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Conserved domains on  [gi|1532581929|ref|WP_125112720|]
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MULTISPECIES: PD-(D/E)XK nuclease-like domain-containing protein [Citrobacter]

Protein Classification

exonuclease family protein( domain architecture ID 1004615)

exonuclease family protein with similarity to E. coli exodeoxyribonuclease VIII (EXO VIII) that catalyzes the degradation of double-stranded DNA; acts progressively in a 5' to 3' direction, releasing 5'-phosphomononucleotides

Gene Ontology:  GO:0004527

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09709 super family cl35886
exodeoxyribonuclease VIII;
1-267 4.43e-100

exodeoxyribonuclease VIII;


The actual alignment was detected with superfamily member PRK09709:

Pssm-ID: 236615 [Multi-domain]  Cd Length: 877  Bit Score: 311.52  E-value: 4.43e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929   1 MNTGIYFDISNEDYHAGDGVSKSQLDMVAKNPALLKWVKAAPEDEEKKSALDMGTALHCLLLEPEEFDKRFIVAPQFNRR 80
Cdd:PRK09709  606 IEPGIYYGISNENYHAGPGVSKSQLDDIADTPALYLWRKNAPVDTTKTKTLDLGTAFHCRVLEPEEFSNRFIVAPEFNRR 685

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929  81 TNQGKADEEAFLKDVAGMGMTVMDAEQGRKLKLMRDSALAHPAARWMLEAPGHCEASMYWNDDETGELCRIRPDKWLNEH 160
Cdd:PRK09709  686 TNAGKEEEKAFLMECASTGKTVITAEEGRKIELMYQSVMALPLGQWLVESAGHAESSIYWEDPETGILCRCRPDKIIPEF 765

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929 161 NVIVDVKKVADMDRFARHIEEFRYHVQDAMYREGALKVTGYPHGFFFLAVSETIDCGRYPVRVFELDAPDVDAGHQLFRR 240
Cdd:PRK09709  766 HWIMDVKTTADIQRFKTAYYDYRYHVQDAFYSDGYEAQFGVQPTFVFLVASTTIECGRYPVEIFMMGEEAKLAGQQEYHR 845

                         250       260
                  ....*....|....*....|....*..
gi 1532581929 241 DLNTYHECRISDEWGGVEIIKRPELAR 267
Cdd:PRK09709  846 NLRTLADCLNTDEWPAIKTLSLPRWAK 872
 
Name Accession Description Interval E-value
PRK09709 PRK09709
exodeoxyribonuclease VIII;
1-267 4.43e-100

exodeoxyribonuclease VIII;


Pssm-ID: 236615 [Multi-domain]  Cd Length: 877  Bit Score: 311.52  E-value: 4.43e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929   1 MNTGIYFDISNEDYHAGDGVSKSQLDMVAKNPALLKWVKAAPEDEEKKSALDMGTALHCLLLEPEEFDKRFIVAPQFNRR 80
Cdd:PRK09709  606 IEPGIYYGISNENYHAGPGVSKSQLDDIADTPALYLWRKNAPVDTTKTKTLDLGTAFHCRVLEPEEFSNRFIVAPEFNRR 685

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929  81 TNQGKADEEAFLKDVAGMGMTVMDAEQGRKLKLMRDSALAHPAARWMLEAPGHCEASMYWNDDETGELCRIRPDKWLNEH 160
Cdd:PRK09709  686 TNAGKEEEKAFLMECASTGKTVITAEEGRKIELMYQSVMALPLGQWLVESAGHAESSIYWEDPETGILCRCRPDKIIPEF 765

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929 161 NVIVDVKKVADMDRFARHIEEFRYHVQDAMYREGALKVTGYPHGFFFLAVSETIDCGRYPVRVFELDAPDVDAGHQLFRR 240
Cdd:PRK09709  766 HWIMDVKTTADIQRFKTAYYDYRYHVQDAFYSDGYEAQFGVQPTFVFLVASTTIECGRYPVEIFMMGEEAKLAGQQEYHR 845

                         250       260
                  ....*....|....*....|....*..
gi 1532581929 241 DLNTYHECRISDEWGGVEIIKRPELAR 267
Cdd:PRK09709  846 NLRTLADCLNTDEWPAIKTLSLPRWAK 872
DUF3799 pfam12684
PDDEXK-like domain of unknown function (DUF3799); This family of proteins is functionally ...
 21-254 4.16e-20

PDDEXK-like domain of unknown function (DUF3799); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 265 and 420 amino acids in length. It appears that these proteins are distantly related to the PDDEXK superfamily and so these domains are likely to be nucleases. This family has a C-terminal cysteine cluster similar to that found in pfam01930.


