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Conserved domains on  [gi|1842004037|ref|YP_009791428|]
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exonuclease [Synechococcus phage Bellamy]

Protein Classification

PD-(D/E)XK nuclease family protein( domain architecture ID 1193)

PD-(D/E)XK nuclease family protein similar to CRISPR-associated exonuclease Cas4

EC:  3.1.-.-
Gene Ontology:  GO:0004527
PubMed:  15972856

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cas4 super family cl43424
CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas ...
 81-182 3.38e-05

CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas system-associated exonuclease Cas4, RecB family is part of the Pathway/BioSystem: CRISPR-Cas system


The actual alignment was detected with superfamily member COG1468:

Pssm-ID: 441077 [Multi-domain]  Cd Length: 184  Bit Score: 43.02  E-value: 3.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842004037  81 YMRNKEINWDEfRPATQF-MFHHAKpyLDKINNVHAIERTLYSEYLGLAGRVDCIAEYEGELAVIDFKTSekiKPEKWlE 159
Cdd:COG1468    24 LIHVIGLEWEE-NERVALgRLLHER--VYKRLERLRREVPLDSERLGLTGKIDLVEFEDGELVPVEYKKS---KPKPW-E 96

                          90       100
                  ....*....|....*....|...
gi 1842004037 160 NYFVQEMFYATAYYELTGIPVKK 182
Cdd:COG1468    97 ADRMQLCAYALLLEEMLGIPVPK 119
 
Name Accession Description Interval E-value
Cas4 COG1468
CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas ...
 81-182 3.38e-05

CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas system-associated exonuclease Cas4, RecB family is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 441077 [Multi-domain]  Cd Length: 184  Bit Score: 43.02  E-value: 3.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842004037  81 YMRNKEINWDEfRPATQF-MFHHAKpyLDKINNVHAIERTLYSEYLGLAGRVDCIAEYEGELAVIDFKTSekiKPEKWlE 159
Cdd:COG1468    24 LIHVIGLEWEE-NERVALgRLLHER--VYKRLERLRREVPLDSERLGLTGKIDLVEFEDGELVPVEYKKS---KPKPW-E 96

                          90       100
                  ....*....|....*....|...
gi 1842004037 160 NYFVQEMFYATAYYELTGIPVKK 182
Cdd:COG1468    97 ADRMQLCAYALLLEEMLGIPVPK 119
PDDEXK_1 pfam12705
PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease ...
 115-172 1.36e-03

PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease superfamily


Pssm-ID: 432731 [Multi-domain]  Cd Length: 250  Bit Score: 38.67  E-value: 1.36e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842004037 115 AIERTLYSEYLGLAGRVDCI-AEYEGELAVIDFKT-SEKIKPEKWLENYFVQEMFYATAY 172
Cdd:pfam12705 115 AVELGFGGTTVRLVGRIDRVdLDGEGYLRIIDYKTgSAPPQSEDLDLYEGLQLLLYLLAL 174
Cas4_I-A_I-B_I-C_I-D_II-B cd09637
CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short ...
 122-182 3.83e-03

CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster


Pssm-ID: 187768 [Multi-domain]  Cd Length: 178  Bit Score: 37.03  E-value: 3.83e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1842004037 122 SEYLGLAGRVDCIAEYEGELAVIDFKTSEKIKPEkwlENYFVQEMFYATAYYELTGIPVKK 182
Cdd:cd09637    62 SKKYGLKGVIDIVLKEDGELVPVEVKSGRAGSPR---EAHKLQLVAYAYLLEEMYGKRVAR 119
 
Name Accession Description Interval E-value
Cas4 COG1468
CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas ...
 81-182 3.38e-05

CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas system-associated exonuclease Cas4, RecB family is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 441077 [Multi-domain]  Cd Length: 184  Bit Score: 43.02  E-value: 3.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842004037  81 YMRNKEINWDEfRPATQF-MFHHAKpyLDKINNVHAIERTLYSEYLGLAGRVDCIAEYEGELAVIDFKTSekiKPEKWlE 159
Cdd:COG1468    24 LIHVIGLEWEE-NERVALgRLLHER--VYKRLERLRREVPLDSERLGLTGKIDLVEFEDGELVPVEYKKS---KPKPW-E 96

                          90       100
                  ....*....|....*....|...
gi 1842004037 160 NYFVQEMFYATAYYELTGIPVKK 182
Cdd:COG1468    97 ADRMQLCAYALLLEEMLGIPVPK 119
PDDEXK_1 pfam12705
PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease ...
 115-172 1.36e-03

PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease superfamily


Pssm-ID: 432731 [Multi-domain]  Cd Length: 250  Bit Score: 38.67  E-value: 1.36e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842004037 115 AIERTLYSEYLGLAGRVDCI-AEYEGELAVIDFKT-SEKIKPEKWLENYFVQEMFYATAY 172
Cdd:pfam12705 115 AVELGFGGTTVRLVGRIDRVdLDGEGYLRIIDYKTgSAPPQSEDLDLYEGLQLLLYLLAL 174
Cas4_I-A_I-B_I-C_I-D_II-B cd09637
CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short ...
 122-182 3.83e-03

CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster


Pssm-ID: 187768 [Multi-domain]  Cd Length: 178  Bit Score: 37.03  E-value: 3.83e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1842004037 122 SEYLGLAGRVDCIAEYEGELAVIDFKTSEKIKPEkwlENYFVQEMFYATAYYELTGIPVKK 182
Cdd:cd09637    62 SKKYGLKGVIDIVLKEDGELVPVEVKSGRAGSPR---EAHKLQLVAYAYLLEEMYGKRVAR 119
RecB COG1074
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 127-184 5.74e-03

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: 37.63  E-value: 5.74e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1842004037 127 LAGRVDCIAEYEGELAVIDFKTSEKIK--PEKWLENYFVQEMFYATAYYELTGI-PVKKLI 184
Cdd:COG1074   795 LKGRIDLVFEDDGRVYIVDYKTNRLGPddEEYLPERYRLQLALYALALERLLPGrPVRAGL 855
Slr0479 COG2887
RecB family exonuclease [Replication, recombination and repair];
35-198 8.06e-03

RecB family exonuclease [Replication, recombination and repair];


Pssm-ID: 442133 [Multi-domain]  Cd Length: 248  Bit Score: 36.55  E-value: 8.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842004037  35 SITSVTSFYN--RQIFAkwrERI-GVEEANRITKKATARGTDFHEAVEVYMRNK-------------EINWDEFRPATQF 98
Cdd:COG2887     4 SPSRIETLLRcpLRYYA---RYIlGLRDPLEPPPDAADRGTLVHAVLERFYKLPadelpaeellallEEAWAELGFEDPW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842004037  99 MFHHAKPYLDKI-------------NNVHAIERTLYSEYLG---LAGRVDCIAEY-EGELAVIDFKTSeKIKPEKWLENY 161
Cdd:COG2887    81 AAALWLERAERLleaflewerapagLEPVAVEVEFELELPGgvrLRGRIDRIDRLpDGRLVVVDYKTG-KAPSTKDEAGE 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1842004037 162 FVQEMFYATAYYE-LTGIPVKKLITIMVTPGGDVKVFD 198
Cdd:COG2887   160 DPQLALYALALERgFEGLVPAGARLVYLGDLGKKKVLD 197
 
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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