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Conserved domains on  [gi|1441214876|ref|WP_114840001|]
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PD-(D/E)XK nuclease family protein [Halarcobacter bivalviorum]

Protein Classification

PD-(D/E)XK nuclease family protein( domain architecture ID 1003949)

PD-(D/E)XK nuclease family protein similar to ATP-dependent helicase/deoxyribonuclease subunit B (AddB), part of a heterodimer that acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease

CATH:  3.90.320.10|3.40.50.300
EC:  3.-.-.-
Gene Ontology:  GO:0005524|GO:0003678|GO:0003677|GO:0032508|GO:0004518
PubMed:  17584917|22398859|21428912
SCOP:  3000104

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AddB super family cl34683
ATP-dependent helicase/DNAse subunit B [Replication, recombination and repair];
47-780 3.43e-38

ATP-dependent helicase/DNAse subunit B [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG3857:

Pssm-ID: 443066 [Multi-domain]  Cd Length: 1019  Bit Score: 153.36  E-value: 3.43e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876   47 ENKKIIDEEQRFLYLNEAVKNV--NLKALGISSSFNSFLKQsdyIYRFFLEISSENVSIESIASADtySYYEEHLEILIQ 124
Cdd:COG3857     76 ATRPLLSDAGKRMLLRKILEEHkdELKVFARAADKPGFIEQ---LAELITELKRYGITPEDLEEAA--ELLKEKLRDLAL 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  125 IYKNYLKILEKNsaidRINMHLFFNLNRDFIERYKKIK---IFFEGY--FTQFEFELVKDISQ-----IVDLEIEFISNE 194
Cdd:COG3857    151 IYEAYEEKLAGR----YIDSEDLLRLLAEKLEKSEFLEgaeIYIDGFtdFTPQELELLEALLKkakevTITLTLDPDELD 226

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  195 Y---NRKSIQKFIDYGFELETDKKYLINLSKKEI---VLSESLNEELDSLKIEGFSSRINQIAFIKNSVVEFI-NKGLDP 267
Cdd:COG3857    227 LfsaTGETYERLLELAKENGVEVEFKKSPELAHLernLFAYPPEEEPEGIEIIEAANRRAEVEAVAREIRRLVrEEGYRY 306

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  268 SKIALILPDES--FAKVLRLFDNEGY-FNYAMGIDIYDTRLYKTLDA-----------------INSSLV----DDEIKV 323
Cdd:COG3857    307 RDIAVVVRDLEayAPLIERVFAEYGIpYFIDEKRPLSHHPLVELILSllelvrsnfryedvfrlLKTGLLrplsREEIDR 386

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  324 IKN------------------------------LEYINIDFEFYNEIFSNSSKSFLTKDKFDKICEYLRSLEENRELLEK 373
Cdd:COG3857    387 LENyvlaygirgrrwleryleeeeeltdeeeedLERLNELRDRLLEPLLPLRERLKKAKTVREWAEALYEFLEELGVPEK 466

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  374 FDEVCFRYEK--LIFSQEQA--------IL-------------LKDAFKIFFQKVSSLTLDDINSGK--ITVMGLLESRL 428
Cdd:COG3857    467 LEEWREAEEAgdLEEAREHEqawnalieLLdelvevlgdeklsLEEFLRILESGLEELTFGLIPPSLdqVQVGGLDRARG 546

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  429 INFDAIIICDFNESLIPKRSLKDKFLSSALKQKVN------LPTVKDREDLQKYY-YQRLISNSKNVAISFVKNDSD--- 498
Cdd:COG3857    547 LDFKAVFVLGLNEGVFPARPREDGLLSDEERERLNelglelPPTSRERLLEERFLfYRALTRASERLYLSYPLADEEgka 626

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  499 -QISRFANRL---FEIKISEKLHDNEYKHILYSQNSLKHFNE--------DIVLDIDLSKLIWSASSLKEFLECKRKYYL 566
Cdd:COG3857    627 lLPSPLIDRLrelFPELEERSLLEEELEYIGTPESALSELAAalrqlelaPLWWDVYKWLLKLSVSRLETYAACPFQFFL 706

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  567 NHILKIKEHNI-SLKPRgyELGNIVHDSLEEYYKQDKRG----------------YEALLSIFNKYRSENPFLNLDLEIW 629
Cdd:COG3857    707 RYGLKLKEREEyELDAP--DRGTLFHAVLERFYKELKEEgldwadlsdeeleellEEAVEELAPELQNGILLSSARYRYL 784

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  630 KRKLKDFIEQEEKRFEK-----GYKIIALEKPF------------LCEYEGVKLQGKIDRIDVLADE---YFVIDYKTSS 689
Cdd:COG3857    785 LERLKRLLKRARRWLEEearrsGFEPVALELSFgpegglppleleLPNGRKIRLRGRIDRIDRLESDgryLRIIDYKSGS 864

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  690 nlKISTKRTFENATDFQLEFYFLALENLYNSNNINT---FYYDLYNMK---------------LLEEVALNEKLELLKS- 750
Cdd:COG3857    865 --KKFDLDDVYYGLALQLPLYLDAALENLEGKEAEPagaLYFHLKNPKlkakkplkklkmkglLLDDPEVLEIIPLKKDg 942

                          890       900       910       920       930       940
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  751 ------------------------------IINGFktTSVSFDKCENNQTCQYCVYKVIC 780
Cdd:COG3857    943 sfknskvlseeefeelldhvrellkeageeILAGD--FAINPYRTKDRTACQYCPYKSIC 1000
 
Name Accession Description Interval E-value
AddB COG3857
ATP-dependent helicase/DNAse subunit B [Replication, recombination and repair];
47-780 3.43e-38

ATP-dependent helicase/DNAse subunit B [Replication, recombination and repair];


Pssm-ID: 443066 [Multi-domain]  Cd Length: 1019  Bit Score: 153.36  E-value: 3.43e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876   47 ENKKIIDEEQRFLYLNEAVKNV--NLKALGISSSFNSFLKQsdyIYRFFLEISSENVSIESIASADtySYYEEHLEILIQ 124
Cdd:COG3857     76 ATRPLLSDAGKRMLLRKILEEHkdELKVFARAADKPGFIEQ---LAELITELKRYGITPEDLEEAA--ELLKEKLRDLAL 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  125 IYKNYLKILEKNsaidRINMHLFFNLNRDFIERYKKIK---IFFEGY--FTQFEFELVKDISQ-----IVDLEIEFISNE 194
Cdd:COG3857    151 IYEAYEEKLAGR----YIDSEDLLRLLAEKLEKSEFLEgaeIYIDGFtdFTPQELELLEALLKkakevTITLTLDPDELD 226

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  195 Y---NRKSIQKFIDYGFELETDKKYLINLSKKEI---VLSESLNEELDSLKIEGFSSRINQIAFIKNSVVEFI-NKGLDP 267
Cdd:COG3857    227 LfsaTGETYERLLELAKENGVEVEFKKSPELAHLernLFAYPPEEEPEGIEIIEAANRRAEVEAVAREIRRLVrEEGYRY 306

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  268 SKIALILPDES--FAKVLRLFDNEGY-FNYAMGIDIYDTRLYKTLDA-----------------INSSLV----DDEIKV 323
Cdd:COG3857    307 RDIAVVVRDLEayAPLIERVFAEYGIpYFIDEKRPLSHHPLVELILSllelvrsnfryedvfrlLKTGLLrplsREEIDR 386

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  324 IKN------------------------------LEYINIDFEFYNEIFSNSSKSFLTKDKFDKICEYLRSLEENRELLEK 373
Cdd:COG3857    387 LENyvlaygirgrrwleryleeeeeltdeeeedLERLNELRDRLLEPLLPLRERLKKAKTVREWAEALYEFLEELGVPEK 466

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  374 FDEVCFRYEK--LIFSQEQA--------IL-------------LKDAFKIFFQKVSSLTLDDINSGK--ITVMGLLESRL 428
Cdd:COG3857    467 LEEWREAEEAgdLEEAREHEqawnalieLLdelvevlgdeklsLEEFLRILESGLEELTFGLIPPSLdqVQVGGLDRARG 546

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  429 INFDAIIICDFNESLIPKRSLKDKFLSSALKQKVN------LPTVKDREDLQKYY-YQRLISNSKNVAISFVKNDSD--- 498
Cdd:COG3857    547 LDFKAVFVLGLNEGVFPARPREDGLLSDEERERLNelglelPPTSRERLLEERFLfYRALTRASERLYLSYPLADEEgka 626

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  499 -QISRFANRL---FEIKISEKLHDNEYKHILYSQNSLKHFNE--------DIVLDIDLSKLIWSASSLKEFLECKRKYYL 566
Cdd:COG3857    627 lLPSPLIDRLrelFPELEERSLLEEELEYIGTPESALSELAAalrqlelaPLWWDVYKWLLKLSVSRLETYAACPFQFFL 706

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  567 NHILKIKEHNI-SLKPRgyELGNIVHDSLEEYYKQDKRG----------------YEALLSIFNKYRSENPFLNLDLEIW 629
Cdd:COG3857    707 RYGLKLKEREEyELDAP--DRGTLFHAVLERFYKELKEEgldwadlsdeeleellEEAVEELAPELQNGILLSSARYRYL 784

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  630 KRKLKDFIEQEEKRFEK-----GYKIIALEKPF------------LCEYEGVKLQGKIDRIDVLADE---YFVIDYKTSS 689
Cdd:COG3857    785 LERLKRLLKRARRWLEEearrsGFEPVALELSFgpegglppleleLPNGRKIRLRGRIDRIDRLESDgryLRIIDYKSGS 864

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  690 nlKISTKRTFENATDFQLEFYFLALENLYNSNNINT---FYYDLYNMK---------------LLEEVALNEKLELLKS- 750
Cdd:COG3857    865 --KKFDLDDVYYGLALQLPLYLDAALENLEGKEAEPagaLYFHLKNPKlkakkplkklkmkglLLDDPEVLEIIPLKKDg 942

                          890       900       910       920       930       940
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  751 ------------------------------IINGFktTSVSFDKCENNQTCQYCVYKVIC 780
Cdd:COG3857    943 sfknskvlseeefeelldhvrellkeageeILAGD--FAINPYRTKDRTACQYCPYKSIC 1000
PDDEXK_1 pfam12705
PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease ...
 549-780 8.97e-30

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: 118.41  E-value: 8.97e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 549 WSASSLKEFLECKRKYYLNHILKIKEhNISLKPRgyELGNIVHDSLEEYYKQDKRGYEALLSIFNKY-----------RS 617
Cdd:pfam12705   2 LSPSRLETYLTCPLRFFLRYLLGLRE-DEELDAP--DLGTLVHAALERFYRWGRLPEEDLEELLQALleelwpelglqSE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 618 ENPFLNLDLEIWKRKLKDFIE--QEEKRFEKGYKIIALEKPFLceYEGVKLQGKIDRIDVLADEYF-VIDYKTSSNLKis 694
Cdd:pfam12705  79 ILPRLPWLAGRLRRRLERMLRrlAEWLRARRGFRPVAVELGFG--GTTVRLVGRIDRVDLDGEGYLrIIDYKTGSAPP-- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 695 TKRTFENATDFQLEFYFLALE--NLYNSNNINTFYYDLYNM-----KLLEEVALNEK---------LELLKSIINGFktt 758
Cdd:pfam12705 155 QSEDLDLYEGLQLLLYLLALAagEKALGGPAGALYLRLDDPlkkdeEVVEPMVLTEDefdallqelRELAEEILAGE--- 231

                         250       260
                  ....*....|....*....|..
gi 1441214876 759 svsFDKCEnNQTCQYCVYKVIC 780
Cdd:pfam12705 232 ---FPARP-GKKCRYCPYRSIC 249
TIGR03623 TIGR03623
probable DNA repair protein; Members of this protein family are bacterial proteins of about ...
 418-713 1.54e-12

probable DNA repair protein; Members of this protein family are bacterial proteins of about 900 amino acids in length. Members show extended homology to proteins in TIGR02786, the AddB protein of double-strand break repair via homologous recombination. Members of this family, therefore, may be DNA repair proteins.


Pssm-ID: 274682 [Multi-domain]  Cd Length: 874  Bit Score: 71.23  E-value: 1.54e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 418 ITVMGLLESRLINFDAIIICDFNESLIPKRSLKDKFLSSALKQKVNLP-TVKDRE-DLQKYYYQRLISNSKNVAISFVKN 495
Cdd:TIGR03623 459 IQVLGLLEAAGLQFDALWVMGLTDEQWPAPPRPNPFLPLALQRAVGMPhASAERElDYARQVTQRLLKSAPEVVFSYPRR 538

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 496 DSDQISR----------FANRLFEIKISEKLHDNEYKhilysQNSLKHFNEDIVLDIDLSKLIWSASS-LKEFLECKRKY 564
Cdd:TIGR03623 539 DGDRELRpspliahlplKAEEDAELADYQDLAAAVAA-----GSRLEVLDDAQAPPLAAGERISGGTGlLKAQAACPFRA 613

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 565 YLNHILKIKEHN-ISLKPRGYELGNIVHDSLEEYYKQDKrGYEALLSI----------------FNKYRSENP------F 621
Cdd:TIGR03623 614 FAQHRLGARALEePVDGLDALERGTLVHRVLELFWERLK-NQEALNALdeaeleqliaeaieeaLAEERARHSqtfperF 692

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 622 LNLDLEIWKRKLKDFIEQEEKRfeKGYKIIALEKPFLCEYEGVKLQGKIDRIDVLAD-EYFVIDYKTSSNlkiSTKRTF- 699
Cdd:TIGR03623 693 LELEQERLLQLLLEWLELERKR--PPFEVVATEQNHSIEIGGLELKLRIDRIDRLADgSRLIIDYKTGAP---SVKDWLg 767

                         330
                  ....*....|....
gi 1441214876 700 ENATDFQLEFYFLA 713
Cdd:TIGR03623 768 ERPVEPQLPLYALL 781
Cas4_I-A_I-B_I-C_I-D_II-B cd09637
CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short ...
 628-780 1.49e-08

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: 55.13  E-value: 1.49e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 628 IWKRKLKDFIEQEEKRFEKGYKI-------------IALEKPFLCEYEGVKLQGKIDRIDVLADEYFVIDYKTSSnlKIS 694
Cdd:cd09637    16 LWYMKCLGISERPTESMELGRLIheraevalkarfgVREEKEVPLKSKKYGLKGVIDIVLKEDGELVPVEVKSGR--AGS 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 695 TKRTFEnatdFQLEFYFLALENLYNsNNINTFYYDLYNMKLLEEVALNEKL--------ELLKSIINGFKTTSVSFDKce 766
Cdd:cd09637    94 PREAHK----LQLVAYAYLLEEMYG-KRVARGYIVYLEGGKRLEVEISEELrkkaekllEEIRKLLEGELPPPVKSSP-- 166

                         170
                  ....*....|....
gi 1441214876 767 nnqTCQYCVYKVIC 780
Cdd:cd09637   167 ---KCKFCPYREIC 177
PRK13909 PRK13909
RecB-like helicase;
587-723 4.99e-03

RecB-like helicase;


Pssm-ID: 237554 [Multi-domain]  Cd Length: 910  Bit Score: 40.34  E-value: 4.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 587 GNIVHDSLEEYYKQDKRGYE-ALLSIFNKYRSenpFLN-LDLEIWKRKLKDFIEQEEKRFEKGYKIIALEKPFlceyegv 664
Cdd:PRK13909  770 GIALHYCLEMLYAFKIENLEvLKNLLKNRYGH---FLDeSDLEDLEKRLELLINNKEFQALLKDGKLLKEQAL------- 839

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1441214876 665 KLQGKIDRIDVLA---DEYFVIDYKTSSNLKISTKRtfenatdfQLEFYFLALENLYNSNNI 723
Cdd:PRK13909  840 LFNGELKQIDLLLekdEEICVIDYKSSKKYQEEHKA--------QVSHYKEAIKEILPKKKV 893
 
Name Accession Description Interval E-value
AddB COG3857
ATP-dependent helicase/DNAse subunit B [Replication, recombination and repair];
47-780 3.43e-38

ATP-dependent helicase/DNAse subunit B [Replication, recombination and repair];


Pssm-ID: 443066 [Multi-domain]  Cd Length: 1019  Bit Score: 153.36  E-value: 3.43e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876   47 ENKKIIDEEQRFLYLNEAVKNV--NLKALGISSSFNSFLKQsdyIYRFFLEISSENVSIESIASADtySYYEEHLEILIQ 124
Cdd:COG3857     76 ATRPLLSDAGKRMLLRKILEEHkdELKVFARAADKPGFIEQ---LAELITELKRYGITPEDLEEAA--ELLKEKLRDLAL 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  125 IYKNYLKILEKNsaidRINMHLFFNLNRDFIERYKKIK---IFFEGY--FTQFEFELVKDISQ-----IVDLEIEFISNE 194
Cdd:COG3857    151 IYEAYEEKLAGR----YIDSEDLLRLLAEKLEKSEFLEgaeIYIDGFtdFTPQELELLEALLKkakevTITLTLDPDELD 226

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  195 Y---NRKSIQKFIDYGFELETDKKYLINLSKKEI---VLSESLNEELDSLKIEGFSSRINQIAFIKNSVVEFI-NKGLDP 267
Cdd:COG3857    227 LfsaTGETYERLLELAKENGVEVEFKKSPELAHLernLFAYPPEEEPEGIEIIEAANRRAEVEAVAREIRRLVrEEGYRY 306

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  268 SKIALILPDES--FAKVLRLFDNEGY-FNYAMGIDIYDTRLYKTLDA-----------------INSSLV----DDEIKV 323
Cdd:COG3857    307 RDIAVVVRDLEayAPLIERVFAEYGIpYFIDEKRPLSHHPLVELILSllelvrsnfryedvfrlLKTGLLrplsREEIDR 386

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  324 IKN------------------------------LEYINIDFEFYNEIFSNSSKSFLTKDKFDKICEYLRSLEENRELLEK 373
Cdd:COG3857    387 LENyvlaygirgrrwleryleeeeeltdeeeedLERLNELRDRLLEPLLPLRERLKKAKTVREWAEALYEFLEELGVPEK 466

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  374 FDEVCFRYEK--LIFSQEQA--------IL-------------LKDAFKIFFQKVSSLTLDDINSGK--ITVMGLLESRL 428
Cdd:COG3857    467 LEEWREAEEAgdLEEAREHEqawnalieLLdelvevlgdeklsLEEFLRILESGLEELTFGLIPPSLdqVQVGGLDRARG 546

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  429 INFDAIIICDFNESLIPKRSLKDKFLSSALKQKVN------LPTVKDREDLQKYY-YQRLISNSKNVAISFVKNDSD--- 498
Cdd:COG3857    547 LDFKAVFVLGLNEGVFPARPREDGLLSDEERERLNelglelPPTSRERLLEERFLfYRALTRASERLYLSYPLADEEgka 626

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  499 -QISRFANRL---FEIKISEKLHDNEYKHILYSQNSLKHFNE--------DIVLDIDLSKLIWSASSLKEFLECKRKYYL 566
Cdd:COG3857    627 lLPSPLIDRLrelFPELEERSLLEEELEYIGTPESALSELAAalrqlelaPLWWDVYKWLLKLSVSRLETYAACPFQFFL 706

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  567 NHILKIKEHNI-SLKPRgyELGNIVHDSLEEYYKQDKRG----------------YEALLSIFNKYRSENPFLNLDLEIW 629
Cdd:COG3857    707 RYGLKLKEREEyELDAP--DRGTLFHAVLERFYKELKEEgldwadlsdeeleellEEAVEELAPELQNGILLSSARYRYL 784

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  630 KRKLKDFIEQEEKRFEK-----GYKIIALEKPF------------LCEYEGVKLQGKIDRIDVLADE---YFVIDYKTSS 689
Cdd:COG3857    785 LERLKRLLKRARRWLEEearrsGFEPVALELSFgpegglppleleLPNGRKIRLRGRIDRIDRLESDgryLRIIDYKSGS 864

