NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1484098566|gb|RJU76011|]
View 

recombinase [Bacteroides sp. AM28-6]

Protein Classification

tyrosine-type recombinase/integrase( domain architecture ID 11471964)

tyrosine-type recombinase/integrase cleaves 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.

Gene Ontology:  GO:0009009|GO:0006310
PubMed:  10047575|9278480

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
96-363 9.77e-74

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 230.65  E-value: 9.77e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  96 YLE-LLEQKRYSPSTIKTYRAYFSDFMEY---HKGRNIDRLKVADINKYILYLVnEKKISVSQQNMRINAIKFYYEQ-VK 170
Cdd:COG4974    10 FLEeLKREKGLSPNTIKAYRRDLRRFLRFleeLGKIPLAEITPEDIRAYLNYLR-ERGLSPSTINRYLAALRSFFRYaVR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 171 GGKRQY--YGGITRAKEYKSLPEVLSKNEIKRILAQIS-----NIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVR 243
Cdd:COG4974    89 EGLLEDnpAAKVKLPKKPRKLPRVLTEEEIEALLEALDtetpeGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIR 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 244 IM-GKGKKCRYSLLSPKLLEELRHYFREYRPQK--WLFEGETpGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFAT 320
Cdd:COG4974   169 VRrGKGGKERTVPLSPEALEALREYLEERRPRDsdYLFPTRR-GRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFAT 247

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1484098566 321 HLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKIPNPLD 363
Cdd:COG4974   248 HLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
96-363 9.77e-74

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 230.65  E-value: 9.77e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  96 YLE-LLEQKRYSPSTIKTYRAYFSDFMEY---HKGRNIDRLKVADINKYILYLVnEKKISVSQQNMRINAIKFYYEQ-VK 170
Cdd:COG4974    10 FLEeLKREKGLSPNTIKAYRRDLRRFLRFleeLGKIPLAEITPEDIRAYLNYLR-ERGLSPSTINRYLAALRSFFRYaVR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 171 GGKRQY--YGGITRAKEYKSLPEVLSKNEIKRILAQIS-----NIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVR 243
Cdd:COG4974    89 EGLLEDnpAAKVKLPKKPRKLPRVLTEEEIEALLEALDtetpeGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIR 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 244 IM-GKGKKCRYSLLSPKLLEELRHYFREYRPQK--WLFEGETpGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFAT 320
Cdd:COG4974   169 VRrGKGGKERTVPLSPEALEALREYLEERRPRDsdYLFPTRR-GRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFAT 247

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1484098566 321 HLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKIPNPLD 363
Cdd:COG4974   248 HLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 189-350 1.49e-66

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: 208.28  E-value: 1.49e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 189 LPEVLSKNEIKRILAQISNIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRI-MGKGKKCRYSLLSPKLLEELRHY 267
Cdd:cd01193     2 LPVVLSPDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVrQGKGGKDRVVPLPEKLLEPLRRY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 268 FREYRPQKWLFEGETPGE------------KYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQEL 335
Cdd:cd01193    82 LKSARPKEELDPAEGRAGvldprtgverrhHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRTIQEL 161

                         170
                  ....*....|....*
gi 1484098566 336 LGHNDIKTTTIYLHV 350
Cdd:cd01193   162 LGHSDLSTTMIYTHV 176
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 96-351 1.41e-53

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: 178.54  E-value: 1.41e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  96 YLELLE-QKRYSPSTIKTYRAYFSDFMEY--HKGRNIDRLKVADINKYILYLVnEKKISVSQQNMRINAIKFYY------ 166
Cdd:TIGR02225   3 FLDYLWvERGLSQNTLEAYRRDLEKFLEFleERGIDLEEVDRGDIVDFLAELK-EAGLSARSIARALSALRSFYrfllre 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 167 --------EQVKGGKRQyyggitrakeyKSLPEVLSKNEIKRILAQISN-----IKHHCMISLVYSAGLRRSELLNLTPQ 233
Cdd:TIGR02225  82 gireddpsALIEPPKVA-----------RKLPKVLTVEEVEALLAAPDVdtplgLRDRAMLELLYATGLRVSELVGLRLE 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 234 DINSETMSVRIMGKGKKCRYSLLSPKLLEELRHYFREYRPQK---------WLFEGeTPGEKYSASALVKVLKEAAHRAG 304
Cdd:TIGR02225 151 DVNLDEGFVRVRGKGNKERLVPLGEEAIEALERYLKEARPLLlkkkvkesdALFLN-RRGGPLSRQGVWKILKEYAKRAG 229

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1484098566 305 IKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVS 351
Cdd:TIGR02225 230 IEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVA 276
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 96-358 1.45e-50

