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Conserved domains on  [gi|818812357|gb|KKU51562|]
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MAG: site-specific tyrosine recombinase XerD [Parcubacteria group bacterium GW2011_GWA2_47_10]

Protein Classification

site-specific integrase( domain architecture ID 332)

tyrosine based site-specific recombinase (integrase) is involved in cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct

CATH:  1.10.443.10
Gene Ontology:  GO:0015074|GO:0003677|GO:0006310
PubMed:  10577069|10047575|9278480
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 1-299 7.07e-89

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


The actual alignment was detected with superfamily member PRK00236:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 297  Bit Score: 267.02  E-value: 7.07e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   1 MNLERLLKDYLEHLEIEKNRSLKTVENYERYLKRFLEFTKVSSPKDISDDVVREFRLQLNRMRDRFDH--TLKRqtqfyH 78
Cdd:PRK00236   4 ADLPAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLDAADLRSFLARRRRQGLSarSLAR-----R 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  79 LIALRNFLKYMAKRD-IKTLAAEKIELGKVSQLQVEFLEGEEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSL 157
Cdd:PRK00236  79 LSALRSFYRWLVRRGlLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSELVGL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 158 NRESVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLDKRADI---EEPLFVSApKGKktqnsnptRLTPRSIQRLIKK 234
Cdd:PRK00236 159 DIDDLDLASGTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFlpdDDALFLGA-RGG--------RLSPRVVQRRVKK 229

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818812357 235 YSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:PRK00236 230 LGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAH 294
 
Name Accession Description Interval E-value
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-299 7.07e-89

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 267.02  E-value: 7.07e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   1 MNLERLLKDYLEHLEIEKNRSLKTVENYERYLKRFLEFTKVSSPKDISDDVVREFRLQLNRMRDRFDH--TLKRqtqfyH 78
Cdd:PRK00236   4 ADLPAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLDAADLRSFLARRRRQGLSarSLAR-----R 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  79 LIALRNFLKYMAKRD-IKTLAAEKIELGKVSQLQVEFLEGEEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSL 157
Cdd:PRK00236  79 LSALRSFYRWLVRRGlLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSELVGL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 158 NRESVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLDKRADI---EEPLFVSApKGKktqnsnptRLTPRSIQRLIKK 234
Cdd:PRK00236 159 DIDDLDLASGTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFlpdDDALFLGA-RGG--------RLSPRVVQRRVKK 229

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818812357 235 YSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:PRK00236 230 LGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAH 294
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
1-299 7.45e-89

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 266.86  E-value: 7.45e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   1 MNLERLLKDYLEHLEIEKNRSLKTVENYERYLKRFLEF---TKVSSPKDISDDVVREFrlqLNRMRDRfdhTLKRQTQFY 77
Cdd:COG4974    1 LTLADLLEAFLEELKREKGLSPNTIKAYRRDLRRFLRFleeLGKIPLAEITPEDIRAY---LNYLRER---GLSPSTINR 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  78 HLIALRNFLKYMAKRD-IKTLAAEKIELGKVSQLQVEFLEGEEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCS 156
Cdd:COG4974   75 YLAALRSFFRYAVREGlLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLG 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 157 LNRESVNLARDEFSIR-GKGQKIRVVFLSSEAKATLKTYLDKRADI-EEPLFVsapkgkktqNSNPTRLTPRSIQRLIKK 234
Cdd:COG4974  155 LKWSDIDLDRGTIRVRrGKGGKERTVPLSPEALEALREYLEERRPRdSDYLFP---------TRRGRPLSRRAIRKILKR 225

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818812357 235 YSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:COG4974  226 LAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 8-299 7.97e-79

tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 241.36  E-value: 7.97e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357    8 KDYLEHLEIEKNRSLKTVENYERYLKRFLEF----TKVSSPKDISDDVVREFRLQLNrmrdrfDHTLKRQTQFYHLIALR 83
Cdd:TIGR02224   1 EAFLEYLRLERNYSPHTVRAYRRDLEAFLEFleeeGGLASLAEVTAADLRSFLAELH------ARGLSRRSLARKLSALR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   84 NFLKYMAKRD-IKTLAAEKIELGKVSQLQVEFLEGEEVNRLLSATS--GNSLQNFRDRALLELLFSTGLRISELCSLNRE 160
Cdd:TIGR02224  75 SFYRFLLRRGlIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEedDEDWLALRDRAILELLYSSGLRVSELVGLDLS 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  161 SVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLDKR------ADIEEPLFVSApKGKktqnsnptRLTPRSIQRLIKK 234
Cdd:TIGR02224 155 DLDLDFGEVRVRGKGNKERIVPFGPYARDALQAYLEARrspllaSEGQDALFLNR-RGG--------RLTPRGVQYRLQQ 225

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818812357  235 YSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:TIGR02224 226 LRAKAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAH 290
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 118-287 9.51e-71

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 216.61  E-value: 9.51e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 118 EEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLDK 197
Cdd:cd00798    2 DEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 198 R------ADIEEPLFVSApKGKktqnsnptRLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQAL 271
Cdd:cd00798   82 RrplllkKKPPDALFLNK-RGK--------RLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQEL 152

                        170
                 ....*....|....*.
gi 818812357 272 LGHSSITTTQRYTHVT 287
Cdd:cd00798  153 LGHASLSTTQIYTHVS 168
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 114-288 4.57e-46

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 153.24  E-value: 4.57e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  114 FLEGEEVNRLLSATSGNSLQnFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSI-RGKGQKIRVVFLSSEAKATLK 192
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLS-IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVhRGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  193 TYLDKRADIEEP---LFVSAPKGkktqnsnptRLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQ 269
Cdd:pfam00589  80 EWLSKRLLEAPKsdyLFASKRGK---------PLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQ 150

                         170
                  ....*....|....*....
gi 818812357  270 ALLGHSSITTTQRYTHVTD 288
Cdd:pfam00589 151 KLLGHSSISTTQIYTHVAD 169
 
Name Accession Description Interval E-value
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-299 7.07e-89

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 267.02  E-value: 7.07e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   1 MNLERLLKDYLEHLEIEKNRSLKTVENYERYLKRFLEFTKVSSPKDISDDVVREFRLQLNRMRDRFDH--TLKRqtqfyH 78
Cdd:PRK00236   4 ADLPAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLDAADLRSFLARRRRQGLSarSLAR-----R 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  79 LIALRNFLKYMAKRD-IKTLAAEKIELGKVSQLQVEFLEGEEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSL 157
Cdd:PRK00236  79 LSALRSFYRWLVRRGlLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSELVGL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 158 NRESVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLDKRADI---EEPLFVSApKGKktqnsnptRLTPRSIQRLIKK 234
Cdd:PRK00236 159 DIDDLDLASGTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFlpdDDALFLGA-RGG--------RLSPRVVQRRVKK 229

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818812357 235 YSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:PRK00236 230 LGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAH 294
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
1-299 7.45e-89

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 266.86  E-value: 7.45e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   1 MNLERLLKDYLEHLEIEKNRSLKTVENYERYLKRFLEF---TKVSSPKDISDDVVREFrlqLNRMRDRfdhTLKRQTQFY 77
Cdd:COG4974    1 LTLADLLEAFLEELKREKGLSPNTIKAYRRDLRRFLRFleeLGKIPLAEITPEDIRAY---LNYLRER---GLSPSTINR 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  78 HLIALRNFLKYMAKRD-IKTLAAEKIELGKVSQLQVEFLEGEEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCS 156
Cdd:COG4974   75 YLAALRSFFRYAVREGlLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLG 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 157 LNRESVNLARDEFSIR-GKGQKIRVVFLSSEAKATLKTYLDKRADI-EEPLFVsapkgkktqNSNPTRLTPRSIQRLIKK 234
Cdd:COG4974  155 LKWSDIDLDRGTIRVRrGKGGKERTVPLSPEALEALREYLEERRPRdSDYLFP---------TRRGRPLSRRAIRKILKR 225

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818812357 235 YSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:COG4974  226 LAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 8-299 7.97e-79

tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 241.36  E-value: 7.97e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357    8 KDYLEHLEIEKNRSLKTVENYERYLKRFLEF----TKVSSPKDISDDVVREFRLQLNrmrdrfDHTLKRQTQFYHLIALR 83
Cdd:TIGR02224   1 EAFLEYLRLERNYSPHTVRAYRRDLEAFLEFleeeGGLASLAEVTAADLRSFLAELH------ARGLSRRSLARKLSALR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   84 NFLKYMAKRD-IKTLAAEKIELGKVSQLQVEFLEGEEVNRLLSATS--GNSLQNFRDRALLELLFSTGLRISELCSLNRE 160
Cdd:TIGR02224  75 SFYRFLLRRGlIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEedDEDWLALRDRAILELLYSSGLRVSELVGLDLS 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  161 SVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLDKR------ADIEEPLFVSApKGKktqnsnptRLTPRSIQRLIKK 234
Cdd:TIGR02224 155 DLDLDFGEVRVRGKGNKERIVPFGPYARDALQAYLEARrspllaSEGQDALFLNR-RGG--------RLTPRGVQYRLQQ 225

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818812357  235 YSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:TIGR02224 226 LRAKAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAH 290
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 9-299 8.59e-78

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 238.64  E-value: 8.59e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357    9 DYLEHLEIEKNRSLKTVENYERYLKRFLEF--TKVSSPKDISDDVVREFrlqLNRMRDRfdhTLKRQTQFYHLIALRNFL 86
Cdd:TIGR02225   2 QFLDYLWVERGLSQNTLEAYRRDLEKFLEFleERGIDLEEVDRGDIVDF---LAELKEA---GLSARSIARALSALRSFY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   87 KYMAKRDIKTL-AAEKIELGKVSQLQVEFLEGEEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLA 165
Cdd:TIGR02225  76 RFLLREGIREDdPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLD 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  166 RDEFSIRGKGQKIRVVFLSSEAKATLKTYLDKRADI--------EEPLFVSApKGKktqnsnptRLTPRSIQRLIKKYSA 237
Cdd:TIGR02225 156 EGFVRVRGKGNKERLVPLGEEAIEALERYLKEARPLllkkkvkeSDALFLNR-RGG--------PLSRQGVWKILKEYAK 226

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 818812357  238 AAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:TIGR02225 227 RAGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHH 288
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
1-296 9.88e-72

Site-specific recombinase XerC [Replication, recombination and repair];


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 223.30  E-value: 9.88e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   1 MNLERLLKDYLEHLEiEKNRSLKTVENYERYLKRFLEF--TKVSSPKDISDDVVREFrlqLNRMRDRfdhTLKRQTQFYH 78
Cdd:COG4973    2 LTLAEALEAYLEHLR-ERRLSPKTLEAYRRDLRRLIPLlgDADLPLEELTPADVRRF---LARLHRR---GLSPRTLNRR 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  79 LIALRNFLKYMAKRD-IKTLAAEKIELGKVSQLQVEFLEGEEVNRLLSATSGNSLqNFRDRALLELLFSTGLRISELCSL 157
Cdd:COG4973   75 LSALRSFFNWAVREGlLEANPAAGVKAPKAPRKLPRALTVDELAQLLDALADDPL-AVRDRAIVELLYSTGLRLGELVGL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 158 NRESVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLDKRADI----EEPLFVSaPKGkktqnsnpTRLTPRSIQRLIK 233
Cdd:COG4973  154 DWEDVDLDAGEVRVRGKTGKSRTVPLGPKALAALREWLAVRPELaapdEGALFPS-RRG--------TRLSPRNVQKRLR 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818812357 234 KYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHK 296
Cdd:COG4973  225 RLAKKAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVYR 287
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 118-287 9.51e-71

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 216.61  E-value: 9.51e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 118 EEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLDK 197
Cdd:cd00798    2 DEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 198 R------ADIEEPLFVSApKGKktqnsnptRLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQAL 271
Cdd:cd00798   82 RrplllkKKPPDALFLNK-RGK--------RLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQEL 152

                        170
                 ....*....|....*.
gi 818812357 272 LGHSSITTTQRYTHVT 287
Cdd:cd00798  153 LGHASLSTTQIYTHVS 168
xerD PRK00283
tyrosine recombinase;
1-299 6.50e-70

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 218.91  E-value: 6.50e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   1 MNLERLLKDYLEHLEIEKNRSLKTVENYERYLKRFLEFTKVS--SPKDISDDVVREFrlqlnrMRDRFDHTLKRQTQFYH 78
Cdd:PRK00283   3 MADRALIEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARglSLAEATRDDLQAF------LAELAEGGYKATSSARR 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  79 LIALRNFLKYmakrdiktLAAEK---------IELGKVSQLQVEFLEGEEVNRLLSATSGNSLQNFRDRALLELLFSTGL 149
Cdd:PRK00283  77 LSALRRFFQF--------LLREGlreddpsalLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGL 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 150 RISELCSLNRESVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLDKRADI------EEPLFVSApKGKktqnsnptRL 223
Cdd:PRK00283 149 RVSELVGLTLDDVSLRQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGRPAllngrsSDALFPSA-RGG--------QL 219

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 818812357 224 TPRSIQRLIKKYSAAAGI-TKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:PRK00283 220 TRQTFWHRIKHYAKRAGIdPKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHH 296
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 113-286 5.06e-48

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 158.59  E-value: 5.06e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 113 EFLEGEEVNRLLsatsgNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIR-GKGQKIRVVFLSSEAKATL 191
Cdd:cd01193    4 VVLSPDEVRRIL-----GALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRqGKGGKDRVVPLPEKLLEPL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 192 KTYLDKRADIEEpLFVSAPKGKKTQNSNPTR----LTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRS 267
Cdd:cd01193   79 RRYLKSARPKEE-LDPAEGRAGVLDPRTGVErrhhISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRT 157

                        170
                 ....*....|....*....
gi 818812357 268 VQALLGHSSITTTQRYTHV 286
Cdd:cd01193  158 IQELLGHSDLSTTMIYTHV 176
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 3-299 5.35e-47

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 161.45  E-value: 5.35e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   3 LERLLKDYLEHLeIEKNRSLKTVENYERYLKRFL---EFTKVSSPKDISDDVVREFRLQLNRMRDRFDHTLKRQTQFYHL 79
Cdd:PRK01287  21 LRQLLERFLAWL-QERNWSERTLKVYTEHLYPFIlwcEERGLYYAADVTLPVLERYQRYLYGYRKANGEPLSTRTQRTQL 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  80 IALRNFLKYMAKRD-IKTLAAEKIELGKVSQ-LQVEFLEGEEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSL 157
Cdd:PRK01287 100 SPLRVWFRWLLKRHhILYNPAEDLELPKEEKrLPRQILSEAETEQVLASPDLTTLQGLRDRALLELLWSTGIRRGELARL 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 158 NRESVNLARDEFSIR-GKGQKIRVVFLSSEAKATLKTYLDK-------RADIEEpLFVSApKGkktqnsnpTRLTPRSIQ 229
Cdd:PRK01287 180 DLYDVDASRGVVTVRqGKGNKDRVVPVGERALAWLQRYLQDvrpqlavRPDSGA-LFVAM-DG--------DGLARNTLT 249

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 230 RLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDIHKKYH 299
Cdd:PRK01287 250 NMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAVHASTH 319
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 114-288 4.57e-46

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 153.24  E-value: 4.57e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  114 FLEGEEVNRLLSATSGNSLQnFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSI-RGKGQKIRVVFLSSEAKATLK 192
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLS-IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVhRGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  193 TYLDKRADIEEP---LFVSAPKGkktqnsnptRLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQ 269
Cdd:pfam00589  80 EWLSKRLLEAPKsdyLFASKRGK---------PLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQ 150

                         170
                  ....*....|....*....
gi 818812357  270 ALLGHSSITTTQRYTHVTD 288
Cdd:pfam00589 151 KLLGHSSISTTQIYTHVAD 169
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 119-284 3.89e-45

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 150.71  E-value: 3.89e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 119 EVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIRGKGQ---KIRVVFLSSEAKATLKTYL 195
Cdd:cd00397    1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTkggKERTVPLPKELAEELKEYL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 196 DKRADIEEPLFVSAPKGKKTQNSNPTRLTPRSIQRLIKKYSAAAGitKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHS 275
Cdd:cd00397   81 KERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAG--RKITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158


                 ....*....
gi 818812357 276 SITTTQRYT 284
Cdd:cd00397  159 SISTTQRYL 167
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 21-288 2.76e-36

integron integrase; Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 132.13  E-value: 2.76e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   21 SLKTVENYERYLKRFLEFTKVSSPKDISDDVVREFrlqLNRMRDRFDHTLKRQTQFYHliALRNFLKYMAKRDIKTLaaE 100
Cdd:TIGR02249  15 AKRTEEAYLHWIKRFIRFHNKRHPSTMGDTEVEAF---LSDLAVDGKVAASTQNQALN--ALLFLYKEILKTPLSLM--E 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  101 KIELGKVSQLQVEFLEGEEVNRLLSATSGnslqnfRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIR-GKGQKIR 179
Cdd:TIGR02249  88 RFVRAKRPRKLPVVLTREEVRRLLEHLEG------KYRLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRqGKGGKDR 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  180 VVFLSSEAKATLKTYLDKRADIEE----PLFVSAPK----GKKTQN------------SNPTRLTPRS------------ 227
Cdd:TIGR02249 162 TVTLPKELIPPLREQIELARAYHEadlaEGYGGVYLphalARKYPNapkewgwqylfpSHRLSRDPESgvirrhhinett 241

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818812357  228 IQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTD 288
Cdd:TIGR02249 242 IQRAVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVLN 302
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 8-293 2.12e-35

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 130.81  E-value: 2.12e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357   8 KDYLEHlEIEKNRSLKTVENYERYLKRFLEF------TKVSSPKDISDDV--------VREFRLQL----NRMRDRFDHT 69
Cdd:PRK05084  22 QEYYQS-KLATPYSPTTLYEYLTEYRRFFNWliseglSDASKIKDIPLSTlenltkkdVEAFILYLrerpLLNGHSTKKG 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  70 LKRQTQFYHLIALRNFLKY------------------MAKRDIK----TLAA------EKIELGKVSQLQVEFLEGEEVN 121
Cdd:PRK05084 101 NSQTTINRTLSALKSLFKYlteeaenedgepyfyrnvMKKIELKkkkeTLAArahnlkQKLFLGDEDYEFLDFIDNEYEQ 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 122 RLlsatSGNSLQNF-----RDRALLELLFSTGLRISELCSLNRESVNLARDEFSIRGKGQKIRVVFLSSEAKATLKTYLD 196
Cdd:PRK05084 181 KL----SNRALSSFkknkeRDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEYLK 256

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 197 KRADI------EEPLFVSAPKGKktqnsnPTRLTPRSIQRLIKKYSAAAGitKRVTPHTLRHSFGTDLLRSGADLRSVQA 270
Cdd:PRK05084 257 IRASRykaekqEKALFLTKYRGK------PNRISARAIEKMVAKYSEAFG--VRLTPHKLRHTLATRLYDATKDQVLVAD 328

                        330       340
                 ....*....|....*....|...
gi 818812357 271 LLGHSSITTTQRYTHVTDSVLRD 293
Cdd:PRK05084 329 QLGHTSTETTDLYTHIVNDEQKE 351
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 115-284 2.34e-34

C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 123.54  E-value: 2.34e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 115 LEGEEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARD-EFSIRGKGQKIRVVFLSSEAKATLKT 193
Cdd:cd01182    1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPaTVRLHGKGRKERTVPLWKETVAALKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 194 YLDKR--ADIEEPLFVSAPkgkktqNSNPTRLTPRSIQRLIKKYSAAA-----GITKRVTPHTLRHSFGTDLLRSGADLR 266
Cdd:cd01182   81 YLQEFhlTPDPKQLFPLFP------NRRGQPLTRDGVAYILNKYVALAsnrcpSLPKRITPHTLRHTKAMHLLQAGVDLT 154

                        170
                 ....*....|....*...
gi 818812357 267 SVQALLGHSSITTTQRYT 284
Cdd:cd01182  155 VIRDWLGHESVETTQIYA 172
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 118-285 7.19e-29

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 108.71  E-value: 7.19e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 118 EEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIRGKGQKIR-VVFLSSEAKATLKTYLD 196
Cdd:cd01195    3 EEARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQReVVTLPPTTREALAAWLA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 197 KRADIEEPLFVSAPKGKKTQnsnptRLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADL-RSVQALLGHS 275
Cdd:cd01195   83 ARGEAEGPLFVSLDRASRGR-----RLSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGLiRKVQDFSRHA 157

                        170
                 ....*....|
gi 818812357 276 SITTTQRYTH 285
Cdd:cd01195  158 DLRTLQVYDD 167
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 122-293 7.96e-29

C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.


Pssm-ID: 271180  Cd Length: 188  Bit Score: 108.93  E-value: 7.96e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 122 RLLSATSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDE----FSIRGKGQ---KIRVVFLSSEAKA----T 190
Cdd:cd00799    3 AMLATLDDTTLRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVDGglliRLRRSKTDqdgEGEIKALPYGPETcpvrA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 191 LKTYLDKRADIEEPLFVSAPKGkktQNSNPTRLTPRSIQRLIKKYSAAAGI-TKRVTPHTLRHSFGTDLLRSGADLRSVQ 269
Cdd:cd00799   83 LRAWLEAAGIPSGPLFRRIRRG---GSVGTTRLSDRSVARIVKRRAALAGLdPGDFSGHSLRRGFATEAARAGASLPEIM 159

                        170       180
                 ....*....|....*....|....
gi 818812357 270 ALLGHSSITTTQRYTHVTDSVLRD 293
Cdd:cd00799  160 AQGGHKSVATVMRYIREADRFKDN 183
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 115-285 5.86e-27

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 103.61  E-value: 5.86e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 115 LEGEEVNRLLSATSGN-SLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIR--GKGQ--KIRVVFLSSEAKA 189
Cdd:cd01194    1 LTLEQARQLLASLPIDdSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYvqGKGKtsKDDFVYLRPDVLK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 190 TLKTYLDKRA--DIEEPLFVSApkgkkTQNSNPTRLTPRSIQRLIKKYSAAAGIT-KRVTPHTLRHSFGTDLLRSGADLR 266
Cdd:cd01194   81 ALQAYLKARGklDFEEPLFTSL-----SNNSKGQRLTTRSIRRIIKKYLRKAGLDdDRLTAHSLRHTAGTLALKAGKSLR 155

                        170
                 ....*....|....*....
gi 818812357 267 SVQALLGHSSITTTQRYTH 285
Cdd:cd01194  156 EVQQLLRHSDPNTTMIYAH 174
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 118-283 2.41e-25

C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; Recombinases RitA (also known as pAE1), RitB, and RitC are encoded by three adjacent and overlapping genes. Collectively they are known as the Recombinase in Trio (RIT). This RitA family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 99.62  E-value: 2.41e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 118 EEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIRG-KGQKIRVVFLSSEAKATLKTYL- 195
Cdd:cd01188    3 DEVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQkKTGRPVELPLTEPVGEALADYLr 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 196 DKRADIEEP-LFVS--APKGKKTqnsnptrlTPRSIQRLIKKYSAAAGITKRVT-PHTLRHSFGTDLLRSGADLRSVQAL 271
Cdd:cd01188   83 DGRPRTDSReVFLRarAPYRPLS--------STSQISSIVRRYLRKAGIEPSHRgTHSLRHSLATRMLRAGTSLKVIADL 154

                        170
                 ....*....|..
gi 818812357 272 LGHSSITTTQRY 283
Cdd:cd01188  155 LGHRSIETTAIY 166
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 113-285 1.31e-24

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 97.01  E-value: 1.31e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 113 EFLEGEEVNRLLSATSGNSLQNFRDRALLELLfsTGLRISELCSLNRESVNLARDEFSIRG-KGQKIRVVFLSSEAKATL 191
Cdd:cd00796    3 RFLTEDEEARLLAALEESTNPHLRLIVLLALY--TGARRGEILSLRWDDIDLEVGLIVLPEtKNGKPRTVPLSDEAIAIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 192 KTYLDKRADIEEPLFVSApkgkktqnsnpTRLTPRSIQRLIKKYSAAAGITKrVTPHTLRHSFGTDLLRSGADLRSVQAL 271
Cdd:cd00796   81 KELKRKRGKDGFFVDGRF-----------FGIPIASLRRAFKKARKRAGLED-LRFHDLRHTFASRLVQAGVPIKTVAKI 148

                        170
                 ....*....|....
gi 818812357 272 LGHSSITTTQRYTH 285
Cdd:cd00796  149 LGHSSIKMTMRYAH 162
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 118-289 2.11e-22

Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain; IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271185 [Multi-domain]  Cd Length: 161  Bit Score: 91.17  E-value: 2.11e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 118 EEVNRLLSATsgNSLQNFRDRALLELLFS--TGLRISELCSLNRESVNLARDEFSI---RGKGQKIRVVFLSSEAKATLK 192
Cdd:cd01185    1 EELKRLMALE--LSDTSRLELVRDMFLFScyTGLRFSDLKNLTWKNIVEASGRTWIryrRKKTGKPVTVPLLPVAREILE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 193 TYLDkrADIEEPLFvsapKGKKTQNSNptrltprsiqRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALL 272
Cdd:cd01185   79 KYKD--DRSEGKLF----PVLSNQKIN----------RYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLL 142

                        170
                 ....*....|....*..
gi 818812357 273 GHSSITTTQRYTHVTDS 289
Cdd:cd01185  143 GHSSIKTTQIYAKIVDS 159
PRK15417 PRK15417
integron integrase;
21-286 3.10e-22

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 94.73  E-value: 3.10e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  21 SLKTVENYERYLKRFLEFTKVSSPKDISDDVVREFRLQLNRMRdRFDHTLKRQTqfyhLIALRNFLKYMAKRDIKTLaaE 100
Cdd:PRK15417  30 SLRTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANER-KVSVSTHRQA----LAALLFFYGKVLCTDLPWL--Q 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 101 KIELGKVSQLQVEFLEGEEVNRLLSATSGNSlqnfrdRALLELLFSTGLRISELCSLNRESVNLARDEFSIR-GKGQKIR 179
Cdd:PRK15417 103 EIGRPRPSRRLPVVLTPDEVVRILGFLEGEH------RLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKDR 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 180 VVFLSSEAKATLKTYLDK------------RADIEEP--LFVSAPKG-----------KKTQNSNPT-------RLTPRS 227
Cdd:PRK15417 177 ALMLPESLAPSLREQLSRarawwlkdqaegRSGVALPdaLERKYPRAghswpwfwvfaQHTHSTDPRsgvvrrhHMYDQT 256

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 818812357 228 IQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHV 286
Cdd:PRK15417 257 FQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 315
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 118-285 5.91e-22

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 89.54  E-value: 5.91e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 118 EEVNRLLSATSgnsLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIRGkgqkirvvflsseakaTLKTYLDK 197
Cdd:cd01189    2 EELKKLLEALK---KRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINR----------------TLVRKKKG 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 198 RADIEEPlfvsapkgkKTQNSNptR---LTPRSIQRL-----IKKYSAAAGItKRVTPHTLRHSFGTDLLRSGADLRSVQ 269
Cdd:cd01189   63 GYVIKPP---------KTKSSI--RtipLPDELIELLkelkaFKKLLKKAGL-PRITPHDLRHTFASLLLEAGVPLKVIA 130

                        170
                 ....*....|....*..
gi 818812357 270 ALLGHSSITTTQR-YTH 285
Cdd:cd01189  131 ERLGHSDISTTLDvYAH 147
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 116-294 4.84e-21

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271196  Cd Length: 183  Bit Score: 88.31  E-value: 4.84e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 116 EGEEVNRLLSATSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIR--GKGQKIRVVFLSSEAKATLKT 193
Cdd:cd01196    1 TAPEARRLLESIDSTHPVGLRDRALIALMVYSFARIGAVLAMRVEDVYDQGRRLWVRlaEKGGKQHEMPCHHDLEEYLRA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 194 YLDK---RADIEEPLFVSAPKGKKTQNSNPtrLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQA 270
Cdd:cd01196   81 YLEAaeiEEDPKGPLFRTTRGGTRKLTHNP--LTQANAYRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTLEDAQN 158

                        170       180
                 ....*....|....*....|....
gi 818812357 271 LLGHSSITTTQRYTHVTDSVLRDI 294
Cdd:cd01196  159 MANHASTRTTQLYDRRSDKITLDE 182
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 118-287 7.16e-20

C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271178 [Multi-domain]  Cd Length: 198  Bit Score: 85.44  E-value: 7.16e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 118 EEVNRLLSA----TSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIR-GKGQKIRVVFLSSEAKATLK 192
Cdd:cd00797    4 AEIRRLLAAadqlPPESPLRPLTYATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRqTKFGKSRLVPLHPSTVGALR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 193 TYLDKRAD-----IEEPLFVSAPKGkktqnsnptRLTPRSIQRLIKKYSAAAGI---TKRVTP--HTLRHSFGTDLL--- 259
Cdd:cd00797   84 DYLARRDRllpspSSSYFFVSQQGG---------RLTGGGVYRVFRRLLRRIGLrgaGDGRGPrlHDLRHTFAVNRLtrw 154

                        170       180       190
                 ....*....|....*....|....*....|...
gi 818812357 260 -RSGAD----LRSVQALLGHSSITTTQRYTHVT 287
Cdd:cd00797  155 yREGADverkLPVLSTYLGHVNVTDTYWYLTAT 187
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 111-284 2.29e-18

FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar to E.coli FimE and FimB and Proteus mirabilis MrpI. FimB and FimE are the regulatory proteins during expression of type 1 fimbriae in Escherichia coli. The fimB and fimE proteins direct the phase switch into the 'on' and 'off' position. MrpI is the regulatory protein of proteus mirabilis fimbriae expression. This family belongs to the integrase/recombinase superfamily.


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 81.01  E-value: 2.29e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 111 QVEFLEGEEVNRLLSAtSGNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIR--GKGQKIRVVFLSSEAK 188
Cdd:cd01197    3 QRKYLTGKEVQALLQA-ACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRrlKNGFSTTHPLRFDERE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 189 AtLKTYLDKRADIEEP----LFVSAPKGkktqnsnptRLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGAD 264
Cdd:cd01197   82 A-LEAWLKERANWKGAdtdwIFLSRRGG---------PLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGAD 151

                        170       180
                 ....*....|....*....|
gi 818812357 265 LRSVQALLGHSSITTTQRYT 284
Cdd:cd01197  152 TRLIQDYLGHRNIRHTVIYT 171
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 134-294 7.24e-17

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 76.95  E-value: 7.24e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 134 NFRDRALLELLFSTGLRISELCSLNRESVnLARDEFSIR-GKGQKIRVVFLSSEAKATLKTYLDKRADIEEPLFVSAPKG 212
Cdd:cd01192   23 NPRNYLLFIVGINTGLRISDLLSLKVEDV-TNKDKLSIKeQKTGKQKTFPLNPTLVKALKEYIDDLDLKRNDYLFKSLKQ 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 213 KKTqnsnpTRLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLR 292
Cdd:cd01192  102 GPE-----KPISRKQAYKILKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYLGIDQEDVD 176


                 ..
gi 818812357 293 DI 294
Cdd:cd01192  177 KA 178
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 115-292 6.58e-16

Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase A from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 74.37  E-value: 6.58e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 115 LEGEEVNRLLsatsgNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSI----------RGKGQKIRVVFLS 184
Cdd:cd01186    2 LTPREVQELI-----NACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELvpredntneaRAKSMRERRIPVS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 185 SEAKATLKTYLdkRADIEEPLFVSAPKGKKTQNSN---PTRLTprSIQRLIKKYSAAAGITkrVTPHTLRHSFGTDLLRS 261
Cdd:cd01186   77 QDLIDLYADYL--TYIYCEEAEFSITVFVNVKGGNqgkAMNYS--DVYDLVRRLKKRTGID--FTPHMFRHTHATALIRA 150

                        170       180       190
                 ....*....|....*....|....*....|..
gi 818812357 262 GADLRSVQALLGHSSI-TTTQRYTHVTDSVLR 292
Cdd:cd01186  151 GWSIEVVARRLGHAHVqTTLNTYGHLSEEDIR 182
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 114-285 4.23e-15

Integrase/recombinase, includes phage integrase [Replication, recombination and repair, Mobilome: prophages, transposons];


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 75.08  E-value: 4.23e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 114 FLEGEEVNRLLSATSGNSLQnFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIRG---KGQKIRVVFLSSEAKAT 190
Cdd:COG0582  205 ALTPEELPELLRALDAYRGS-PVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAermKTRRPHIVPLSRQALEI 283

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 191 LKTyLDKRADIEEPLFVSAPKGKKtqnsnptRLTPRSIQRLIKKysaaAGItKRVTPHTLRHSFGTDLLRSGADLRSVQA 270
Cdd:COG0582  284 LKE-LKPLTGDSEYVFPSRRGPKK-------PMSENTLNKALRR----MGY-GRFTPHGFRHTASTLLNEAGFPPDVIER 350

                        170
                 ....*....|....*.
gi 818812357 271 LLGHSSITTTQR-YTH 285
Cdd:COG0582  351 QLAHKDGNKVRAaYNR 366
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 144-294 2.69e-13

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271191  Cd Length: 176  Bit Score: 66.68  E-value: 2.69e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 144 LFSTGLRISELCSLNRESVNLARdeFSIRGKGQKIRVVFLSSEAKATLKTYLDKRADIEEPLFVsapkgkktqNSNPTRL 223
Cdd:cd01191   29 LAATGARVSELIKIKVEHVELGY--FDIYSKGGKLRRLYIPKKLRNEALEWLKSTNRKSGYIFL---------NRFGERI 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 818812357 224 TPRSIQRLIKKYSAAAGITKRVT-PHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRDI 294
Cdd:cd01191   98 TTRGIAQQLKNYARKYGLNPKVVyPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRKTASEQQEI 169
int PHA02601
integrase; Provisional
 76-293 7.59e-13

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 67.83  E-value: 7.59e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  76 FYHLIALRNFLKYMAKRDIKTLAAEKIELGkvsqlqveFLEGEEVNRLLSAtsgnsLQNFRDRALL---ELLFSTGLRIS 152
Cdd:PHA02601 142 FNELIKLGKWSGPNPLDGIRPFKEAEPELA--------FLTKEEIERLLDA-----CDGSRSPDLGliaKICLATGARWS 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 153 ELCSLNRESVNLARDEFsIRGKGQKIRVVflsseakatlktyldkraDIEEPLFVSAPKgkktqnsNPTRLTPRSiqrli 232
Cdd:PHA02601 209 EAETLKRSQISPYKITF-VKTKGKKNRTV------------------PISEELYKMLPK-------RRGRLFKDA----- 257

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818812357 233 kkYSAAAGITKRVTP--------HTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTHVTDSVLRD 293
Cdd:PHA02601 258 --YESFERAVKRAGIdlpegqatHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAHFAPDHLED 324
PRK09870 PRK09870
tyrosine recombinase; Provisional
 114-284 3.60e-12

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 64.19  E-value: 3.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 114 FLEGEEVNRLLSATSgNSLQNFRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIR--GKGQKIRVVFLSSEAKAtL 191
Cdd:PRK09870  12 FLTHSEIESLLKAAN-TGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHrlKKGFSTTHPLLNKEIQA-L 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 192 KTYLDKRADIE----EPLFVSapkgkktQNSNPtrLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRS 267
Cdd:PRK09870  90 KNWLSIRTSYPhaesEWVFLS-------RKGNP--LSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRL 160

                        170
                 ....*....|....*..
gi 818812357 268 VQALLGHSSITTTQRYT 284
Cdd:PRK09870 161 IQDYLGHRNIRHTVWYT 177
PRK09871 PRK09871
tyrosine recombinase; Provisional
 114-284 4.81e-12

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 63.85  E-value: 4.81e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 114 FLEGEEVNRLLSATSGNSLQNfRDRALLELLFSTGLRISELCSLNRESVNLARDEFSIRGKGQKIRVV----FLSSEA-- 187
Cdd:PRK09871   6 YLTGKEVQAMMQAVCYGATGA-RDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVhplrFDEREAve 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 188 KATLKTYLDKRADIEEPLFVSApKGkktqnsnpTRLTPRSIQRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRS 267
Cdd:PRK09871  85 RWTQERANWKGADRTDAIFISR-RG--------SRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRL 155

                        170
                 ....*....|....*..
gi 818812357 268 VQALLGHSSITTTQRYT 284
Cdd:PRK09871 156 IQDYLGHRNIRHTVRYT 172
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 138-275 8.98e-11

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 59.98  E-value: 8.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 138 RALLELLFSTGLRISELCSLNRESVNLARDEFSI---RGKGQKIRVVFLSSEAKATLKTYLDKRADiEEPLFVSAPKGKK 214
Cdd:cd00801   22 KLALRLLLLTGQRIGELARARWSEIDLEEKTWTIpaeRTKNKRPHRVPLSDQALEILEELKEFTGD-SGYLFPSRRKKKK 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818812357 215 TQNSNptrltprSIQRLIKKYSAAAGITkrvTPHTLRHSFGTDLLRSGADLRSVQALLGHS 275
Cdd:cd00801  101 PISEN-------TINKALKRLGYKGKEF---TPHDLRRTFSTLLNELGIDPEVIERLLNHV 151
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 118-285 1.42e-10

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 59.24  E-value: 1.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 118 EEVNRLLSA---TSGNSLQNFRDRALLELLFsTGLRISELCSLNRESVNLARD----EFSIRGKGQK------IRVVFLS 184
Cdd:cd01184    4 EELAKIFSSplyTGCKKKDPALYWLPLIGLY-TGARLNEICQLRVDDIKEEDGiwciDINDDAEGRRlktkasRRLVPIH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 185 SEAKAT--LKTYLDKRADIEEPLFVSAPKGKKTQNSNPTRLTPRSIQRLIKKysaaagITKRVTPHTLRHSFGTDLLRSG 262
Cdd:cd01184   83 PRLIELgfLDYVEALRADGKLFLFPEKRDKDGKYSKAASKWFNRLLRKLGIK------DDERKSFHSFRHTFITALKRAG 156

                        170       180
                 ....*....|....*....|....
gi 818812357 263 ADLRSVQALLGHS-SITTTQRYTH 285
Cdd:cd01184  157 VPEELIAQIVGHSrGGVTHDTYGK 180
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 139-285 4.27e-07

Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase B from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 48.58  E-value: 4.27e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 139 ALLELLFSTGLRISELCSLnrESVNLARDEfsirgkgqkirvvflsSEAKATLKTYLDKRADIEEPLFVSAPKGK---KT 215
Cdd:cd01187   17 PVVQAAVFTGARASELATL--KFGCLHAQT----------------SDDGTFLYWLKWENKGGKQLDIPISKKVAeliKT 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 216 QNSNPTRLtprsiqRLIKKYSAAAGITKRVTPHTLRHSFGTDLLRSGADLRSVQALLGHSSITTTQRYTH 285
Cdd:cd01187   79 INWTLNEL------SELKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
6-94 2.68e-06

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 44.53  E-value: 2.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357    6 LLKDYLEHLEIeKNRSLKTVENYERYLKRFLEFTKVSSPKDISDDVVREFRLQLNRMRdrfdhTLKRQTQFYHLIALRNF 85
Cdd:pfam13495   1 LLERFREALRL-RGYAERTIKAYLRWIRRFLRFHDKKHPEELTEEDIEAYLSHLANER-----NVSASTQNQALNALSFF 74


                  ....*....
gi 818812357   86 LKYMAKRDI 94
Cdd:pfam13495  75 YRWVLEREL 83
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 138-290 1.83e-05

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 44.26  E-value: 1.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 138 RALLELLFSTGLRISELCSLNREsvNLARD----EFSIRGKGQKIRVVFLSSEAKATLKTYLDKRADIeeplFVSAPKGK 213
Cdd:cd00800   15 RLAMELALLTGQRQGDLLRLKWS--DITDGgllvEQSKTGKKLLIPWTPSLRALVDRIRALPRKRSEY----LINSRKGG 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357 214 KtqnsnptrLTPRSIQRLIKKYSAAAGITKRVTP---HTLRHSFGTDLLRSGaDLRSVQALLGHSSITTTQRYTHVTDSV 290
Cdd:cd00800   89 P--------LSYDTLKSAWRRARKAAGLKGETEGftfHDLRAKAATDYAEQG-GSTDAQALLGHKSDAMTERYTRKRGQK 159
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
7-92 2.10e-05

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 42.25  E-value: 2.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357    7 LKDYLEHLEIEKNRSLKTVENYERYLKRFLEFTKV--SSPKDISDDVVREFrlqlnrMRDRFDHTLKRQTQFYHLIALRN 84
Cdd:pfam02899   1 IDQFLEYLSLERGLSPHTLRAYRRDLLAFLKFLSEggSSLEQITTSDVRAF------LAELRAQGLSASSLARRLSALRS 74


                  ....*...
gi 818812357   85 FLKYMAKR 92
Cdd:pfam02899  75 FYQFLIRE 82
COG4342 COG4342
Phage integrase/recombinase [Mobilome: prophages, transposons];
19-153 2.55e-03

Phage integrase/recombinase [Mobilome: prophages, transposons];


Pssm-ID: 443483 [Multi-domain]  Cd Length: 278  Bit Score: 38.92  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818812357  19 NRSLKTVENYERYLKRFLEFTKVSSPKDISDDVVREFR--LQLNRMRDRFDHTLKRQTQFYHLiALRNFLKYMAKRDIKT 96
Cdd:COG4342   10 PSGLRVIILTEGLLEEFLEWLVKRVSEKTAKDYISALDryLSILTPEDLREIELAKEKKNLVK-ALRNLANFLVERGIIS 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818812357  97 L-AAEKI-ELGKV--SQLQVEFLEGEEVNRLLSATSGNslqNFRDRALLELLFSTGLRISE 153
Cdd:COG4342   89 EeVAEKIkEVLKVkrSGVDLYVPTDEEIREALKYLKEK---DEEVYLLYKLLLFSGLRLSE 146
 
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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