSADRFVSIadtGRSLKVVcgsEKISIIAEDGIEY-----AYWTRDQLKNAFEKKYKNKFv 76
Cdd:cd22347   86 KYGYEDD--DGRRKALYCTVSANPNNSG---GLLLVVD---LDNDILRELLLKRkiedvVVWTFDDLRKRLLEKHKETF- 156

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 400189748  77 YAKAQSRGKGASEEFRFVEAYEVAGFNYEAFVDLLEQGKIYIDLRIG 123
Cdd:cd22347  157 WVKAESKKIDGKEEFHYNKVTHTKNPSVSQFLPLIEAGLITLDLRIH 203
 
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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