NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|971757228|ref|YP_009210761|]
View 

exonuclease [Mycobacterium phage Serenity]

Protein Classification

PD-(D/E)XK nuclease family protein( domain architecture ID 10578103)

PD-(D/E)XK nuclease family protein similar to uncharacterized Fromanvirus gene 69 protein

Gene Ontology:  GO:0004518
PubMed:  15972856

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
PDDEXK_1 pfam12705
PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease ...
12-285 7.76e-24

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: 96.83  E-value: 7.76e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228   12 SVSQLNQYTRCPQAYKLARIDKV-WARPAAWLPQGTAFHTVAEIYEKALAEGREMSLERAQEIFREEyAKDIGALCEETP 90
Cdd:pfam12705   3 SPSRLETYLTCPLRFFLRYLLGLrEDEELDAPDLGTLVHAALERFYRWGRLPEEDLEELLQALLEEL-WPELGLQSEILP 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228   91 NFEWWfwsgpyngerdIERRFHLGLEQVEKFIAWRQTKGQEIWTtpggicttetwhdpsceecrpkpAIELPFNIELdgI 170
Cdd:pfam12705  82 RLPWL-----------AGRLRRRLERMLRRLAEWLRARRGFRPV-----------------------AVELGFGGTT--V 125
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  171 RVRGFIDAVVV-VNGELRVRDYKTGNKPG--------DDFQLGVYALAVAMTFGVEAPKTGD--YFMAGKKGVKPKPTAP 239
Cdd:pfam12705 126 RLVGRIDRVDLdGEGYLRIIDYKTGSAPPqsedldlyEGLQLLLYLLALAAGEKALGGPAGAlyLRLDDPLKKDEEVVEP 205
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 971757228  240 YDLTEWTRERITERFHEVEDRIQAGDFEPLPEPdKCGFCDVNYSCP 285
Cdd:pfam12705 206 MVLTEDEFDALLQELRELAEEILAGEFPARPGK-KCRYCPYRSICP 250
 
Name Accession Description Interval E-value
PDDEXK_1 pfam12705
PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease ...
12-285 7.76e-24

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: 96.83  E-value: 7.76e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228   12 SVSQLNQYTRCPQAYKLARIDKV-WARPAAWLPQGTAFHTVAEIYEKALAEGREMSLERAQEIFREEyAKDIGALCEETP 90
Cdd:pfam12705   3 SPSRLETYLTCPLRFFLRYLLGLrEDEELDAPDLGTLVHAALERFYRWGRLPEEDLEELLQALLEEL-WPELGLQSEILP 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228   91 NFEWWfwsgpyngerdIERRFHLGLEQVEKFIAWRQTKGQEIWTtpggicttetwhdpsceecrpkpAIELPFNIELdgI 170
Cdd:pfam12705  82 RLPWL-----------AGRLRRRLERMLRRLAEWLRARRGFRPV-----------------------AVELGFGGTT--V 125
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  171 RVRGFIDAVVV-VNGELRVRDYKTGNKPG--------DDFQLGVYALAVAMTFGVEAPKTGD--YFMAGKKGVKPKPTAP 239
Cdd:pfam12705 126 RLVGRIDRVDLdGEGYLRIIDYKTGSAPPqsedldlyEGLQLLLYLLALAAGEKALGGPAGAlyLRLDDPLKKDEEVVEP 205
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 971757228  240 YDLTEWTRERITERFHEVEDRIQAGDFEPLPEPdKCGFCDVNYSCP 285
Cdd:pfam12705 206 MVLTEDEFDALLQELRELAEEILAGEFPARPGK-KCRYCPYRSICP 250
COG2887 COG2887
RecB family exonuclease [Replication, recombination and repair];
12-283 4.41e-10

RecB family exonuclease [Replication, recombination and repair];


Pssm-ID: 225441 [Multi-domain]  Cd Length: 269  Bit Score: 59.03  E-value: 4.41e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  12 SVSQLNQYTRCPQAYKLARIDKVWARPAAWLP-----QGTAFHTVAEIYEKALAEGREMSLERAQEIFREEYAKDigALC 86
Cdd:COG2887    2 SVSRAEALRRCPYLFYARRILALPPLGTRAEEpeaavRGTLLHAILEALVGERYHAAAAALAKLAWLLRKELAEA--ELP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  87 EETPNfEWWFwsgpyngerdierRFhLGLEQVEKFIAWRQTKGQEIWTtpggicttetwhdpSCEECRpkpaiELPFNIE 166
Cdd:COG2887   80 GYTDA-EWLD-------------RL-RARARAFLVYDWERERGTAFHA--------------WLEEER-----GAELLID 125
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228 167 lDGIRVRGFIDAVVVV-NGELRVRDYKTGNKPGDD---------FQLGVYALAVAMTFGVE-APKTGDYFMAGKK-GVKP 234
Cdd:COG2887  126 -GGIRLRGRADRIDKDaDGELEILDYKTGKSPSAArapaavspqLALEALALIEGRFRGVEpGQLRLVYLRKSGRvGEAP 204
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 971757228 235 KPTAPYDLTEWTRE---RITERFHEVEDRIQ--AGDFEPLPEPDKCGF---CDVNYS 283
Cdd:COG2887  205 DNREQLPQLALAREalaELAELLAGLEVRPRgySSRCDLCPHQDLCPAyggLARLLE 261
Cas4_I-A_I-B_I-C_I-D_II-B cd09637
CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short ...
165-285 4.56e-06