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  690 nlKISTKRTFENATDFQLEFYFLALENLYNSNNINT---FYYDLYNMK---------------LLEEVALNEKLELLKS- 750
Cdd:COG3857    865 --KKFDLDDVYYGLALQLPLYLDAALENLEGKEAEPagaLYFHLKNPKlkakkplkklkmkglLLDDPEVLEIIPLKKDg 942

                          890       900       910       920       930       940
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876  751 ------------------------------IINGFktTSVSFDKCENNQTCQYCVYKVIC 780
Cdd:COG3857    943 sfknskvlseeefeelldhvrellkeageeILAGD--FAINPYRTKDRTACQYCPYKSIC 1000
Slr0479 COG2887
RecB family exonuclease [Replication, recombination and repair];
549-780 2.89e-32

RecB family exonuclease [Replication, recombination and repair];


Pssm-ID: 442133 [Multi-domain]  Cd Length: 248  Bit Score: 125.53  E-value: 2.89e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 549 WSASSLKEFLECKRKYYLNHILKIKEhNISLKPRGYELGNIVHDSLEEYYKQ--DKRGYEALLSI----FNKYRSENP-F 621
Cdd:COG2887     3 LSPSRIETLLRCPLRYYARYILGLRD-PLEPPPDAADRGTLVHAVLERFYKLpaDELPAEELLALleeaWAELGFEDPwA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 622 LNLDLEIWKRKLKDFIEQEEKRfeKGYKIIALEKPFLCEYE-GVKLQGKIDRIDVLAD-EYFVIDYKTSSNlkISTKrtF 699
Cdd:COG2887    82 AALWLERAERLLEAFLEWERAP--AGLEPVAVEVEFELELPgGVRLRGRIDRIDRLPDgRLVVVDYKTGKA--PSTK--D 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 700 ENATDFQLEFYFLALENLYNSNNINT--FYY--DLYNMKLLE--EVALNEKLELLKSIINGFKTTSVSFDKCENNQTCQY 773
Cdd:COG2887   156 EAGEDPQLALYALALERGFEGLVPAGarLVYlgDLGKKKVLDplEEELEEAEERLEELAAAIADPEGPFPARPNPPLCRY 235


                  ....*..
gi 1441214876 774 CVYKVIC 780
Cdd:COG2887   236 CDYRHLC 242
PDDEXK_1 pfam12705
PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease ...
 549-780 8.97e-30

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: 118.41  E-value: 8.97e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 549 WSASSLKEFLECKRKYYLNHILKIKEhNISLKPRgyELGNIVHDSLEEYYKQDKRGYEALLSIFNKY-----------RS 617
Cdd:pfam12705   2 LSPSRLETYLTCPLRFFLRYLLGLRE-DEELDAP--DLGTLVHAALERFYRWGRLPEEDLEELLQALleelwpelglqSE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 618 ENPFLNLDLEIWKRKLKDFIE--QEEKRFEKGYKIIALEKPFLceYEGVKLQGKIDRIDVLADEYF-VIDYKTSSNLKis 694
Cdd:pfam12705  79 ILPRLPWLAGRLRRRLERMLRrlAEWLRARRGFRPVAVELGFG--GTTVRLVGRIDRVDLDGEGYLrIIDYKTGSAPP-- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 695 TKRTFENATDFQLEFYFLALE--NLYNSNNINTFYYDLYNM-----KLLEEVALNEK---------LELLKSIINGFktt 758
Cdd:pfam12705 155 QSEDLDLYEGLQLLLYLLALAagEKALGGPAGALYLRLDDPlkkdeEVVEPMVLTEDefdallqelRELAEEILAGE--- 231

                         250       260
                  ....*....|....*....|..
gi 1441214876 759 svsFDKCEnNQTCQYCVYKVIC 780
Cdd:pfam12705 232 ---FPARP-GKKCRYCPYRSIC 249
TIGR03623 TIGR03623
probable DNA repair protein; Members of this protein family are bacterial proteins of about ...
 418-713 1.54e-12

probable DNA repair protein; Members of this protein family are bacterial proteins of about 900 amino acids in length. Members show extended homology to proteins in TIGR02786, the AddB protein of double-strand break repair via homologous recombination. Members of this family, therefore, may be DNA repair proteins.