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 171.11  E-value: 1.45e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  96 YLELLE-QKRYSPSTIKTYR---AYFSDFMEYHKGRNIDRLKVADINKYILYLVNE--KKISVSQqnmRINAIK-F--YY 166
Cdd:PRK00236   13 FLEYLRvERGLSPHTLRAYRrdlRAFLAFLEEHGISSLQDLDAADLRSFLARRRRQglSARSLAR---RLSALRsFyrWL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 167 EQVKGGKRQYYGGITRAKEYKSLPEVLSKNEIKRILAQISN-----IKHHCMISLVYSAGLRRSELLNLTPQDINSETMS 241
Cdd:PRK00236   90 VRRGLLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEddplaLRDRAILELLYGSGLRLSELVGLDIDDLDLASGT 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 242 VRIMGKGKKCRYSLLSPKLLEELRHYF--REY--RPQKWLFEGETpGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHS 317
Cdd:PRK00236  170 LRVLGKGNKERTVPLGRAAREALEAYLalRPLflPDDDALFLGAR-GGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHS 248

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1484098566 318 FATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKI 358
Cdd:PRK00236  249 FATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEV 289
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 192-351 1.46e-33

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: 122.43  E-value: 1.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 192 VLSKNEIKRILAQISN----IKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRI-MGKGKKCRYSLLSPKLLEELRH 266
Cdd:pfam00589   1 RLTEDEVERLLDAAETgplsIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVhRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 267 Y----FREYRPQKWLFEGeTPGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIK 342
Cdd:pfam00589  81 WlskrLLEAPKSDYLFAS-KRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIS 159


                  ....*....
gi 1484098566 343 TTTIYLHVS 351
Cdd:pfam00589 160 TTQIYTHVA 168
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
96-363 9.77e-74

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 230.65  E-value: 9.77e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  96 YLE-LLEQKRYSPSTIKTYRAYFSDFMEY---HKGRNIDRLKVADINKYILYLVnEKKISVSQQNMRINAIKFYYEQ-VK 170
Cdd:COG4974    10 FLEeLKREKGLSPNTIKAYRRDLRRFLRFleeLGKIPLAEITPEDIRAYLNYLR-ERGLSPSTINRYLAALRSFFRYaVR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 171 GGKRQY--YGGITRAKEYKSLPEVLSKNEIKRILAQIS-----NIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVR 243
Cdd:COG4974    89 EGLLEDnpAAKVKLPKKPRKLPRVLTEEEIEALLEALDtetpeGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIR 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 244 IM-GKGKKCRYSLLSPKLLEELRHYFREYRPQK--WLFEGETpGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFAT 320
Cdd:COG4974   169 VRrGKGGKERTVPLSPEALEALREYLEERRPRDsdYLFPTRR-GRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFAT 247

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1484098566 321 HLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKIPNPLD 363
Cdd:COG4974   248 HLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 189-350 1.49e-66

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: 208.28  E-value: 1.49e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 189 LPEVLSKNEIKRILAQISNIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRI-MGKGKKCRYSLLSPKLLEELRHY 267
Cdd:cd01193     2 LPVVLSPDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVrQGKGGKDRVVPLPEKLLEPLRRY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 268 FREYRPQKWLFEGETPGE------------KYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQEL 335
Cdd:cd01193    82 LKSARPKEELDPAEGRAGvldprtgverrhHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRTIQEL 161

                         170
                  ....*....|....*
gi 1484098566 336 LGHNDIKTTTIYLHV 350
Cdd:cd01193   162 LGHSDLSTTMIYTHV 176
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
96-358 1.26e-54

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 181.31  E-value: 1.26e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  96 YLELLEQKRYSPSTIKTYRAYFSDFMEY--HKGRNIDRLKVADINKYILYLVnEKKISVSQQNMRINAIK-FYYEQVKGG 172
Cdd:COG4973    11 YLEHLRERRLSPKTLEAYRRDLRRLIPLlgDADLPLEELTPADVRRFLARLH-RRGLSPRTLNRRLSALRsFFNWAVREG 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 173 KRQY--YGGITRAKEYKSLPEVLSKNEIKRILAQISN----IKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRIMG 246
Cdd:COG4973    90 LLEAnpAAGVKAPKAPRKLPRALTVDELAQLLDALADdplaVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 247 KGKKCRYSLLSPKLLEELRHYFRE-----YRPQKWLFEGETpGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATH 321
Cdd:COG4973   170 KTGKSRTVPLGPKALAALREWLAVrpelaAPDEGALFPSRR-GTRLSPRNVQKRLRRLAKKAGLPKHVHPHDLRHSFATH 248

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1484098566 322 LLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKI 358
Cdd:COG4973   249 LLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEV 285
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 96-351 1.41e-53

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: 178.54  E-value: 1.41e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  96 YLELLE-QKRYSPSTIKTYRAYFSDFMEY--HKGRNIDRLKVADINKYILYLVnEKKISVSQQNMRINAIKFYY------ 166
Cdd:TIGR02225   3 FLDYLWvERGLSQNTLEAYRRDLEKFLEFleERGIDLEEVDRGDIVDFLAELK-EAGLSARSIARALSALRSFYrfllre 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 167 --------EQVKGGKRQyyggitrakeyKSLPEVLSKNEIKRILAQISN-----IKHHCMISLVYSAGLRRSELLNLTPQ 233
Cdd:TIGR02225  82 gireddpsALIEPPKVA-----------RKLPKVLTVEEVEALLAAPDVdtplgLRDRAMLELLYATGLRVSELVGLRLE 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 234 DINSETMSVRIMGKGKKCRYSLLSPKLLEELRHYFREYRPQK---------WLFEGeTPGEKYSASALVKVLKEAAHRAG 304
Cdd:TIGR02225 151 DVNLDEGFVRVRGKGNKERLVPLGEEAIEALERYLKEARPLLlkkkvkesdALFLN-RRGGPLSRQGVWKILKEYAKRAG 229

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1484098566 305 IKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVS 351
Cdd:TIGR02225 230 IEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVA 276
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 96-358 2.15e-53

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: 178.18  E-value: 2.15e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  96 YLELLE-QKRYSPSTIKTYR---AYFSDFMEYHKG-RNIDRLKVADINKYILYLvNEKKISVSQQNMRINAIKFYYEQVK 170
Cdd:TIGR02224   3 FLEYLRlERNYSPHTVRAYRrdlEAFLEFLEEEGGlASLAEVTAADLRSFLAEL-HARGLSRRSLARKLSALRSFYRFLL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 171 ggKRQY-----YGGITRAKEYKSLPEVLSKNEIKRILAQISN-------IKHHCMISLVYSAGLRRSELLNLTPQDINSE 238
Cdd:TIGR02224  82 --RRGLidanpAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEddedwlaLRDRAILELLYSSGLRVSELVGLDLSDLDLD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 239 TMSVRIMGKGKKCRYSLLSPKLLEELRHYfREYRPQKWLFEGETP-------GEKYSASALVKVLKEAAHRAGIKHRVHV 311
Cdd:TIGR02224 160 FGEVRVRGKGNKERIVPFGPYARDALQAY-LEARRSPLLASEGQDalflnrrGGRLTPRGVQYRLQQLRAKAGLPKHVHP 238

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1484098566 312 HMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKI 358
Cdd:TIGR02224 239 HALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKV 285
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 98-365 3.06e-53

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: 178.36  E-value: 3.06e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  98 ELLEQKRYSPSTIKTYRAYFSDFMEYHKGRNIDRLKVADINKYILYLVNEKKISVSQQNMRINAIKFYYEQVKGGKRQYY 177
Cdd:TIGR02249   7 EHMRTRHYAKRTEEAYLHWIKRFIRFHNKRHPSTMGDTEVEAFLSDLAVDGKVAASTQNQALNALLFLYKEILKTPLSLM 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 178 GGITRAKEYKSLPEVLSKNEIKRILAQISNiKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRIM-GKGKKCRYSLL 256
Cdd:TIGR02249  87 ERFVRAKRPRKLPVVLTREEVRRLLEHLEG-KYRLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRqGKGGKDRTVTL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 257 SPKLLEELR--------HYFREYRPQ-----------------------KWLFegetPGEKYS--------------ASA 291
Cdd:TIGR02249 166 PKELIPPLReqielaraYHEADLAEGyggvylphalarkypnapkewgwQYLF----PSHRLSrdpesgvirrhhinETT 241

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1484098566 292 LVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKIPNPLDTL 365
Cdd:TIGR02249 242 IQRAVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVLNRGASGVLSPLDRL 315
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 96-358 1.45e-50

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 171.11  E-value: 1.45e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  96 YLELLE-QKRYSPSTIKTYR---AYFSDFMEYHKGRNIDRLKVADINKYILYLVNE--KKISVSQqnmRINAIK-F--YY 166
Cdd:PRK00236   13 FLEYLRvERGLSPHTLRAYRrdlRAFLAFLEEHGISSLQDLDAADLRSFLARRRRQglSARSLAR---RLSALRsFyrWL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 167 EQVKGGKRQYYGGITRAKEYKSLPEVLSKNEIKRILAQISN-----IKHHCMISLVYSAGLRRSELLNLTPQDINSETMS 241
Cdd:PRK00236   90 VRRGLLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEddplaLRDRAILELLYGSGLRLSELVGLDIDDLDLASGT 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 242 VRIMGKGKKCRYSLLSPKLLEELRHYF--REY--RPQKWLFEGETpGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHS 317
Cdd:PRK00236  170 LRVLGKGNKERTVPLGRAAREALEAYLalRPLflPDDDALFLGAR-GGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHS 248

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1484098566 318 FATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKI 358
Cdd:PRK00236  249 FATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEV 289
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 197-354 4.42e-48

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: 160.37  E-value: 4.42e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 197 EIKRILAQISNIKHH-----CMISLVYSAGLRRSELLNLTPQDINSETMSVRIMGKGKKCRYSLLSPKLLEELRHYFREY 271
Cdd:cd00798     3 EVERLLDAPDTDTPLglrdrAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLEER 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 272 RPqkWLFEGETP--------GEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKT 343
Cdd:cd00798    83 RP--LLLKKKPPdalflnkrGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLST 160

                         170
                  ....*....|.
gi 1484098566 344 TTIYLHVSSAH 354
Cdd:cd00798   161 TQIYTHVSFER 171
xerD PRK00283
tyrosine recombinase;
94-354 7.45e-42

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 148.03  E-value: 7.45e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  94 KGYLELLEQKR-YSPSTIKTYRAYFSDFMEYHKGRNIDRLKV--ADINKYILYLVnEKKISVSQQNMRINAIKFYYEQVK 170
Cdd:PRK00283   10 EQFLDALWVERgLAENTLSSYRRDLELFAEWLAARGLSLAEAtrDDLQAFLAELA-EGGYKATSSARRLSALRRFFQFLL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 171 G-GKRQY--YGGITRAKEYKSLPEVLSKNEIKRILAQIS-----NIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSV 242
Cdd:PRK00283   89 ReGLREDdpSALLDSPKLPRRLPKTLSEAQVEALLDAPDidtplGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQGVV 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 243 RIMGKGKKCRYSLLSPKLLEELRHYFREYRPQ-------KWLFegetP---GEKYSASALVKVLKEAAHRAGIKH-RVHV 311
Cdd:PRK00283  169 RVTGKGNKERLVPLGEEAVYAIERYLERGRPAllngrssDALF----PsarGGQLTRQTFWHRIKHYAKRAGIDPkKLSP 244

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1484098566 312 HMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAH 354
Cdd:PRK00283  245 HVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATER 287
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 192-351 1.46e-33

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: 122.43  E-value: 1.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 192 VLSKNEIKRILAQISN----IKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRI-MGKGKKCRYSLLSPKLLEELRH 266
Cdd:pfam00589   1 RLTEDEVERLLDAAETgplsIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVhRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 267 Y----FREYRPQKWLFEGeTPGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIK 342
Cdd:pfam00589  81 WlskrLLEAPKSDYLFAS-KRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIS 159


                  ....*....
gi 1484098566 343 TTTIYLHVS 351
Cdd:pfam00589 160 TTQIYTHVA 168
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 197-348 1.45e-32

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: 119.89  E-value: 1.45e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 197 EIKRILAQIS-----NIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRIMGKG---KKCRYSLLSPKLLEELRHYF 268
Cdd:cd00397     1 ELEKLLDAIDedkkiDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkgGKERTVPLPKELAEELKEYL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 269 REYRPQKWLFEGETP-----GEKYSASALVKVLKEAAHRAGIK--HRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDI 341
Cdd:cd00397    81 KERRDKRGPLLKSLYlnklfGTKLGERLSRRTLRRIFKKAGIEagRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSI 160


                  ....*..
gi 1484098566 342 KTTTIYL 348
Cdd:cd00397   161 STTQRYL 167
PRK15417 PRK15417
integron integrase;
98-365 3.33e-30

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 118.23  E-value: 3.33e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  98 ELLEQKRYSPSTIKTYRAYF---SDFMEYHKGRNIDRLKVADINKYILYLVNEKKISVSQQNMRINAIKFYYEQVKGGKR 174
Cdd:PRK15417   19 QLRERIRYLHYSLRTEQAYVhwvRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDL 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 175 QYYGGITRAKEYKSLPEVLSKNEIKRILAQISNIkHHCMISLVYSAGLRRSELLNLTPQDINSE--TMSVRiMGKGKKCR 252
Cdd:PRK15417   99 PWLQEIGRPRPSRRLPVVLTPDEVVRILGFLEGE-HRLFAQLLYGTGMRISEGLQLRVKDLDFDhgTIIVR-EGKGSKDR 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 253 YSLLSPKLLEELRHYFREYR-------------------------------PQKWLFEGETPGEKYSASAL--------- 292
Cdd:PRK15417  177 ALMLPESLAPSLREQLSRARawwlkdqaegrsgvalpdalerkypraghswPWFWVFAQHTHSTDPRSGVVrrhhmydqt 256

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1484098566 293 -VKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKIPNPLDTL 365
Cdd:PRK15417  257 fQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDAL 330
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 82-358 1.87e-28

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 113.69  E-value: 1.87e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566  82 RHPKPQREYILpkGYLELLEQKRYSPSTIKTYRAYFSDFMEYHKGRNIdrLKVADINKYIL-----YL-----VNEKKIS 151
Cdd:PRK01287   16 HDPKTLRQLLE--RFLAWLQERNWSERTLKVYTEHLYPFILWCEERGL--YYAADVTLPVLeryqrYLygyrkANGEPLS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 152 VSQQNMRINAIKFYYEQVKggKRQYY-----GGITRAKEYKSLP-EVLSKNEIKRILAQIS-----NIKHHCMISLVYSA 220
Cdd:PRK01287   92 TRTQRTQLSPLRVWFRWLL--KRHHIlynpaEDLELPKEEKRLPrQILSEAETEQVLASPDlttlqGLRDRALLELLWST 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 221 GLRRSELLNLTPQDINS--ETMSVRiMGKGKKCRYSLLSPKLLEELRHYFREYRPQ-------KWLFEGETpGEKYSASA 291
Cdd:PRK01287  170 GIRRGELARLDLYDVDAsrGVVTVR-QGKGNKDRVVPVGERALAWLQRYLQDVRPQlavrpdsGALFVAMD-GDGLARNT 247

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1484098566 292 LVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKI 358
Cdd:PRK01287  248 LTNMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAV 314
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 193-355 3.33e-27

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: 106.21  E-value: 3.33e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 193 LSKNEIKRILAQI-----SNIKHHCMISLVYSAGLRRSELLNLTPQDINSETMS-VRIMGKGKKCRYSLLSPKLLEELRH 266
Cdd:cd01182     1 LTREEMKALLAAPdrntsLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPAtVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 267 YFREYRPQKWLFEGET-----PGEKYSASA----LVKVLKEAA-HRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELL 336
Cdd:cd01182    81 YLQEFHLTPDPKQLFPlfpnrRGQPLTRDGvayiLNKYVALASnRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                         170
                  ....*....|....*....
gi 1484098566 337 GHNDIKTTTIYLHVSSAHK 355
Cdd:cd01182   161 GHESVETTQIYAEADLEMK 179
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 191-349 2.19e-26

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: 103.18  E-value: 2.19e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 191 EVLSKNEIKRILAQISNIKHHC---MISLVYSAGLRRSELLNLTPQDINSETMSVRI-MGKGKKCRYSLLSPKLLEELRH 266
Cdd:cd00796     3 RFLTEDEEARLLAALEESTNPHlrlIVLLALYTGARRGEILSLRWDDIDLEVGLIVLpETKNGKPRTVPLSDEAIAILKE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 267 YFREyrPQKWLFEGETPGEKYSASALVKVLKEAAHRAGIkHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTI 346
Cdd:cd00796    83 LKRK--RGKDGFFVDGRFFGIPIASLRRAFKKARKRAGL-EDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMR 159


                  ...
gi 1484098566 347 YLH 349
Cdd:cd00796   160 YAH 162
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 195-349 4.98e-25

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: 98.79  E-value: 4.98e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 195 KNEIKRIL--AQISNIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRI---MGKGKKCRYSLLSPK---------L 260
Cdd:cd01189     1 PEELKKLLeaLKKRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRInrtLVRKKKGGYVIKPPKtkssirtipL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 261 LEELRHYFREYrpqkwlfegetpgekysasalvKVLKEAAHRAGIKHrVHVHMLRHSFATHLLEQGTDLHTIQELLGHND 340
Cdd:cd01189    81 PDELIELLKEL----------------------KAFKKLLKKAGLPR-ITPHDLRHTFASLLLEAGVPLKVIAERLGHSD 137

                         170
                  ....*....|
gi 1484098566 341 IKTTT-IYLH 349
Cdd:cd01189   138 ISTTLdVYAH 147
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 194-350 1.01e-22

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: 93.85  E-value: 1.01e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 194 SKNEIKRILAQISN-----IKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRIMG-KGKKCRYSLLSPKLLEELRHY 267
Cdd:cd01188     1 SPDEVRRLLAAIDRltpvgLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQkKTGRPVELPLTEPVGEALADY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 268 FREYRPQ---KWLFEGET-PGEKYS-ASALVKVLKEAAHRAGI-KHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDI 341
Cdd:cd01188    81 LRDGRPRtdsREVFLRARaPYRPLSsTSQISSIVRRYLRKAGIePSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSI 160


                  ....*....
gi 1484098566 342 KTTTIYLHV 350
Cdd:cd01188   161 ETTAIYAKI 169
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 221-350 2.65e-20

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: 86.55  E-value: 2.65e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 221 GLRRSELLNLTPQDINSETMSVRIMGKGKKC--RYSL-LSPKLLEELRHYfREYRPQKWLFEGetpgekYSASALVKVLK 297
Cdd:cd01185    31 GLRFSDLKNLTWKNIVEASGRTWIRYRRKKTgkPVTVpLLPVAREILEKY-KDDRSEGKLFPV------LSNQKINRYLK 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1484098566 298 EAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHV 350
Cdd:cd01185   104 EIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKI 156
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 193-349 3.68e-18

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: 80.88  E-value: 3.68e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 193 LSKNEIKRILAQISNIKH------HCMISLVYSAGLRRSELLNLTPQDIN--SETMSVRIMGKGK--KCRYSLLSPKLLE 262
Cdd:cd01194     1 LTLEQARQLLASLPIDDSiiglrdRAIISLMVTEGLRTVEIVRADVGDLRqeGEGTILYVQGKGKtsKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 263 ELRHYFR---EYRPQKWLFEGETP---GEKYSASALVKVLKEAAHRAGIK-HRVHVHMLRHSFATHLLEQGTDLHTIQEL 335
Cdd:cd01194    81 ALQAYLKargKLDFEEPLFTSLSNnskGQRLTTRSIRRIIKKYLRKAGLDdDRLTAHSLRHTAGTLALKAGKSLREVQQL 160

                         170
                  ....*....|....
gi 1484098566 336 LGHNDIKTTTIYLH 349
Cdd:cd01194   161 LRHSDPNTTMIYAH 174
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 194-349 1.31e-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: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 79.44  E-value: 1.31e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 194 SKNEIKRILAQISN-----IKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRIMGKGKKCRYSL-LSPKLLEELRHY 267
Cdd:cd01195     1 SREEARQRLDAADRhtakgKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQREVVtLPPTTREALAAW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 268 FREYRPQK---WL-FEGETPGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDL-HTIQELLGHNDIK 342
Cdd:cd01195    81 LAARGEAEgplFVsLDRASRGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGLiRKVQDFSRHADLR 160


                  ....*..
gi 1484098566 343 TTTIYLH 349
Cdd:cd01195   161 TLQVYDD 167
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 212-366 2.82e-16

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 79.19  E-value: 2.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 212 CMISLVYSAGLRRSELLNLTPQDINSETMSVRIMGKGKKCRYSLLSPKLLEELRHYF----REYRPQKW---LFEGETPG 284
Cdd:PRK05084  199 AIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEYLkiraSRYKAEKQekaLFLTKYRG 278

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 285 E--KYSASALVKVLKEAAhrAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSahkAKIPNPL 362
Cdd:PRK05084  279 KpnRISARAIEKMVAKYS--EAFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVN---DEQKEAL 353


                  ....
gi 1484098566 363 DTLD 366
Cdd:PRK05084  354 DRLE 357
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 193-349 2.36e-15

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: 73.88  E-value: 2.36e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 193 LSKNEIKRILAQ---------ISNIKHHCMISLVYSAGLRRSELLNLTPQDIN--SETMSVRiMGKGKKCRYSLLSPKLL 261
Cdd:cd00797     1 YTDAEIRRLLAAadqlppespLRPLTYATLFGLLYATGLRVGEALRLRLEDVDldSGILTIR-QTKFGKSRLVPLHPSTV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 262 EELRHYFREYR-----PQKWLFEGETPGEKYSASALVKVLKEAAHRAGIKHRV-----HVHMLRHSFATHLL----EQGT 327
Cdd:cd00797    80 GALRDYLARRDrllpsPSSSYFFVSQQGGRLTGGGVYRVFRRLLRRIGLRGAGdgrgpRLHDLRHTFAVNRLtrwyREGA 159

                         170       180
                  ....*....|....*....|....*.
gi 1484098566 328 DLHT----IQELLGHNDIKTTTIYLH 349
Cdd:cd00797   160 DVERklpvLSTYLGHVNVTDTYWYLT 185
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 193-347 6.69e-15

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: 72.15  E-value: 6.69e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 193 LSKNEIKRILAQI----SNIKHHCMISLVYSAGLRRSELLNLTPQDI--NSETMSVRIMGKGkkcrYSLLSPKLLEEL-- 264
Cdd:cd01197     7 LTGKEVQALLQAAcrgrTPARDYCLLLLAFRHGFRVSELCDLHLSDVdlESRRLHIRRLKNG----FSTTHPLRFDERea 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 265 -------RHYFREYRPQkWLFEGETPGeKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLG 337
Cdd:cd01197    83 leawlkeRANWKGADTD-WIFLSRRGG-PLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLG 160

                         170
                  ....*....|
gi 1484098566 338 HNDIKTTTIY 347
Cdd:cd01197   161 HRNIRHTVIY 170
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
96-171 1.88e-14

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 68.02  E-value: 1.88e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1484098566  96 YLELLEQKRYSPSTIKTYRAYFSDFMEYHKGRNIDRLKVADINKYILYLVNEKKISVSQQNMRINAIKFYYEQVKG 171
Cdd:pfam13495   5 FREALRLRGYAERTIKAYLRWIRRFLRFHDKKHPEELTEEDIEAYLSHLANERNVSASTQNQALNALSFFYRWVLE 80
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 193-344 2.51e-14

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 73.53  E-value: 2.51e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 193 LSKNEIKRILAQISNIKHH----CMISLVYSAGLRRSELLNLTPQDINSETMSVRI----MgKGKKCRYSLLSPKLLEEL 264
Cdd:COG0582   206 LTPEELPELLRALDAYRGSpvtrLALRLLLLTGVRPGELRGARWSEIDLEAALWTIpaerM-KTRRPHIVPLSRQALEIL 284

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 265 RHYFREYRPQKWLFEGETPGEK-YSASALVKVLKeaahRAGIKHRVhVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKT 343
Cdd:COG0582   285 KELKPLTGDSEYVFPSRRGPKKpMSENTLNKALR----RMGYGRFT-PHGFRHTASTLLNEAGFPPDVIERQLAHKDGNK 359


                  .
gi 1484098566 344 T 344
Cdd:COG0582   360 V 360
PRK09870 PRK09870
tyrosine recombinase; Provisional
 193-347 8.87e-13

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 66.50  E-value: 8.87e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 193 LSKNEIKRILAQISN----IKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRI--MGKGkkcrYSLLSPKLLEELRH 266
Cdd:PRK09870   13 LTHSEIESLLKAANTgphaARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIhrLKKG----FSTTHPLLNKEIQA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 267 Y-----FREYRPQ---KWLFEGETpGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGH 338
Cdd:PRK09870   89 LknwlsIRTSYPHaesEWVFLSRK-GNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLGH 167


                  ....*....
gi 1484098566 339 NDIKTTTIY 347
Cdd:PRK09870  168 RNIRHTVWY 176
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 192-351 3.23e-12

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: 64.36  E-value: 3.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 192 VLSKNEIKRILAQISNIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRIMGKG---KKCRYSLLSPK-------LL 261
Cdd:cd01186     1 VLTPREVQELINACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPREdntNEARAKSMRERripvsqdLI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 262 EELRHYFREYRPQK-----WLF---EGETPGEKYSASALVKVLKEAAHRAGIKhrVHVHMLRHSFATHLLEQGTDLHTIQ 333
Cdd:cd01186    81 DLYADYLTYIYCEEaefsiTVFvnvKGGNQGKAMNYSDVYDLVRRLKKRTGID--FTPHMFRHTHATALIRAGWSIEVVA 158

                         170
                  ....*....|....*....
gi 1484098566 334 ELLGHNDIKTT-TIYLHVS 351
Cdd:cd01186   159 RRLGHAHVQTTlNTYGHLS 177
int PHA02601
integrase; Provisional
 179-362 3.63e-12

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 66.67  E-value: 3.63e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 179 GITRAKEYKSLPEVLSKNEIKRILAQISNIKHH--CMISLV-YSAGLRRSELLNLTPQDInSETMSVRIMGKGKKCRYSL 255
Cdd:PHA02601  159 GIRPFKEAEPELAFLTKEEIERLLDACDGSRSPdlGLIAKIcLATGARWSEAETLKRSQI-SPYKITFVKTKGKKNRTVP 237

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 256 LSPKLLEELrhyfreyrPQKwlfegetpgekysASALVKVLKEAAHRAGIKHRVHV------HMLRHSFATHLLEQGTDL 329
Cdd:PHA02601  238 ISEELYKML--------PKR-------------RGRLFKDAYESFERAVKRAGIDLpegqatHVLRHTFASHFMMNGGNI 296

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1484098566 330 HTIQELLGHNDIKTTTIYLHVSSAH--KAKIPNPL 362
Cdd:PHA02601  297 LVLQRILGHATIEMTMAYAHFAPDHleDAVSLNPL 331
PRK09871 PRK09871
tyrosine recombinase; Provisional
 209-363 3.99e-12

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 64.62  E-value: 3.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 209 KHHCMISLVYSAGLRRSELLNLTPQD--INSETMSVRIMGKGkkcrYSLLSPKLLEELRHYFREYRPQK-WLFEGETP-- 283
Cdd:PRK09871   27 RDYCLILLAYRHGMRISELLDLHYQDldLNEGRINIRRLKNG----FSTVHPLRFDEREAVERWTQERAnWKGADRTDai 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 284 -----GEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHKAKI 358
Cdd:PRK09871  103 fisrrGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTASNAARFAGL 182


                  ....*...
gi 1484098566 359 ---PNPLD 363
Cdd:PRK09871  183 werNNLIN 190
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 194-348 7.44e-12

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: 63.47  E-value: 7.44e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 194 SKNEIKRILA--QISNIKHHCMISLVYSAGLRRSELLNLTPQDI-NSETMSVRIMGKGKKcRYSLLSPKLLEELRHYFRE 270
Cdd:cd01192     8 DKKLIKEIKLylKKANPRNYLLFIVGINTGLRISDLLSLKVEDVtNKDKLSIKEQKTGKQ-KTFPLNPTLVKALKEYIDD 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 271 YRPQ----KWLFEGETPGEKYSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTI 346
Cdd:cd01192    87 LDLKrndyLFKSLKQGPEKPISRKQAYKILKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLR 166


                  ..
gi 1484098566 347 YL 348
Cdd:cd01192   167 YL 168
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 193-349 1.36e-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: 62.71  E-value: 1.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 193 LSKNEIKRILAQISNIKHH---------CMISLvYSaGLRRSELLNLTPQDINSE--TMSVRIM----GKGKKCRYSL-- 255
Cdd:cd01184     1 FTPEELAKIFSSPLYTGCKkkdpalywlPLIGL-YT-GARLNEICQLRVDDIKEEdgIWCIDINddaeGRRLKTKASRrl 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 256 --LSPKLLEE-LRHYFREYR--PQKWLFEGETPGEKYSASALVKVLKEAAHRAGIKH--RVHVHMLRHSFATHLLEQGTD 328
Cdd:cd01184    79 vpIHPRLIELgFLDYVEALRadGKLFLFPEKRDKDGKYSKAASKWFNRLLRKLGIKDdeRKSFHSFRHTFITALKRAGVP 158

                         170       180
                  ....*....|....*....|..
gi 1484098566 329 LHTIQELLGH-NDIKTTTIYLH 349
Cdd:cd01184   159 EELIAQIVGHsRGGVTHDTYGK 180
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 221-349 4.75e-10

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: 58.05  E-value: 4.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 221 GLRRSELLNLTPQDINSETMSVRIMGKGKKCRYSL---LSPKLLEELRHYFREYRPQKWLFEGET-PGEKYSASALVKVL 296
Cdd:cd00801    32 GQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHrvpLSDQALEILEELKEFTGDSGYLFPSRRkKKKPISENTINKAL 111

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1484098566 297 KEAAHRAgikHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTT-IYLH 349
Cdd:cd00801   112 KRLGYKG---KEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGVVRaAYNR 162
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 216-348 9.64e-09

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: 53.89  E-value: 9.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 216 LVYSAGLRRSELLNLTPQDINSETMSVRIMGKGKKCRYSlLSPKL---LEELRHYFReyRPQKWLFEGETpGEKYSASAL 292
Cdd:cd00800    20 LALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIP-WTPSLralVDRIRALPR--KRSEYLINSRK-GGPLSYDTL 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1484098566 293 VKVLKEAAHRAGIK---HRVHVHMLRHSFATHLLEQGtDLHTIQELLGHNDIKTTTIYL 348
Cdd:cd00800    96 KSAWRRARKAAGLKgetEGFTFHDLRAKAATDYAEQG-GSTDAQALLGHKSDAMTERYT 153
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 198-358 3.32e-08

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: 52.81  E-value: 3.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 198 IKRILAQISNIKHHCMISLVYSAGLRRSELLNLTPQDInsETMSVRIMGKGKKCRYSLLSPKLLEELRHYFREY-RPQKW 276
Cdd:cd01191    10 LKKCLKKDGNLEWYFVVRFLAATGARVSELIKIKVEHV--ELGYFDIYSKGGKLRRLYIPKKLRNEALEWLKSTnRKSGY 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 277 LFEGETpGEKYSASALVKVLKEAAHRAGIKHRV-HVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLHVSSAHK 355
Cdd:cd01191    88 IFLNRF-GERITTRGIAQQLKNYARKYGLNPKVvYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRKTASEQ 166


                  ...
gi 1484098566 356 AKI 358
Cdd:cd01191   167 QEI 169
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 198-348 2.50e-07

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: 50.38  E-value: 2.50e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 198 IKRILAQIS-----NIKHHCMISLVYSAGLRRSELLNL---TPQDINSETMSVRImGKGK-----------KCRYSLLSP 258
Cdd:cd00799     1 LKAMLATLDdttlrGLRDRALLLLGFAGALRRSELVALrveDLTRFVDGGLLIRL-RRSKtdqdgegeikaLPYGPETCP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 259 -----KLLEELR----HYFReyRPQKWlfeGETPGEKYSASALVKVLKEAAHRAGI-KHRVHVHMLRHSFATHLLEQGTD 328
Cdd:cd00799    80 vralrAWLEAAGipsgPLFR--RIRRG---GSVGTTRLSDRSVARIVKRRAALAGLdPGDFSGHSLRRGFATEAARAGAS 154

                         170       180
                  ....*....|....*....|
gi 1484098566 329 LHTIQELLGHNDIKTTTIYL 348
Cdd:cd00799   155 LPEIMAQGGHKSVATVMRYI 174
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 209-349 1.34e-06

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: 47.42  E-value: 1.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 209 KHHCMISLVYSA---GLRRSELLNL-----TPQDINSETMSV--RIMGKGKKCRYSLLSPKLLEELRHYFREYRPqkwlf 278
Cdd:cd01187    11 LLPQPIPVVQAAvftGARASELATLkfgclHAQTSDDGTFLYwlKWENKGGKQLDIPISKKVAELIKTINWTLNE----- 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1484098566 279 egetpgekysasalvkvLKEAAHRAGIKHRV---HVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIYLH 349
Cdd:cd01187    86 -----------------LSELKNISDDHGERfrfHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
INT_StrepXerD_C_like cd01190
Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; ...
 194-343 3.52e-04

Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; This family includes a putative XerD recombinase in Streptococcus pneumonia and similar tyrosine recombinases. However, the members of this family contain unusual active site motifs from the XerD from Escherichia coli. E. coli XerD and homologous enzymes show four conserved amino acids R-H-R-H that are spaced along the C-terminal domain. The putative S. pneumoniae XerD contains three unique replacements at the conserved positions resulting in L-Q-R-L. Severe growth defects in a loss-of-function xerD mutant demonstrate an important in vivo function of the S. pneumoniae XerD protein. 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: 271190  Cd Length: 150  Bit Score: 40.41  E-value: 3.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 194 SKNEIKRILA--QISNIKHHCMISLVYSAGLRRSELLNLTPQDINSETMSVRIMgKGKKCRYSLLSPKLLEELRHYFREY 271
Cdd:cd01190     1 EPPEILDLSSfyQGDFLKGQLIALLILELGLTPSEIANLKWADFDLDFQVLTIE-KGGIKRVLPLPKKLLPFLEQHIKAD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1484098566 272 RPQkWLFEGETPGEKYSASALVKVLKEAAhragiKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKT 343
Cdd:cd01190    80 YLE-FDHEGKAYSRQWLFNQLKKFLNSIG-----LSGLTAQKLREQYILKQKEAGKSIYELAKLLGLKSPVT 145
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 216-347 2.63e-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: 271196  Cd Length: 183  Bit Score: 38.62  E-value: 2.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484098566 216 LVYSAGlRRSELLNLTPQD--INSETMSVRIMGKGKKCRYSLLSPKLLEELRHYFR----EYRPQKWLFEGETPGEK--- 286
Cdd:cd01196    29 MVYSFA-RIGAVLAMRVEDvyDQGRRLWVRLAEKGGKQHEMPCHHDLEEYLRAYLEaaeiEEDPKGPLFRTTRGGTRklt 107

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1484098566 287 ---YSASALVKVLKEAAHRAGIKHRVHVHMLRHSFATHLLEQGTDLHTIQELLGHNDIKTTTIY 347
Cdd:cd01196   108 hnpLTQANAYRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQLY 171
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH