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Conserved domains on  [gi|2124955637|ref|WP_227160451|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Bacillota]

Protein Classification

site-specific integrase( domain architecture ID 11139622)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
96-394 2.67e-44

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 155.15  E-value: 2.67e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637  96 RKNIKRATEKGRQYLMNALKN--DPLGMRAIDTVKQSDAKEWAIRMSEKGYAYKTIDNYKRSLKASFYMAIQDDCIRKNP 173
Cdd:COG4974    17 EKGLSPNTIKAYRRDLRRFLRflEELGKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYAVREGLLEDNP 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 174 FEfKLSDVLEDDTEQKViLTPEQEERLLAFMETDKIYSKYYDEVV-LLLETGLRISEFCGLT-THIDMQNRILNIdhqll 251
Cdd:COG4974    97 AA-KVKLPKKPRKLPRV-LTEEEIEALLEALDTETPEGLRDRALLlLLYATGLRVSELLGLKwSDIDLDRGTIRV----- 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 252 kdseigyyietPKTKNGK-RELPLTERAYQAIQRILKNRGKAQplivggySNFLFLNREGLPKvagnYEGMVRGLIKKYN 330
Cdd:COG4974   170 -----------RRGKGGKeRTVPLSPEALEALREYLEERRPRD-------SDYLFPTRRGRPL----SRRAIRKILKRLA 227

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2124955637 331 KyHTDKLPNITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLgYYAHGTFQSAKAELERL 394
Cdd:COG4974   228 K-RAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQ-IYTHVSDEELREAVEKL 289
Integrase_DNA pfam02920
DNA binding domain of tn916 integrase;
5-72 6.49e-24

DNA binding domain of tn916 integrase;


:

Pssm-ID: 427054  Cd Length: 58  Bit Score: 93.44  E-value: 6.49e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2124955637   5 KRKDSKNRNLRNGESQRKDGRYVYKYTDIYGKPQFIYSWKLVptdktpagkrddiSLREKEAQIKKDL 72
Cdd:pfam02920   4 KRKDSKGRVLRTGESQRKDGRYQYKYTDVDGKRKYVYSWDLV-------------ELREKEKEIQKDL 58
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
96-394 2.67e-44

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 155.15  E-value: 2.67e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637  96 RKNIKRATEKGRQYLMNALKN--DPLGMRAIDTVKQSDAKEWAIRMSEKGYAYKTIDNYKRSLKASFYMAIQDDCIRKNP 173
Cdd:COG4974    17 EKGLSPNTIKAYRRDLRRFLRflEELGKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYAVREGLLEDNP 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 174 FEfKLSDVLEDDTEQKViLTPEQEERLLAFMETDKIYSKYYDEVV-LLLETGLRISEFCGLT-THIDMQNRILNIdhqll 251
Cdd:COG4974    97 AA-KVKLPKKPRKLPRV-LTEEEIEALLEALDTETPEGLRDRALLlLLYATGLRVSELLGLKwSDIDLDRGTIRV----- 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 252 kdseigyyietPKTKNGK-RELPLTERAYQAIQRILKNRGKAQplivggySNFLFLNREGLPKvagnYEGMVRGLIKKYN 330
Cdd:COG4974   170 -----------RRGKGGKeRTVPLSPEALEALREYLEERRPRD-------SDYLFPTRRGRPL----SRRAIRKILKRLA 227

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2124955637 331 KyHTDKLPNITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLgYYAHGTFQSAKAELERL 394
Cdd:COG4974   228 K-RAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQ-IYTHVSDEELREAVEKL 289
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 192-381 2.94e-39

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: 138.22  E-value: 2.94e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 192 LTPEQEERLLAFMETDKIYSKYYDEVVLLLETGLRISEFCGLTT-HIDMQNRILNIDHqllkdseigyyietpkTKNGK- 269
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWsDIDFENGVIRVHR----------------GKGNKe 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 270 RELPLTERAYQAIQRILKNRGKAQPlivggYSNFLFLNREGLPKVAGNYEGMVRGLIKKYNKYhtdklPNITPHSFRHTY 349
Cdd:pfam00589  66 RTVPLSDAALELLKEWLSKRLLEAP-----KSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLE-----LPLHPHMLRHSF 135

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2124955637 350 CTNMANRGMNPNTLQYLMGHANITMTlGYYAH 381
Cdd:pfam00589 136 ATHLLEAGVDLRVVQKLLGHSSISTT-QIYTH 166
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 194-381 5.97e-39

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: 136.53  E-value: 5.97e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 194 PEQEERLLAFMETDKiySKYYDEVVLLLETGLRISEFCGLT-THIDMQNRILNIDHQLLKDSEIGYYIETPKTKNGKREL 272
Cdd:cd01189     1 PEELKKLLEALKKRG--DRYYLLFLLALLTGLRRGELLALTwSDIDFENGTIRINRTLVRKKKGGYVIKPPKTKSSIRTI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 273 PLTERAYQAIQRILKnrgkaqplivggysnflfLNReglpkvagnyegmvrgLIKKYNkyhtdkLPNITPHSFRHTYCTN 352
Cdd:cd01189    79 PLPDELIELLKELKA------------------FKK----------------LLKKAG------LPRITPHDLRHTFASL 118

                         170       180
                  ....*....|....*....|....*....
gi 2124955637 353 MANRGMNPNTLQYLMGHANITMTLGYYAH 381
Cdd:cd01189   119 LLEAGVPLKVIAERLGHSDISTTLDVYAH 147
Integrase_DNA pfam02920
DNA binding domain of tn916 integrase;
5-72 6.49e-24

DNA binding domain of tn916 integrase;


Pssm-ID: 427054  Cd Length: 58  Bit Score: 93.44  E-value: 6.49e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2124955637   5 KRKDSKNRNLRNGESQRKDGRYVYKYTDIYGKPQFIYSWKLVptdktpagkrddiSLREKEAQIKKDL 72
Cdd:pfam02920   4 KRKDSKGRVLRTGESQRKDGRYQYKYTDVDGKRKYVYSWDLV-------------ELREKEKEIQKDL 58
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 124-375 2.12e-20

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: 90.33  E-value: 2.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 124 IDTVKQSDAKEWAIRMSEKGYAYKTIDNYKRSLKASFYMAIQDDCIRKNPFEF--------KLSDVLeddteqkvilTPE 195
Cdd:TIGR02225  39 LEEVDRGDIVDFLAELKEAGLSARSIARALSALRSFYRFLLREGIREDDPSALieppkvarKLPKVL----------TVE 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 196 QEERLLAFMETDKIYSkYYDEVVLLL--ETGLRISEFCGLT-THIDMQNRILNIdhqllkdseIGyyietpktKNGK-RE 271
Cdd:TIGR02225 109 EVEALLAAPDVDTPLG-LRDRAMLELlyATGLRVSELVGLRlEDVNLDEGFVRV---------RG--------KGNKeRL 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 272 LPLTERAYQAIQRILKNRGKAQPLIVGGYSNFLFLNREGlpkvagnyEGMVR----GLIKKYNKYhTDKLPNITPHSFRH 347
Cdd:TIGR02225 171 VPLGEEAIEALERYLKEARPLLLKKKVKESDALFLNRRG--------GPLSRqgvwKILKEYAKR-AGIEKPISPHTLRH 241

                         250       260
                  ....*....|....*....|....*...
gi 2124955637 348 TYCTNMANRGMNPNTLQYLMGHANITMT 375
Cdd:TIGR02225 242 SFATHLLENGADLRVVQELLGHADISTT 269
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 192-375 1.36e-18

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 85.21  E-value: 1.36e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 192 LTPEQEERLLAFM-ETDKIYSKYYDEVVLLLETGLRISEFCGLT-THIDMQNRILNIdhqllkdseIGyyietpktKNGK 269
Cdd:PRK00236  116 LDVDQAKRLLDAIdEDDPLALRDRAILELLYGSGLRLSELVGLDiDDLDLASGTLRV---------LG--------KGNK 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 270 -RELPLTERAYQAIQRILKNRGKAQPlivggYSNFLFLNREGLPKVAGNYEGMVRGLIKKYNkyhtdkLP-NITPHSFRH 347
Cdd:PRK00236  179 eRTVPLGRAAREALEAYLALRPLFLP-----DDDALFLGARGGRLSPRVVQRRVKKLGKKAG------LPsHITPHKLRH 247

                         170       180
                  ....*....|....*....|....*...
gi 2124955637 348 TYCTNMANRGMNPNTLQYLMGHANITMT 375
Cdd:PRK00236  248 SFATHLLESGGDLRAVQELLGHASLSTT 275
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
96-394 2.67e-44

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 155.15  E-value: 2.67e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637  96 RKNIKRATEKGRQYLMNALKN--DPLGMRAIDTVKQSDAKEWAIRMSEKGYAYKTIDNYKRSLKASFYMAIQDDCIRKNP 173
Cdd:COG4974    17 EKGLSPNTIKAYRRDLRRFLRflEELGKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYAVREGLLEDNP 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 174 FEfKLSDVLEDDTEQKViLTPEQEERLLAFMETDKIYSKYYDEVV-LLLETGLRISEFCGLT-THIDMQNRILNIdhqll 251
Cdd:COG4974    97 AA-KVKLPKKPRKLPRV-LTEEEIEALLEALDTETPEGLRDRALLlLLYATGLRVSELLGLKwSDIDLDRGTIRV----- 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 252 kdseigyyietPKTKNGK-RELPLTERAYQAIQRILKNRGKAQplivggySNFLFLNREGLPKvagnYEGMVRGLIKKYN 330
Cdd:COG4974   170 -----------RRGKGGKeRTVPLSPEALEALREYLEERRPRD-------SDYLFPTRRGRPL----SRRAIRKILKRLA 227

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2124955637 331 KyHTDKLPNITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLgYYAHGTFQSAKAELERL 394
Cdd:COG4974   228 K-RAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQ-IYTHVSDEELREAVEKL 289
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 192-381 2.94e-39

