Conserved Protein Domain Family
PDDEXK_7
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pfam04411: PDDEXK_7 
PD-(D/E)XK nuclease superfamily
This domain has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches. The domain has two additional beta-strands inserted to the core fold after the first core alpha-helix. It has been speculated that it could function as s methylation-dependent restriction. The domain has two additional beta-strands inserted into the core fold after the first core alpha-helix. The PD-(D/E)XK signature is clearly conserved corresponding to an invariant PD (motif II) and DAK (motif III) motifs. There is also a conserved glutamic acid in motif I that is most likely to be involved in metal ion binding. The second core alpha-helix contains an invariant MHXYRD motif. It has been speculated that it could function as s methylation-dependent restriction enzyme.
Links
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Statistics
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PSSM-Id: 398217
Aligned: 16 rows
Threshold Bit Score: 138.684
Threshold Setting Gi: 500594548
Created: 11-May-2020
Updated: 7-Aug-2020
Structure
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Aligned Rows:
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PubMed ReferencesClick to see Conserved Features Help
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Q67PW5        293 TLYEYWVFLQLVKVMERLcGKEFHLSQLVEVRPDGM-GVALRRGRAraIKGTVQ-RlGRTLQVELWFNRSFGhrt----- 365 Symbiobacteriu...
WP_000989793  392 RLYEYWTYLKLGQILSKK--YIPLHQDVIQVKQDGL-YVTLDESKT--AKRTFK-HpETDEVIELYFQKRNG-------- 457 Bacillus anthr...
Q5LBA9        375 KLYEIWCFIELKNIIKELlG-NEVETNYSKRPEKKF-ITQLGKGKL--SKVIFS-K-HNIELAKICYNPKSYvgeeqlst 448 Bacteroides fr...
WP_012072032  386 DIYEVWCFIEVMSIVKSL-GFIEKERTLNHLKQVQFeKHFPDDEMA--AAFVYF-RaSDGMTIELAHEPSFTpkg----- 456 Marinomonas sp...
Q6LVP0        398 ETYEVWCFLAVRKVLTDVlGFKETEQNKAKLKLNDYfELQLEDGLSgaGAFVFE-R-SDGLKARLAHEPVFRrag----- 470 Photobacterium...
WP_011940895  391 ELYEVWCLLEIRRMLMAL-GFTEVETRKAALRTKGL-EKDLADGMG--TAFRFT-R-RDGLEIRLAHEPPFSvtrnp--- 461 Geobacter uran...
O26602        370 ELYEYWCYFRILRILEDItGDRVNPRDIFVRDGW---RVRLRTGNS-----ILR-FsMDDTEIALSYNGRFAgdt----- 435 Methanothermob...
Q7P254        408 QIYEYWCFFVLRDVLRSLc-LETGGGNFLSVSADGL-RVQLAKGRRseCRFEYTcGnGTSLGVSLFYNRRFLrprvp--- 482 Chromobacteriu...
WP_011956975  353 LLYERWCVLRAVWSLLDL-GVDVHSHNLLITPPGETdAWAINLPSD--APLLIA-Gy-KGWDLTVRYQPRYPpavsaq-s 426 Roseiflexus sp...
jgi:Haur_4160 337 TLYEQWCALAVAQVLAELg--QVEAQHLLIDNPQRE-RWVLELNSA--TPLLSV-Ri-GSQLWHLRYQARFSaqpds--- 406 Herpetosiphon ...

Q67PW5        366 --gnqGSWTRPMRPDYSIRIKPDMTYGepdeVWIHFDAKYRVESVTELfgedprteeeEGRlldeeqtaesrqlaRRADL 443 Symbiobacteriu...
WP_000989793  458 -----RLPTVTQKPDTMLAIEKKGKNYq---YQYIFDAKYRIDFAERShykr--kygtPGP--------------MEEDI 513 Bacillus anthr...
Q5LBA9        449 iipctTSYTVSQQPDIILQLTRRDIKQgi-kLTYLFDAKYRIGDTQDNv---------DTP--------------PDDAI 504 Bacteroides fr...
WP_012072032  457 --mvnRTWLAKQRPDIVLRVTLVNHES----FFILFDAKYRIDTQQLKdk-------dGVP---------------EDAL 508 Marinomonas sp...
Q6LVP0        471 --kkiRSFWVTQKPDILLEVTFPDGKK----CIWLFDAKYRIKTKNDRyeqddidqqdFVP---------------DDAI 529 Photobacterium...
WP_011940895  462 dargiYSWTTPQKPDILLEAALPDGSR----INWIFDAKYRIDAEDGKd--------dLIP---------------DDAI 514 Geobacter uran...
O26602        436 ---pcRSYSLPFKPDYSILVAVDECT-----CFIHLDAKYRSTVRPDDlyesidmrdsEEEler---------rfRDGDV 498 Methanothermob...
Q7P254        483 qndwsGSYTAAFDPDYSILIRSPNGPA----HWLHFDAKYRLERQQAEamfeadedsdDDAgvmadyeaelvrvhKQEDL 558 Chromobacteriu...
WP_011956975  427 gdtfvSLDRHTRIPDLAIEATRPGHPP----RIIVLDAKYRLDADERAv--------------------------pADAL 476 Roseiflexus sp...
jgi:Haur_4160 407 -dgfySLDRYLRIPDLVLQTATANAK-----QVLVLDAKYRRAPDQRVp---------------------------QSAL 453 Herpetosiphon ...

Q67PW5        444 LKMHAYRDAI--------------RRSAGAYVIYPGTER 468 Symbiobacterium thermophilum
WP_000989793  514 NTMHRYRDALvveqe-----gpfeRTAYGAYVLFPWNQe 547 Bacillus anthracis
Q5LBA9        505 NQMHRYRDAIyyidqd---tkqlkKEVIGGYILFPGNGE 540 Bacteroides fragilis NCTC 9343
WP_012072032  509 NQMHRYRDAIihqhrfeyesplksRPVMGAFALYPGFFN 547 Marinomonas sp. MWYL1
Q6LVP0        530 NQMHRYRDALiriegqe-glhsksRPVFGAFALYPGFYD 567 Photobacterium profundum
WP_011940895  515 NQMHRYRDALihlkkaddgvteksRPVVGAFVLYPGWFD 553 Geobacter uraniireducens
O26602        499 YKMHSYKDAI--------------LRSVGAYILYPGDED 523 Methanothermobacter thermautotrophicus str. Delta H
Q7P254        559 FKMHTYRDGI--------------LSTRGAYVLFPGDGV 583 Chromobacterium violaceum
WP_011956975  477 AEAYAYAGAIgaa---------dpPSVVAALILYPGTGA 506 Roseiflexus sp. RS-1
jgi:Haur_4160 454 DDVYAYRGSLgyn---------gqPCVLAAAILYPQANT 483 Herpetosiphon aurantiacus DSM 785
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