Pssm-ID: 274682 [Multi-domain]  Cd Length: 874  Bit Score: 71.23  E-value: 1.54e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 418 ITVMGLLESRLINFDAIIICDFNESLIPKRSLKDKFLSSALKQKVNLP-TVKDRE-DLQKYYYQRLISNSKNVAISFVKN 495
Cdd:TIGR03623 459 IQVLGLLEAAGLQFDALWVMGLTDEQWPAPPRPNPFLPLALQRAVGMPhASAERElDYARQVTQRLLKSAPEVVFSYPRR 538

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 496 DSDQISR----------FANRLFEIKISEKLHDNEYKhilysQNSLKHFNEDIVLDIDLSKLIWSASS-LKEFLECKRKY 564
Cdd:TIGR03623 539 DGDRELRpspliahlplKAEEDAELADYQDLAAAVAA-----GSRLEVLDDAQAPPLAAGERISGGTGlLKAQAACPFRA 613

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 565 YLNHILKIKEHN-ISLKPRGYELGNIVHDSLEEYYKQDKrGYEALLSI----------------FNKYRSENP------F 621
Cdd:TIGR03623 614 FAQHRLGARALEePVDGLDALERGTLVHRVLELFWERLK-NQEALNALdeaeleqliaeaieeaLAEERARHSqtfperF 692

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 622 LNLDLEIWKRKLKDFIEQEEKRfeKGYKIIALEKPFLCEYEGVKLQGKIDRIDVLAD-EYFVIDYKTSSNlkiSTKRTF- 699
Cdd:TIGR03623 693 LELEQERLLQLLLEWLELERKR--PPFEVVATEQNHSIEIGGLELKLRIDRIDRLADgSRLIIDYKTGAP---SVKDWLg 767

                         330
                  ....*....|....
gi 1441214876 700 ENATDFQLEFYFLA 713
Cdd:TIGR03623 768 ERPVEPQLPLYALL 781
COG3893 COG3893
Inactivated superfamily I helicase [Replication, recombination and repair];
418-507 5.12e-10

Inactivated superfamily I helicase [Replication, recombination and repair];


Pssm-ID: 443100 [Multi-domain]  Cd Length: 965  Bit Score: 63.27  E-value: 5.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 418 ITVMGLLESRLINFDAIIICDFNE-SLiPKRSLKDKFLSSALKQKVNLPTVKDREDLQKYYYQRLISNsKNVAISFVKND 496
Cdd:COG3893   551 VQILGLLEARLQRFDAVILGGLNEgVW-PPAPRPDPWLSRPMRRALGLPTPERRIGLAAHDFAQALGA-PEVVLSRARRS 628

                          90
                  ....*....|....
gi 1441214876 497 SDQ---ISRFANRL 507
Cdd:COG3893   629 DGAptvPSRWLQRL 642
cas4 TIGR00372
CRISPR-associated protein Cas4; This model represents a family of proteins associated with ...
 637-780 4.17e-09

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: 56.65  E-value: 4.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 637 IEQEEKRFEKGYKIIALEKPFLCEYEGVKLQGKIDRIDVLADEYFVIDYKTSsnlkistKRTFENATDFQLEFYFLALEN 716
Cdd:TIGR00372  38 IHEEAESFLKSLGEVREEKEVPLKSKKYGLKGVIDIVLEEDGELVPVEVKSG-------KPSPREAHKYQLLAYAYLLEE 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1441214876 717 LYNSNNINTFYYDLYNMKLleEVALNEKL--------ELLKSIINGFKTTSVSFDKCEnnqtCQYCVYKVIC 780
Cdd:TIGR00372 111 MYGEIVRGYILYINAGKKL--EVEISEELrkkavkliEKIRELLEGGKPPSPPKSGPK----CKFCPYREIC 176
Cas4_I-A_I-B_I-C_I-D_II-B cd09637
CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short ...
 628-780 1.49e-08

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: 55.13  E-value: 1.49e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 628 IWKRKLKDFIEQEEKRFEKGYKI-------------IALEKPFLCEYEGVKLQGKIDRIDVLADEYFVIDYKTSSnlKIS 694
Cdd:cd09637    16 LWYMKCLGISERPTESMELGRLIheraevalkarfgVREEKEVPLKSKKYGLKGVIDIVLKEDGELVPVEVKSGR--AGS 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 695 TKRTFEnatdFQLEFYFLALENLYNsNNINTFYYDLYNMKLLEEVALNEKL--------ELLKSIINGFKTTSVSFDKce 766
Cdd:cd09637    94 PREAHK----LQLVAYAYLLEEMYG-KRVARGYIVYLEGGKRLEVEISEELrkkaekllEEIRKLLEGELPPPVKSSP-- 166

                         170
                  ....*....|....
gi 1441214876 767 nnqTCQYCVYKVIC 780
Cdd:cd09637   167 ---KCKFCPYREIC 177
RecB COG1074
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 585-728 3.01e-06

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: 50.73  E-value: 3.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 585 ELGNIVHDSLEEYykqDKRGYEALLSIFNKYRSENPFLNLDLEIWKRKLKDFIEQEE-KRFEKGYKIIAlEKPF----LC 659
Cdd:COG1074   713 RRGTLVHRLLEHL---DFSAPAELRAALARLLARGGLDEEEAEALAEALLAFLATPLlAELFAAAEVLR-EVPFllpdLY 788

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1441214876 660 EYEGVKLQGKIDRIDVLADEYFVIDYKTSSNLKISTKRTFEnATDFQLEFYFLALENLYNSNNINTFYY 728
Cdd:COG1074   789 RGLGGLLKGRIDLVFEDDGRVYIVDYKTNRLGPDDEEYLPE-RYRLQLALYALALERLLPGRPVRAGLY 856
Cas4 COG1468
CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas ...
 552-780 5.28e-06

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: 47.65  E-value: 5.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 552 SSLKEFLECKRKYYLNHILKIKEHNislkPRGYELGNIVHDSLEEYYKQDKRgyeallsifnkyrsenpflnlDLEIWKR 631
Cdd:COG1468    10 SAIQYYLYCPRKLWLIHVIGLEWEE----NERVALGRLLHERVYKRLERLRR---------------------EVPLDSE 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 632 KLKdfieqeekrfekgykiialekpflceyegvkLQGKIDRIDVLADEYFVIDYKTSsnlkistKRTFENATDFQLEFYF 711
Cdd:COG1468    65 RLG-------------------------------LTGKIDLVEFEDGELVPVEYKKS-------KPKPWEADRMQLCAYA 106

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1441214876 712 LALENLYNSNNINTF-YYdlYNMKLLEEVALNEKL--------ELLKSIINGFKTTSVSFDKCEnnqtCQYCVYKVIC 780
Cdd:COG1468   107 LLLEEMLGIPVPKGYlYY--PEERKREEVELTEELreeveeaiEEIREILESEKPPPPTKSKKK----CKKCSYREFC 178
PRK13909 PRK13909
RecB-like helicase;
587-723 4.99e-03

RecB-like helicase;


Pssm-ID: 237554 [Multi-domain]  Cd Length: 910  Bit Score: 40.34  E-value: 4.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1441214876 587 GNIVHDSLEEYYKQDKRGYE-ALLSIFNKYRSenpFLN-LDLEIWKRKLKDFIEQEEKRFEKGYKIIALEKPFlceyegv 664
Cdd:PRK13909  770 GIALHYCLEMLYAFKIENLEvLKNLLKNRYGH---FLDeSDLEDLEKRLELLINNKEFQALLKDGKLLKEQAL------- 839

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1441214876 665 KLQGKIDRIDVLA---DEYFVIDYKTSSNLKISTKRtfenatdfQLEFYFLALENLYNSNNI 723
Cdd:PRK13909  840 LFNGELKQIDLLLekdEEICVIDYKSSKKYQEEHKA--------QVSHYKEAIKEILPKKKV 893
 
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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