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: 45.89  E-value: 4.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228 165 IELDGIRVRGFIDAVVVVNGELRVRDYKTGNKPG----DDFQLGVYALAVAMTFGVEAPKTGDYFMAGKKGVKPKPTapy 240
Cdd:cd09637   60 LKSKKYGLKGVIDIVLKEDGELVPVEVKSGRAGSpreaHKLQLVAYAYLLEEMYGKRVARGYIVYLEGGKRLEVEIS--- 136
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 971757228 241 dlTEWTRErITERFHEVEDRIQAGDFEPLPEPDKCGFCDVNYSCP 285
Cdd:cd09637  137 --EELRKK-AEKLLEEIRKLLEGELPPPVKSSPKCKFCPYREICL 178
cas4 TIGR00372
CRISPR-associated protein Cas4; This model represents a family of proteins associated with ...
165-286 2.02e-03

CRISPR-associated protein Cas4; This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.


Pssm-ID: 273040 [Multi-domain]  Cd Length: 178  Bit Score: 38.16  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  165 IELDGIRVRGFIDAVVVVNGELRVRDYKTGnKPG----DDFQLGVYALAVAMTfGVEAPKTGDYFMAGKKGVKpkptapY 240
Cdd:TIGR00372  60 LKSKKYGLKGVIDIVLEEDGELVPVEVKSG-KPSpreaHKYQLLAYAYLLEEM-YGEIVRGYILYINAGKKLE------V 131
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 971757228  241 DLTEWTRERITERFHEVEDRIQaGDFEPLPE--PDKCGFCDVNYSCPV 286
Cdd:TIGR00372 132 EISEELRKKAVKLIEKIRELLE-GGKPPSPPksGPKCKFCPYREICLP 178
 
Name Accession Description Interval E-value
PDDEXK_1 pfam12705
PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease ...
12-285 7.76e-24

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: 96.83  E-value: 7.76e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228   12 SVSQLNQYTRCPQAYKLARIDKV-WARPAAWLPQGTAFHTVAEIYEKALAEGREMSLERAQEIFREEyAKDIGALCEETP 90
Cdd:pfam12705   3 SPSRLETYLTCPLRFFLRYLLGLrEDEELDAPDLGTLVHAALERFYRWGRLPEEDLEELLQALLEEL-WPELGLQSEILP 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228   91 NFEWWfwsgpyngerdIERRFHLGLEQVEKFIAWRQTKGQEIWTtpggicttetwhdpsceecrpkpAIELPFNIELdgI 170
Cdd:pfam12705  82 RLPWL-----------AGRLRRRLERMLRRLAEWLRARRGFRPV-----------------------AVELGFGGTT--V 125
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  171 RVRGFIDAVVV-VNGELRVRDYKTGNKPG--------DDFQLGVYALAVAMTFGVEAPKTGD--YFMAGKKGVKPKPTAP 239
Cdd:pfam12705 126 RLVGRIDRVDLdGEGYLRIIDYKTGSAPPqsedldlyEGLQLLLYLLALAAGEKALGGPAGAlyLRLDDPLKKDEEVVEP 205
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 971757228  240 YDLTEWTRERITERFHEVEDRIQAGDFEPLPEPdKCGFCDVNYSCP 285
Cdd:pfam12705 206 MVLTEDEFDALLQELRELAEEILAGEFPARPGK-KCRYCPYRSICP 250
COG2887 COG2887
RecB family exonuclease [Replication, recombination and repair];
12-283 4.41e-10

RecB family exonuclease [Replication, recombination and repair];