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: 138.22  E-value: 2.94e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 192 LTPEQEERLLAFMETDKIYSKYYDEVVLLLETGLRISEFCGLTT-HIDMQNRILNIDHqllkdseigyyietpkTKNGK- 269
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWsDIDFENGVIRVHR----------------GKGNKe 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 270 RELPLTERAYQAIQRILKNRGKAQPlivggYSNFLFLNREGLPKVAGNYEGMVRGLIKKYNKYhtdklPNITPHSFRHTY 349
Cdd:pfam00589  66 RTVPLSDAALELLKEWLSKRLLEAP-----KSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLE-----LPLHPHMLRHSF 135

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2124955637 350 CTNMANRGMNPNTLQYLMGHANITMTlGYYAH 381
Cdd:pfam00589 136 ATHLLEAGVDLRVVQKLLGHSSISTT-QIYTH 166
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 194-381 5.97e-39

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: 136.53  E-value: 5.97e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 194 PEQEERLLAFMETDKiySKYYDEVVLLLETGLRISEFCGLT-THIDMQNRILNIDHQLLKDSEIGYYIETPKTKNGKREL 272
Cdd:cd01189     1 PEELKKLLEALKKRG--DRYYLLFLLALLTGLRRGELLALTwSDIDFENGTIRINRTLVRKKKGGYVIKPPKTKSSIRTI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 273 PLTERAYQAIQRILKnrgkaqplivggysnflfLNReglpkvagnyegmvrgLIKKYNkyhtdkLPNITPHSFRHTYCTN 352
Cdd:cd01189    79 PLPDELIELLKELKA------------------FKK----------------LLKKAG------LPRITPHDLRHTFASL 118

                         170       180
                  ....*....|....*....|....*....
gi 2124955637 353 MANRGMNPNTLQYLMGHANITMTLGYYAH 381
Cdd:cd01189   119 LLEAGVPLKVIAERLGHSDISTTLDVYAH 147
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
122-385 6.26e-37

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 135.47  E-value: 6.26e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 122 RAIDTVKQSDAKEWAIRMSEKGYAYKTIDNYKRSLKASFYMAIQDDCIRKNPFE----FKLSDVLEDdteqkvILTPEQE 197
Cdd:COG4973    44 LPLEELTPADVRRFLARLHRRGLSPRTLNRRLSALRSFFNWAVREGLLEANPAAgvkaPKAPRKLPR------ALTVDEL 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 198 ERLLAFMETDKIYSKYYDEVVLLLETGLRISEFCGLT-THIDMQNRILNIdhqllkdseigyyietpKTKNGK-RELPLT 275
Cdd:COG4973   118 AQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDwEDVDLDAGEVRV-----------------RGKTGKsRTVPLG 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 276 ERAYQAIQRILKNRgkaqPLIVGGYSNFLFLNREGLPKVAGNYEGMVRGLIKKYNkyhtdkLP-NITPHSFRHTYCTNMA 354
Cdd:COG4973   181 PKALAALREWLAVR----PELAAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAG------LPkHVHPHDLRHSFATHLL 250

                         250       260       270
                  ....*....|....*....|....*....|.
gi 2124955637 355 NRGMNPNTLQYLMGHANITMTLGyYAHGTFQ 385
Cdd:COG4973   251 ESGGDLRAVQELLGHASISTTQI-YTHLDFQ 280
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 198-378 2.42e-28

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: 109.11  E-value: 2.42e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 198 ERLLAFMETDKIYSKYYDEVV-LLLETGLRISEFCGLTT-HIDMQNRILNIDhqllkdseigyyiETPKTKNGKRELPLT 275
Cdd:cd00397     3 EKLLDAIDEDKKIDLRDRAILlLLLETGLRISELLALKVkDIDLDNGTIRVR-------------GKKTKGGKERTVPLP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 276 ERAYQAIQRILKN-RGKAQPLIVGGYSNFLFLNREGLPKVAGnyegMVRGLIKKYNKyhtDKLPNITPHSFRHTYCTNMA 354
Cdd:cd00397    70 KELAEELKEYLKErRDKRGPLLKSLYLNKLFGTKLGERLSRR----TLRRIFKKAGI---EAGRKITPHSLRHTFATNLL 142

                         170       180
                  ....*....|....*....|....
gi 2124955637 355 NRGMNPNTLQYLMGHANITMTLGY 378
Cdd:cd00397   143 ENGVDIKVVQKLLGHSSISTTQRY 166
Integrase_DNA pfam02920
DNA binding domain of tn916 integrase;
5-72 6.49e-24

DNA binding domain of tn916 integrase;


Pssm-ID: 427054  Cd Length: 58  Bit Score: 93.44  E-value: 6.49e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2124955637   5 KRKDSKNRNLRNGESQRKDGRYVYKYTDIYGKPQFIYSWKLVptdktpagkrddiSLREKEAQIKKDL 72
Cdd:pfam02920   4 KRKDSKGRVLRTGESQRKDGRYQYKYTDVDGKRKYVYSWDLV-------------ELREKEKEIQKDL 58
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 191-381 2.24e-23

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: 95.47  E-value: 2.24e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 191 ILTPEQEERLLAFMETDKIYsKYYDEVVLLLETGLRISEFCGLT-THIDMQNRILNIdhqllkdseigyyietPKTKNGK 269
Cdd:cd00796     4 FLTEDEEARLLAALEESTNP-HLRLIVLLALYTGARRGEILSLRwDDIDLEVGLIVL----------------PETKNGK 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 270 -RELPLTERAYQAIQRILKNRGKAQPLIVGGysnFLFLNREGLPKVagnyegmVRGLIKKYnkyhtdKLPNITPHSFRHT 348
Cdd:cd00796    67 pRTVPLSDEAIAILKELKRKRGKDGFFVDGR---FFGIPIASLRRA-------FKKARKRA------GLEDLRFHDLRHT 130

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2124955637 349 YCTNMANRGMNPNTLQYLMGHANITMTLgYYAH 381
Cdd:cd00796   131 FASRLVQAGVPIKTVAKILGHSSIKMTM-RYAH 162
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 124-375 2.12e-20

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: 90.33  E-value: 2.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 124 IDTVKQSDAKEWAIRMSEKGYAYKTIDNYKRSLKASFYMAIQDDCIRKNPFEF--------KLSDVLeddteqkvilTPE 195
Cdd:TIGR02225  39 LEEVDRGDIVDFLAELKEAGLSARSIARALSALRSFYRFLLREGIREDDPSALieppkvarKLPKVL----------TVE 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 196 QEERLLAFMETDKIYSkYYDEVVLLL--ETGLRISEFCGLT-THIDMQNRILNIdhqllkdseIGyyietpktKNGK-RE 271
Cdd:TIGR02225 109 EVEALLAAPDVDTPLG-LRDRAMLELlyATGLRVSELVGLRlEDVNLDEGFVRV---------RG--------KGNKeRL 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 272 LPLTERAYQAIQRILKNRGKAQPLIVGGYSNFLFLNREGlpkvagnyEGMVR----GLIKKYNKYhTDKLPNITPHSFRH 347
Cdd:TIGR02225 171 VPLGEEAIEALERYLKEARPLLLKKKVKESDALFLNRRG--------GPLSRqgvwKILKEYAKR-AGIEKPISPHTLRH 241

                         250       260
                  ....*....|....*....|....*...
gi 2124955637 348 TYCTNMANRGMNPNTLQYLMGHANITMT 375
Cdd:TIGR02225 242 SFATHLLENGADLRVVQELLGHADISTT 269
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 5-384 3.12e-20

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 91.25  E-value: 3.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637   5 KRKDSKNRNLRNGESQRKDGRYVYKYTDIYGKPQFIYSWKLVPTDKTPA-GKRDDISL---REKEAQIKKDLNDGIDTAG 80
Cdd:COG0582     3 TDTAKKKAKPKDKPYKLGDGGGLLLLVGPSGGKRWRYRYRFRGKRKRLAlGVYPGVSLalaRARRAEARALLALGIDPSP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637  81 GK------------MTVCQLYDK-KNSQRKNIKRATekGRQYLmNALKND---PLGMRAIDTVKQSDAKEWAIRMSEKGy 144
Cdd:COG0582    83 ARkaakaaaaaaaaNTFEEVAEEwLEEKKPEWKEKT--AAQVR-RTLEKHifpVLGDRPIAEITPPDLLAVLRPIEARG- 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 145 AYKTIDNYKRSLKASFYMAIQDDCIRKNPFEfKLSDVLEDDTEQKV-ILTPEQEERLLAFMETDKIYSKYYDEVVLLLET 223
Cdd:COG0582   159 APETARRVRQRLRQVFRYAVARGLIERNPAA-DLKGALPKPKVKHHpALTPEELPELLRALDAYRGSPVTRLALRLLLLT 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 224 GLRISEFCGLT-THIDMQNRILNIDHQllkdseigyyietpKTKNGK-RELPLTErayQAIqRILKNRGKAQplivgGYS 301
Cdd:COG0582   238 GVRPGELRGARwSEIDLEAALWTIPAE--------------RMKTRRpHIVPLSR---QAL-EILKELKPLT-----GDS 294

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 302 NFLFLNREGLPKVAgnYEGMVRGLIKKYnkyhtdKLPNITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGYYAH 381
Cdd:COG0582   295 EYVFPSRRGPKKPM--SENTLNKALRRM------GYGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNR 366


                  ...
gi 2124955637 382 GTF 384
Cdd:COG0582   367 ADY 369
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 192-375 1.36e-18

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 85.21  E-value: 1.36e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 192 LTPEQEERLLAFM-ETDKIYSKYYDEVVLLLETGLRISEFCGLT-THIDMQNRILNIdhqllkdseIGyyietpktKNGK 269
Cdd:PRK00236  116 LDVDQAKRLLDAIdEDDPLALRDRAILELLYGSGLRLSELVGLDiDDLDLASGTLRV---------LG--------KGNK 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 270 -RELPLTERAYQAIQRILKNRGKAQPlivggYSNFLFLNREGLPKVAGNYEGMVRGLIKKYNkyhtdkLP-NITPHSFRH 347
Cdd:PRK00236  179 eRTVPLGRAAREALEAYLALRPLFLP-----DDDALFLGARGGRLSPRVVQRRVKKLGKKAG------LPsHITPHKLRH 247

                         170       180
                  ....*....|....*....|....*...
gi 2124955637 348 TYCTNMANRGMNPNTLQYLMGHANITMT 375
Cdd:PRK00236  248 SFATHLLESGGDLRAVQELLGHASLSTT 275
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 219-375 2.25e-18

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: 81.79  E-value: 2.25e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 219 LLLETGLRISEFCGLT-THIDMQNRILNIdhqllkdseIGyyietpktKNGK-RELPLTERAYQAIQRILKNRGKAqpLI 296
Cdd:cd00798    27 LLYASGLRVSELVGLDlSDVDLDEGLVRV---------TG--------KGNKeRLVPFGSYAVEALEEYLEERRPL--LL 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2124955637 297 VGGYSNFLFLNREGlpkvAGNYEGMVRGLIKKYNKyHTDKLPNITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMT 375
Cdd:cd00798    88 KKKPPDALFLNKRG----KRLSRRGVWRILKKYAE-RAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTT 161
xerD PRK00283
tyrosine recombinase;
191-375 4.06e-12

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 66.37  E-value: 4.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 191 ILTPEQEERLLAFMETDkiyskyyDEVVL----LLE----TGLRISEFCGLTT-HIDMQNRILNIdhqllkdseIGyyie 261
Cdd:PRK00283  113 TLSEAQVEALLDAPDID-------TPLGLrdraMLEllyaTGLRVSELVGLTLdDVSLRQGVVRV---------TG---- 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 262 tpktKNGK-RELPLTERAYQAIQRILKnrgKAQPLIVGG-YSNFLFLNREGlpkvagnyEGMVR----GLIKKYNKYHTD 335
Cdd:PRK00283  173 ----KGNKeRLVPLGEEAVYAIERYLE---RGRPALLNGrSSDALFPSARG--------GQLTRqtfwHRIKHYAKRAGI 237

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2124955637 336 KLPNITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMT 375
Cdd:PRK00283  238 DPKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTT 277
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 190-378 1.23e-11

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: 62.68  E-value: 1.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 190 VILTPEQEERLLAFMETdkiySKYYDEVVLLLETGLRISEFCGL-TTHIDMQNRILNIDHqllkdseigyyietpkTKNG 268
Cdd:cd01193     4 VVLSPDEVRRILGALTE----LRHRLILSLLYGAGLRISELLRLrVKDIDFERGVIRVRQ----------------GKGG 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 269 K-RELPLTERAYQAIQRILKNRGKAQPLivggysnFLFLNREGLPKVAGN-------YEGMVRGLIKKYNKyHTDKLPNI 340
Cdd:cd01193    64 KdRVVPLPEKLLEPLRRYLKSARPKEEL-------DPAEGRAGVLDPRTGverrhhiSETTVQRALKKAVE-QAGITKRV 135

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2124955637 341 TPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGY 378
Cdd:cd01193   136 TPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIY 173
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 192-381 7.30e-11

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: 60.78  E-value: 7.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 192 LTPEQEERLLAFMETDKIYSKYYDE--VVLL-LETGLRISEFCGLTTHiDMQnRILNIDHQLLKDseiGYYIETPKTKNG 268
Cdd:cd01184     1 FTPEELAKIFSSPLYTGCKKKDPALywLPLIgLYTGARLNEICQLRVD-DIK-EEDGIWCIDIND---DAEGRRLKTKAS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 269 KRELPLTERAYQA--IQRILKNRGKAQPlivggysnFLFLNREGLPKVAGNYEGmvrgliKKYNKYHTDKLPNITP---- 342
Cdd:cd01184    76 RRLVPIHPRLIELgfLDYVEALRADGKL--------FLFPEKRDKDGKYSKAAS------KWFNRLLRKLGIKDDErksf 141

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2124955637 343 HSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGYYAH 381
Cdd:cd01184   142 HSFRHTFITALKRAGVPEELIAQIVGHSRGGVTHDTYGK 180
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 217-378 1.81e-10

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: 58.60  E-value: 1.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 217 VVLLLETGLRISEFCGLTTHidmqnrilNIDHQLLKDSEIGYYIETPKTKNGKRELPLTerayqaiqrilknrgkaqpli 296
Cdd:cd01187    19 VQAAVFTGARASELATLKFG--------CLHAQTSDDGTFLYWLKWENKGGKQLDIPIS--------------------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 297 vggysnflflnreglPKVAGnyegmvrgLIKKYNKY------------HTDKLPNITPHSFRHTYCTNMANRGMNPNTLQ 364
Cdd:cd01187    70 ---------------KKVAE--------LIKTINWTlnelselknisdDHGERFRFHTHRFRHTVATRLANSGMGILVLQ 126

                         170
                  ....*....|....
gi 2124955637 365 YLMGHANITMTLGY 378
Cdd:cd01187   127 QLLGHSSPEMTLRY 140
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 188-380 3.44e-10

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: 58.67  E-value: 3.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 188 QKVILTPEQEERLLAFMETDKIYSKYYDEVVLLLETGLRISEFCGLT-THIDMQNRILNIDhqllkdseigyyietpKTK 266
Cdd:cd01197     3 QRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHlSDVDLESRRLHIR----------------RLK 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 267 NGKREL-PLTERAYQAIQRILKNRGKAQplivGGYSNFLFLNREGLPKVagnyEGMVRGLIKKYNKYHTDKLPNiTPHSF 345
Cdd:cd01197    67 NGFSTThPLRFDEREALEAWLKERANWK----GADTDWIFLSRRGGPLS----RQQAYRIIRDLGKEAGTVTQT-HPHML 137

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2124955637 346 RHTYCTNMANRGMNPNTLQYLMGHANITMTLGYYA 380
Cdd:cd01197   138 RHACGYALADRGADTRLIQDYLGHRNIRHTVIYTA 172
PRK09870 PRK09870
tyrosine recombinase; Provisional
 185-380 2.07e-09

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 56.87  E-value: 2.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 185 DTEQKVILTPEQEERLLAFMETDKIYSKYYDEVVLLLETGLRISEFCGLtthidmqnRILNIDhqlLKDSEIgyYIETPK 264
Cdd:PRK09870    6 DNKKRNFLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRL--------RISDID---LKAKCI--YIHRLK 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 265 tKNGKRELPLTERAYQAIQRILKNRGKAQPlivgGYSNFLFLNREGLPKVAGNYEGMVRGLIKKYnkyhtdKLP-NITPH 343
Cdd:PRK09870   73 -KGFSTTHPLLNKEIQALKNWLSIRTSYPH----AESEWVFLSRKGNPLSRQQFYHIISTSGGNA------GLSlEIHPH 141

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2124955637 344 SFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGYYA 380
Cdd:PRK09870  142 MLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTA 178
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 198-378 4.12e-09

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: 55.35  E-value: 4.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 198 ERLLAFMETDKIYSKYYDEV----VLLLETGLRISEfcgltthidmqnrILNIDHQLLKDSEIGYYIETPKTKNGKR-EL 272
Cdd:cd01185     1 EELKRLMALELSDTSRLELVrdmfLFSCYTGLRFSD-------------LKNLTWKNIVEASGRTWIRYRRKKTGKPvTV 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 273 PLTERAYQAIQRILKNRGKaqPLIVGGYSNFLFlnREGLPKVAGNYEgmvrglIKKynkyhtdklpNITPHSFRHTYCTN 352
Cdd:cd01185    68 PLLPVAREILEKYKDDRSE--GKLFPVLSNQKI--NRYLKEIAKIAG------IDK----------HLTFHVARHTFATL 127

                         170       180
                  ....*....|....*....|....*.
gi 2124955637 353 MANRGMNPNTLQYLMGHANITMTLGY 378
Cdd:cd01185   128 LLLKGVDIETISKLLGHSSIKTTQIY 153
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 193-370 4.63e-09

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: 55.35  E-value: 4.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 193 TPEQEERLLAFMETDKIYSKYYDEVVLLLETGLRISEFCGLT-THIDMQNRILNIDHQllkdseigyyietpKTKNGK-R 270
Cdd:cd00801     1 SPDELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARwSEIDLEEKTWTIPAE--------------RTKNKRpH 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 271 ELPLTERAYQAIQRILKnrgkaqpliVGGYSNFLFlnreglPKVAGNYEGMVRGLIKKYNKYHTDKLPNITPHSFRHTYC 350
Cdd:cd00801    67 RVPLSDQALEILEELKE---------FTGDSGYLF------PSRRKKKKPISENTINKALKRLGYKGKEFTPHDLRRTFS 131

                         170       180
                  ....*....|....*....|
gi 2124955637 351 TNMANRGMNPNTLQYLMGHA 370
Cdd:cd00801   132 TLLNELGIDPEVIERLLNHV 151
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 193-395 5.30e-09

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: 55.33  E-value: 5.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 193 TPEQEERLLAFMETDKIYSKY-YDEVVLLLETGLRISEFCGLtthidmqnRILNIDHqllKDSEIGYYietpKTKNGK-R 270
Cdd:cd01188     1 SPDEVRRLLAAIDRLTPVGLRdYAILLLLARLGLRAGDVAGL--------RLDDIDW---RSGTITVR----QKKTGRpV 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 271 ELPLTERAYQAIQRILKNRGKAQPlivggySNFLFLnREGLPKVAGNYEGMVRGLIKKYnkYHTDKLPNIT--PHSFRHT 348
Cdd:cd01188    66 ELPLTEPVGEALADYLRDGRPRTD------SREVFL-RARAPYRPLSSTSQISSIVRRY--LRKAGIEPSHrgTHSLRHS 136

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2124955637 349 YCTNMANRGMNPNTLQYLMGHANITMTLGYyahgtfqsAKAELERLA 395
Cdd:cd01188   137 LATRMLRAGTSLKVIADLLGHRSIETTAIY--------AKIDVDDLR 175
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 217-390 9.20e-08

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: 51.65  E-value: 9.20e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 217 VVLLLETGLRISEFCGLtthidmqnRILNI---DHQL-LKDSEIGYYIETpKTKNGKRELPLTerayQAIQRILKNRGKA 292
Cdd:cd01186    23 LALLYETGLRIGEALGL--------RIEDIdmaDNQIeLVPREDNTNEAR-AKSMRERRIPVS----QDLIDLYADYLTY 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 293 ---QPLIVGGYsnfLFLNREGLPKVAGNYEGMVRGLIKKYNKyHTDKlpNITPHSFRHTYCTNMANRGMNPNTLQYLMGH 369
Cdd:cd01186    90 iycEEAEFSIT---VFVNVKGGNQGKAMNYSDVYDLVRRLKK-RTGI--DFTPHMFRHTHATALIRAGWSIEVVARRLGH 163

                         170       180
                  ....*....|....*....|.
gi 2124955637 370 ANITMTLGYYAHGTFQSAKAE 390
Cdd:cd01186   164 AHVQTTLNTYGHLSEEDIRRE 184
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 191-378 1.16e-07

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 53.21  E-value: 1.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 191 ILTPEQEERLLAFMETDKIYSkYYDEVVL--LLETGLRISEFCGLTTH-IDMQNRILNIDhqllkdseigyyietpKTKN 267
Cdd:PRK01287  136 ILSEAETEQVLASPDLTTLQG-LRDRALLelLWSTGIRRGELARLDLYdVDASRGVVTVR----------------QGKG 198

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 268 GK-RELPLTERAYQAIQRILKNrgkAQP-LIVGGYSNFLF-------LNREGLPKVAGNYegMVRGLIKKYNkyhtdklp 338
Cdd:PRK01287  199 NKdRVVPVGERALAWLQRYLQD---VRPqLAVRPDSGALFvamdgdgLARNTLTNMVGRY--IRAAGIEKAG-------- 265

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2124955637 339 niTPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGY 378
Cdd:PRK01287  266 --ACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 192-395 2.68e-07

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: 50.77  E-value: 2.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 192 LTPEQEERLLA----FMETDKIYSKYYDEVVLLLE-TGLRISEFCGLTTH-IDMQNRILNIDhqllkdseigyyietpKT 265
Cdd:cd00797     1 YTDAEIRRLLAaadqLPPESPLRPLTYATLFGLLYaTGLRVGEALRLRLEdVDLDSGILTIR----------------QT 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 266 KNGK-RELPLTERAYQAIQRILKNRGKAQPLIVGGYsnfLFLNREGLPKVAGNYEGMVRGLIKKYNKYHTD--KLPNItp 342
Cdd:cd00797    65 KFGKsRLVPLHPSTVGALRDYLARRDRLLPSPSSSY---FFVSQQGGRLTGGGVYRVFRRLLRRIGLRGAGdgRGPRL-- 139

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2124955637 343 HSFRHTYCTNMANR----GMNP-NTLQYL---MGHANITMTlGYYAHGTfqsakAELERLA 395
Cdd:cd00797   140 HDLRHTFAVNRLTRwyreGADVeRKLPVLstyLGHVNVTDT-YWYLTAT-----PELMELA 194
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 192-393 4.03e-07

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: 49.97  E-value: 4.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 192 LTPEQEERLLAFMETDKiYSKYYDEVVLLL--ETGLRISEFCGLTthidmqnrilnidhqllkdseIGYYIETPKTK--- 266
Cdd:cd01182     1 LTREEMKALLAAPDRNT-SLGRRDHALLLLlyDTGARVQELADLT---------------------IRDLRLDDPATvrl 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 267 NGK----RELPLTERAYQAIQRILKNRgkaQPLIVGGYSNFLFLNREGLPKVAGNyegmVRGLIKKYNKYHTDKLPN--- 339
Cdd:cd01182    59 HGKgrkeRTVPLWKETVAALKAYLQEF---HLTPDPKQLFPLFPNRRGQPLTRDG----VAYILNKYVALASNRCPSlpk 131

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2124955637 340 -ITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGYyahgtfqsAKAELER 393
Cdd:cd01182   132 rITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIY--------AEADLEM 178
int PHA02601
integrase; Provisional
 192-381 2.39e-06

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 48.96  E-value: 2.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 192 LTPEQEERLLAFMETDKiySKYYDEVVLL-LETGLRISEFCGLTTHIDMQNRILNIdhqllkdseigyyietpKTKNGK- 269
Cdd:PHA02601  173 LTKEEIERLLDACDGSR--SPDLGLIAKIcLATGARWSEAETLKRSQISPYKITFV-----------------KTKGKKn 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 270 RELPLTERAYQAIQrilKNRGKaqplivggysnfLFlnreglPKVAGNYEGMVRglikkynKYHTDKLPNITPHSFRHTY 349
Cdd:PHA02601  234 RTVPISEELYKMLP---KRRGR------------LF------KDAYESFERAVK-------RAGIDLPEGQATHVLRHTF 285

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2124955637 350 CTN-MANRGmNPNTLQYLMGHANITMTLGyYAH 381
Cdd:PHA02601  286 ASHfMMNGG-NILVLQRILGHATIEMTMA-YAH 316
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 192-380 3.51e-06

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: 46.98  E-value: 3.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 192 LTPEQEERLLAFMETDKIYSKYYDEVV--LLLETGLRISEFCGLTTHiDMQNRilnidhqllkDSEIGYYIETpKTKNGK 269
Cdd:cd01194     1 LTLEQARQLLASLPIDDSIIGLRDRAIisLMVTEGLRTVEIVRADVG-DLRQE----------GEGTILYVQG-KGKTSK 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 270 RE-LPLTERAYQAIQRILKNRGKAQPlivggySNFLFLNreglpkVAGNYEGM------VRGLIKKYNKYHTDKLPNITP 342
Cdd:cd01194    69 DDfVYLRPDVLKALQAYLKARGKLDF------EEPLFTS------LSNNSKGQrlttrsIRRIIKKYLRKAGLDDDRLTA 136

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2124955637 343 HSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGYYA 380
Cdd:cd01194   137 HSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIYAH 174
PRK15417 PRK15417
integron integrase;
190-378 3.09e-04

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 42.34  E-value: 3.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 190 VILTPEQEERLLAFMETD-KIYSKyydevvLLLETGLRISEfcGLTTHIdmqnRILNIDHQLL-----KDSEIGYYIETP 263
Cdd:PRK15417  115 VVLTPDEVVRILGFLEGEhRLFAQ------LLYGTGMRISE--GLQLRV----KDLDFDHGTIivregKGSKDRALMLPE 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 264 KTKNGKRELPLTERAY---------------QAIQRILKNRGKAQPLI-VGGYSNFLFLNREGLPKVAGNYEGMVRGLIK 327
Cdd:PRK15417  183 SLAPSLREQLSRARAWwlkdqaegrsgvalpDALERKYPRAGHSWPWFwVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFK 262

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2124955637 328 KYNKYHTDKLPnITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGY 378
Cdd:PRK15417  263 RAVEQAGITKP-ATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIY 312
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 212-378 7.96e-04

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: 40.10  E-value: 7.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 212 KYYDEVVLLLETGLRISEFCGLtthidmqnrilNIDHqllkdSEIGYYieTPKTKNGKrelplTERAYqaIQRILKNRGK 291
Cdd:cd01191    21 EWYFVVRFLAATGARVSELIKI-----------KVEH-----VELGYF--DIYSKGGK-----LRRLY--IPKKLRNEAL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 292 AQPLIVGGYSNFLFLNREGLPKVAgnyEGMVRGLIKKYNKYHTDKlPNITPHSFRHTYCTNMANRGMNPNTLQYLMGHAN 371
Cdd:cd01191    76 EWLKSTNRKSGYIFLNRFGERITT---RGIAQQLKNYARKYGLNP-KVVYPHSFRHRFAKNFLEKYNDIALLADLMGHES 151


                  ....*..
gi 2124955637 372 ITMTLGY 378
Cdd:cd01191   152 IETTRIY 158
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 219-394 2.79e-03

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 39.52  E-value: 2.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 219 LLLETGLRISEFCGLTT-HIDMQNRILNIDHqllkdseigyyietpktKNGKRE-LPLTERAYQAIQRILK---NRGKAQ 293
Cdd:PRK05084  203 LILGSGLRVSELVNLDLsDLNLKQMTIDVTR-----------------KGGKRDsVNIAPFALPYLEEYLKiraSRYKAE 265

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 294 PlivggYSNFLFLNREGlpkvaGNYEGM-VRGLIKKYNKYHTDKLPNITPHSFRHTYCTNMANRGMNPNTLQYLMGHANi 372
Cdd:PRK05084  266 K-----QEKALFLTKYR-----GKPNRIsARAIEKMVAKYSEAFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTS- 334

                         170       180
                  ....*....|....*....|..
gi 2124955637 373 TMTLGYYAHGTFQSAKAELERL 394
Cdd:PRK05084  335 TETTDLYTHIVNDEQKEALDRL 356
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 190-378 2.94e-03

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: 39.30  E-value: 2.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 190 VILTPEQEERLLAFMETdkiysKYYDEVVLLLETGLRISEFcgltthidMQNRIlnidhqllKDSEIGY-YIETPKTKNG 268
Cdd:TIGR02249 100 VVLTREEVRRLLEHLEG-----KYRLIAKLLYGSGMRLMEC--------LRLRI--------QDIDFDYgEIRIRQGKGG 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 269 K-RELPLTERAYQAIQRILK----------NRGKAQPLIVGG----YSN--------FLF----LNREGLPKVAG----N 317
Cdd:TIGR02249 159 KdRTVTLPKELIPPLREQIElarayheadlAEGYGGVYLPHAlarkYPNapkewgwqYLFpshrLSRDPESGVIRrhhiN 238

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2124955637 318 YEGMVRGLIKKYNKYHTDKlpNITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGY 378
Cdd:TIGR02249 239 ETTIQRAVRRAVERAGIEK--PVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 221-378 5.30e-03

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: 37.66  E-value: 5.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124955637 221 LETGLRISEFCGLTthidmQNRILNIDHQLLKDSeigyyietpktKNGK-RELPLTERAYQAIQRILKNRGKAQPLIvgg 299
Cdd:cd01192    34 INTGLRISDLLSLK-----VEDVTNKDKLSIKEQ-----------KTGKqKTFPLNPTLVKALKEYIDDLDLKRNDY--- 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2124955637 300 YSNFLFLNREGLPKVAGNYEGMVRGLIKKYNKYhtdklpNITPHSFRHTYCTNMANRGMNPNTLQYLMGHANITMTLGY 378
Cdd:cd01192    95 LFKSLKQGPEKPISRKQAYKILKKAADDLGLNY------NIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
 
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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