Pssm-ID: 432717 [Multi-domain]  Cd Length: 231  Bit Score: 86.20  E-value: 4.16e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929  21 SKSQLDMVAKNPALLKWVKAAPEDEEKKSALDMGTALHCLLlEPEEFDKRFIvapqfnrrtnqgKADEEAFLKDVAGMGm 100
Cdd:pfam12684   1 SVSQYKDFLKCEAHALAKLNGEWQPSDTTALLVGSYVHSYF-ESTLFHEEFK------------KENKEAYTTRRPPKG- 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929 101 tVMDAEQgRKLKLMRDSALAHPAARWMLEAPghcEASMYWNDdETGELCRIRPDkWLNEHNVIVDVKKVADM--DRFARH 178
Cdd:pfam12684  67 -ELKAEF-QIANQMIERLKNDPLFMKLYSGE---KEVIFTGE-LFGVPWKIKID-SLNPEGYFVDLKTTRDIhkRKWNED 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929 179 ------IEEFRYHVQDAMYREGALKVTGYPHGFFFLAVS-ETIdcgrYPVRVFELDAPDVDAGHQLFRRDLNTYHECRIS 251
Cdd:pfam12684 140 agrrvtIEAYGYDLQMAVYQEGLRQNTGKTLPPYIIAVEkETP----PDKAIITAGQSFLDEGLDEVEENLERLKKVKNG 215


                  ...
gi 1532581929 252 DEW 254
Cdd:pfam12684 216 EVE 218
 
Name Accession Description Interval E-value
PRK09709 PRK09709
exodeoxyribonuclease VIII;
1-267 4.43e-100

exodeoxyribonuclease VIII;


Pssm-ID: 236615 [Multi-domain]  Cd Length: 877  Bit Score: 311.52  E-value: 4.43e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929   1 MNTGIYFDISNEDYHAGDGVSKSQLDMVAKNPALLKWVKAAPEDEEKKSALDMGTALHCLLLEPEEFDKRFIVAPQFNRR 80
Cdd:PRK09709  606 IEPGIYYGISNENYHAGPGVSKSQLDDIADTPALYLWRKNAPVDTTKTKTLDLGTAFHCRVLEPEEFSNRFIVAPEFNRR 685

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929  81 TNQGKADEEAFLKDVAGMGMTVMDAEQGRKLKLMRDSALAHPAARWMLEAPGHCEASMYWNDDETGELCRIRPDKWLNEH 160
Cdd:PRK09709  686 TNAGKEEEKAFLMECASTGKTVITAEEGRKIELMYQSVMALPLGQWLVESAGHAESSIYWEDPETGILCRCRPDKIIPEF 765

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929 161 NVIVDVKKVADMDRFARHIEEFRYHVQDAMYREGALKVTGYPHGFFFLAVSETIDCGRYPVRVFELDAPDVDAGHQLFRR 240
Cdd:PRK09709  766 HWIMDVKTTADIQRFKTAYYDYRYHVQDAFYSDGYEAQFGVQPTFVFLVASTTIECGRYPVEIFMMGEEAKLAGQQEYHR 845

                         250       260
                  ....*....|....*....|....*..
gi 1532581929 241 DLNTYHECRISDEWGGVEIIKRPELAR 267
Cdd:PRK09709  846 NLRTLADCLNTDEWPAIKTLSLPRWAK 872
DUF3799 pfam12684
PDDEXK-like domain of unknown function (DUF3799); This family of proteins is functionally ...
 21-254 4.16e-20

PDDEXK-like domain of unknown function (DUF3799); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 265 and 420 amino acids in length. It appears that these proteins are distantly related to the PDDEXK superfamily and so these domains are likely to be nucleases. This family has a C-terminal cysteine cluster similar to that found in pfam01930.


Pssm-ID: 432717 [Multi-domain]  Cd Length: 231  Bit Score: 86.20  E-value: 4.16e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929  21 SKSQLDMVAKNPALLKWVKAAPEDEEKKSALDMGTALHCLLlEPEEFDKRFIvapqfnrrtnqgKADEEAFLKDVAGMGm 100
Cdd:pfam12684   1 SVSQYKDFLKCEAHALAKLNGEWQPSDTTALLVGSYVHSYF-ESTLFHEEFK------------KENKEAYTTRRPPKG- 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929 101 tVMDAEQgRKLKLMRDSALAHPAARWMLEAPghcEASMYWNDdETGELCRIRPDkWLNEHNVIVDVKKVADM--DRFARH 178
Cdd:pfam12684  67 -ELKAEF-QIANQMIERLKNDPLFMKLYSGE---KEVIFTGE-LFGVPWKIKID-SLNPEGYFVDLKTTRDIhkRKWNED 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532581929 179 ------IEEFRYHVQDAMYREGALKVTGYPHGFFFLAVS-ETIdcgrYPVRVFELDAPDVDAGHQLFRRDLNTYHECRIS 251
Cdd:pfam12684 140 agrrvtIEAYGYDLQMAVYQEGLRQNTGKTLPPYIIAVEkETP----PDKAIITAGQSFLDEGLDEVEENLERLKKVKNG 215


                  ...
gi 1532581929 252 DEW 254
Cdd:pfam12684 216 EVE 218
 
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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