Pssm-ID: 225441 [Multi-domain]  Cd Length: 269  Bit Score: 59.03  E-value: 4.41e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  12 SVSQLNQYTRCPQAYKLARIDKVWARPAAWLP-----QGTAFHTVAEIYEKALAEGREMSLERAQEIFREEYAKDigALC 86
Cdd:COG2887    2 SVSRAEALRRCPYLFYARRILALPPLGTRAEEpeaavRGTLLHAILEALVGERYHAAAAALAKLAWLLRKELAEA--ELP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  87 EETPNfEWWFwsgpyngerdierRFhLGLEQVEKFIAWRQTKGQEIWTtpggicttetwhdpSCEECRpkpaiELPFNIE 166
Cdd:COG2887   80 GYTDA-EWLD-------------RL-RARARAFLVYDWERERGTAFHA--------------WLEEER-----GAELLID 125
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228 167 lDGIRVRGFIDAVVVV-NGELRVRDYKTGNKPGDD---------FQLGVYALAVAMTFGVE-APKTGDYFMAGKK-GVKP 234
Cdd:COG2887  126 -GGIRLRGRADRIDKDaDGELEILDYKTGKSPSAArapaavspqLALEALALIEGRFRGVEpGQLRLVYLRKSGRvGEAP 204
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 971757228 235 KPTAPYDLTEWTRE---RITERFHEVEDRIQ--AGDFEPLPEPDKCGF---CDVNYS 283
Cdd:COG2887  205 DNREQLPQLALAREalaELAELLAGLEVRPRgySSRCDLCPHQDLCPAyggLARLLE 261
Cas4_I-A_I-B_I-C_I-D_II-B cd09637
CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short ...
165-285 4.56e-06

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: 45.89  E-value: 4.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228 165 IELDGIRVRGFIDAVVVVNGELRVRDYKTGNKPG----DDFQLGVYALAVAMTFGVEAPKTGDYFMAGKKGVKPKPTapy 240
Cdd:cd09637   60 LKSKKYGLKGVIDIVLKEDGELVPVEVKSGRAGSpreaHKLQLVAYAYLLEEMYGKRVARGYIVYLEGGKRLEVEIS--- 136
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 971757228 241 dlTEWTRErITERFHEVEDRIQAGDFEPLPEPDKCGFCDVNYSCP 285
Cdd:cd09637  137 --EELRKK-AEKLLEEIRKLLEGELPPPVKSSPKCKFCPYREICL 178
RecB COG1074
ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) ...
66-228 1.37e-04

ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [Replication, recombination and repair];


Pssm-ID: 224000 [Multi-domain]  Cd Length: 1139  Bit Score: 43.22  E-value: 1.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228   66 SLERAQEIFREEyakdIGALCEETpnFEWWFWSGPYNGE--RDIERRFHLGLEQVEKFIAWRQtkgqeIWTTpggICTTE 143
Cdd:COG1074   969 NLDFSAPVDAAE----IGTAIHEL--LQHLPFEEDWEQElaEWLEAMLSTPLEDAERAIILSQ-----ILAF---FRDPE 1034
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  144 TwhDPSCEECRPKPAIELPFNIELDGIRVRGFIDAVVVVNGELRVRDYKTgNKPGD----------------DFQLGVYA 207
Cdd:COG1074  1035 L--EFLFPINSRPFSLLDPLSAGSERGLLQGIIDLLFRHEGRYYILDYKT-NRLGDdsaayspaeamlkqryDLQLQLYA 1111
                         170       180
                  ....*....|....*....|.
gi 971757228  208 LAVAMTFGVEAPKTGDYFMAG 228
Cdd:COG1074  1112 EALHRILRKRVKDYALARHFG 1132
Cas4 COG1468
CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms];
160-286 1.46e-03

CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms];


Pssm-ID: 224385  Cd Length: 190  Bit Score: 38.93  E-value: 1.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228 160 ELPFNIELDGIRV-RGFIDAVVVVNGELRVRDYKTGNKP---GDDFQLgVYALAVAMTFGVEAPKTGDYFmagkkgVKPK 235
Cdd:COG1468   65 RDEKEVELEGEWIkIDFLKGRMDLEVKDVVVEIKKSKKMekaPHKLQL-AYYLYLEEKLGIAVAKGYIYY------PKLK 137
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 971757228 236 PTAPYDLTEWTRERITERFHEVEdRIQAGDFEPLPEPD-KCGFCDVNYSCPV 286
Cdd:COG1468  138 KRVEVELTEELREEVERVLKEIE-EILEGGKPPPPKKKkKCKKCAYREICFP 188
cas4 TIGR00372
CRISPR-associated protein Cas4; This model represents a family of proteins associated with ...
165-286 2.02e-03

CRISPR-associated protein Cas4; This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.


Pssm-ID: 273040 [Multi-domain]  Cd Length: 178  Bit Score: 38.16  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971757228  165 IELDGIRVRGFIDAVVVVNGELRVRDYKTGnKPG----DDFQLGVYALAVAMTfGVEAPKTGDYFMAGKKGVKpkptapY 240
Cdd:TIGR00372  60 LKSKKYGLKGVIDIVLEEDGELVPVEVKSG-KPSpreaHKYQLLAYAYLLEEM-YGEIVRGYILYINAGKKLE------V 131
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 971757228  241 DLTEWTRERITERFHEVEDRIQaGDFEPLPE--PDKCGFCDVNYSCPV 286
Cdd:TIGR00372 132 EISEELRKKAVKLIEKIRELLE-GGKPPSPPksGPKCKFCPYREICLP 178
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH