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Conserved domains on  [gi|2047447479|ref|YP_010102202|]
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integrase [Gordonia phage Barb]

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

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List of domain hits

 Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
23-294 4.07e-53

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 175.18  E-value: 4.07e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  23 SWQPLIAGFLRHLRAA-GQPNTTINTRRQQIERMARALEGE----PSEVTRDAITDYHA---AQTWALETRRGHRNAAVS 94
Cdd:COG4974     2 TLADLLEAFLEELKREkGLSPNTIKAYRRDLRRFLRFLEELgkipLAEITPEDIRAYLNylrERGLSPSTINRYLAALRS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  95 FFAWAHSCGHIPENPAQHLPIVKSSVPAPRPAPDRVVNVALKTPEK------RIQLMLRLSCELGLRRAEVAVVSTTDVE 168
Cdd:COG4974    82 FFRYAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTetpeglRDRALLLLLYATGLRVSELLGLKWSDID 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 169 DGVGgaMLRVH-GKGGKIRVIPISDELALRIEDGAAGHTPGAprTGYLFPGNDGGHLSPRWVGT----LCAEA-LPGGWT 242
Cdd:COG4974   162 LDRG--TIRVRrGKGGKERTVPLSPEALEALREYLEERRPRD--SDYLFPTRRGRPLSRRAIRKilkrLAKRAgIPKRVT 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2047447479 243 MHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRAAMNSA 294
Cdd:COG4974   238 PHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
23-294 4.07e-53

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 175.18  E-value: 4.07e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  23 SWQPLIAGFLRHLRAA-GQPNTTINTRRQQIERMARALEGE----PSEVTRDAITDYHA---AQTWALETRRGHRNAAVS 94
Cdd:COG4974     2 TLADLLEAFLEELKREkGLSPNTIKAYRRDLRRFLRFLEELgkipLAEITPEDIRAYLNylrERGLSPSTINRYLAALRS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  95 FFAWAHSCGHIPENPAQHLPIVKSSVPAPRPAPDRVVNVALKTPEK------RIQLMLRLSCELGLRRAEVAVVSTTDVE 168
Cdd:COG4974    82 FFRYAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTetpeglRDRALLLLLYATGLRVSELLGLKWSDID 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 169 DGVGgaMLRVH-GKGGKIRVIPISDELALRIEDGAAGHTPGAprTGYLFPGNDGGHLSPRWVGT----LCAEA-LPGGWT 242
Cdd:COG4974   162 LDRG--TIRVRrGKGGKERTVPLSPEALEALREYLEERRPRD--SDYLFPTRRGRPLSRRAIRKilkrLAKRAgIPKRVT 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2047447479 243 MHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRAAMNSA 294
Cdd:COG4974   238 PHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 25-294 1.23e-35

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 129.50  E-value: 1.23e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  25 QPLIAGFLRHLRAAGQ--PNTTINTRRQqIERMARALEG----EPSEVT----RDAITDYHAAQtwaLETR-RGHRNAAV 93
Cdd:PRK00236    7 PAALEAFLEYLRVERGlsPHTLRAYRRD-LRAFLAFLEEhgisSLQDLDaadlRSFLARRRRQG---LSARsLARRLSAL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  94 -SFFAWAHSCGHIPENPAQHLPIVKSSVPAPRP-APDRVV----NVALKTPEK-RIQLMLRL--SCelGLRRAEVAVVST 164
Cdd:PRK00236   83 rSFYRWLVRRGLLKANPAAGLRAPKIPKRLPKPlDVDQAKrlldAIDEDDPLAlRDRAILELlyGS--GLRLSELVGLDI 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 165 TDVEDGVGgaMLRVHGKGGKIRVIPISDELALRIEDGAAGHTPGAPRTGYLFPGNDGGHLSPRWVGTLCAEA-----LPG 239
Cdd:PRK00236  161 DDLDLASG--TLRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDDALFLGARGGRLSPRVVQRRVKKLgkkagLPS 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2047447479 240 GWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRAAMNSA 294
Cdd:PRK00236  239 HITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 31-294 1.86e-35

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: 129.26  E-value: 1.86e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  31 FLRHLRAAGQ--PNTTINTRR--QQIERMARALEG--EPSEVTRDAITDYHAAQTWALETRR--GHRNAAV-SFFAWAHS 101
Cdd:TIGR02224   3 FLEYLRLERNysPHTVRAYRRdlEAFLEFLEEEGGlaSLAEVTAADLRSFLAELHARGLSRRslARKLSALrSFYRFLLR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 102 CGHIPENPAQ--HLPIVKSSVPAPRPAPD--RVVNVALKTPEKRIQLMLRLSCEL----GLRRAEVAV--VSTTDVEDGV 171
Cdd:TIGR02224  83 RGLIDANPAAgvRAPKQPKKLPKFLSEDEmeALLDAPEEDDEDWLALRDRAILELlyssGLRVSELVGldLSDLDLDFGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 172 ggamLRVHGKGGKIRVIPISDELALRIEDG-AAGHTPGAPR--TGYLFPGNDGGHLSPRWVGTLCAE-----ALPGGWTM 243
Cdd:TIGR02224 163 ----VRVRGKGNKERIVPFGPYARDALQAYlEARRSPLLASegQDALFLNRRGGRLTPRGVQYRLQQlrakaGLPKHVHP 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2047447479 244 HTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRAAMNSA 294
Cdd:TIGR02224 239 HALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQA 289
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 131-283 1.65e-27

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: 104.90  E-value: 1.65e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 131 VNVALKTPEKRIQLMLRLSC--EL----GLRRAEVAVVSTTDVEDGVGgaMLRVHGKGGKIRVIPISDELALRIE---DG 201
Cdd:cd00798     4 VERLLDAPDTDTPLGLRDRAilELlyasGLRVSELVGLDLSDVDLDEG--LVRVTGKGNKERLVPFGSYAVEALEeylEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 202 AAGHTPGAPRTGYLFPGNDGGHLSPRWVGTLCAEA-----LPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATT 276
Cdd:cd00798    82 RRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYaeragLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTT 161


                  ....*..
gi 2047447479 277 QRYTAVD 283
Cdd:cd00798   162 QIYTHVS 168
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 141-284 4.79e-25

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: 98.16  E-value: 4.79e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 141 RIQLMLRLSCELGLRRAEVAVVSTTDVEDGVGgaMLRVH-GKGGKIRVIPISDELALRIEDGAAGHTPGAPRTGYLFPGN 219
Cdd:pfam00589  22 RDKALLELLYATGLRISELCSLRWSDIDFENG--VIRVHrGKGNKERTVPLSDAALELLKEWLSKRLLEAPKSDYLFASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 220 DGGHLSPR----WVGTLCAEA-LPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDE 284
Cdd:pfam00589 100 RGKPLSRQtvrkIFKRAGKEAgLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVAD 169
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
23-294 4.07e-53

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 175.18  E-value: 4.07e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  23 SWQPLIAGFLRHLRAA-GQPNTTINTRRQQIERMARALEGE----PSEVTRDAITDYHA---AQTWALETRRGHRNAAVS 94
Cdd:COG4974     2 TLADLLEAFLEELKREkGLSPNTIKAYRRDLRRFLRFLEELgkipLAEITPEDIRAYLNylrERGLSPSTINRYLAALRS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  95 FFAWAHSCGHIPENPAQHLPIVKSSVPAPRPAPDRVVNVALKTPEK------RIQLMLRLSCELGLRRAEVAVVSTTDVE 168
Cdd:COG4974    82 FFRYAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTetpeglRDRALLLLLYATGLRVSELLGLKWSDID 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 169 DGVGgaMLRVH-GKGGKIRVIPISDELALRIEDGAAGHTPGAprTGYLFPGNDGGHLSPRWVGT----LCAEA-LPGGWT 242
Cdd:COG4974   162 LDRG--TIRVRrGKGGKERTVPLSPEALEALREYLEERRPRD--SDYLFPTRRGRPLSRRAIRKilkrLAKRAgIPKRVT 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2047447479 243 MHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRAAMNSA 294
Cdd:COG4974   238 PHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
23-291 2.22e-45

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 154.73  E-value: 2.22e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  23 SWQPLIAGFLRHLRAAGQPNTTINTRRQQIERMARALEG---EPSEVTRDAITDYHA---AQTWALETRRGHRNAAVSFF 96
Cdd:COG4973     3 TLAEALEAYLEHLRERRLSPKTLEAYRRDLRRLIPLLGDadlPLEELTPADVRRFLArlhRRGLSPRTLNRRLSALRSFF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  97 AWAHSCGHIPENPAQHLPIVKSSVPAPRPAPDRVVNVALKTP-----EKRIQLMLRLSCELGLRRAEVAVVSTTDV--ED 169
Cdd:COG4973    83 NWAVREGLLEANPAAGVKAPKAPRKLPRALTVDELAQLLDALaddplAVRDRAIVELLYSTGLRLGELVGLDWEDVdlDA 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 170 GVggamLRVHGKGGKIRVIPISDEL--ALRiEDGAAGHTPGAPRTGYLFPGNDGGHLSPRWVGTLCAEA-----LPGGWT 242
Cdd:COG4973   163 GE----VRVRGKTGKSRTVPLGPKAlaALR-EWLAVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRLakkagLPKHVH 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2047447479 243 MHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRAAM 291
Cdd:COG4973   238 PHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 25-294 1.23e-35

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 129.50  E-value: 1.23e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  25 QPLIAGFLRHLRAAGQ--PNTTINTRRQqIERMARALEG----EPSEVT----RDAITDYHAAQtwaLETR-RGHRNAAV 93
Cdd:PRK00236    7 PAALEAFLEYLRVERGlsPHTLRAYRRD-LRAFLAFLEEhgisSLQDLDaadlRSFLARRRRQG---LSARsLARRLSAL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  94 -SFFAWAHSCGHIPENPAQHLPIVKSSVPAPRP-APDRVV----NVALKTPEK-RIQLMLRL--SCelGLRRAEVAVVST 164
Cdd:PRK00236   83 rSFYRWLVRRGLLKANPAAGLRAPKIPKRLPKPlDVDQAKrlldAIDEDDPLAlRDRAILELlyGS--GLRLSELVGLDI 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 165 TDVEDGVGgaMLRVHGKGGKIRVIPISDELALRIEDGAAGHTPGAPRTGYLFPGNDGGHLSPRWVGTLCAEA-----LPG 239
Cdd:PRK00236  161 DDLDLASG--TLRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDDALFLGARGGRLSPRVVQRRVKKLgkkagLPS 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2047447479 240 GWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRAAMNSA 294
Cdd:PRK00236  239 HITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 31-294 1.86e-35

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: 129.26  E-value: 1.86e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  31 FLRHLRAAGQ--PNTTINTRR--QQIERMARALEG--EPSEVTRDAITDYHAAQTWALETRR--GHRNAAV-SFFAWAHS 101
Cdd:TIGR02224   3 FLEYLRLERNysPHTVRAYRRdlEAFLEFLEEEGGlaSLAEVTAADLRSFLAELHARGLSRRslARKLSALrSFYRFLLR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 102 CGHIPENPAQ--HLPIVKSSVPAPRPAPD--RVVNVALKTPEKRIQLMLRLSCEL----GLRRAEVAV--VSTTDVEDGV 171
Cdd:TIGR02224  83 RGLIDANPAAgvRAPKQPKKLPKFLSEDEmeALLDAPEEDDEDWLALRDRAILELlyssGLRVSELVGldLSDLDLDFGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 172 ggamLRVHGKGGKIRVIPISDELALRIEDG-AAGHTPGAPR--TGYLFPGNDGGHLSPRWVGTLCAE-----ALPGGWTM 243
Cdd:TIGR02224 163 ----VRVRGKGNKERIVPFGPYARDALQAYlEARRSPLLASegQDALFLNRRGGRLTPRGVQYRLQQlrakaGLPKHVHP 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2047447479 244 HTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRAAMNSA 294
Cdd:TIGR02224 239 HALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQA 289
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 131-283 1.65e-27

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: 104.90  E-value: 1.65e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 131 VNVALKTPEKRIQLMLRLSC--EL----GLRRAEVAVVSTTDVEDGVGgaMLRVHGKGGKIRVIPISDELALRIE---DG 201
Cdd:cd00798     4 VERLLDAPDTDTPLGLRDRAilELlyasGLRVSELVGLDLSDVDLDEG--LVRVTGKGNKERLVPFGSYAVEALEeylEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 202 AAGHTPGAPRTGYLFPGNDGGHLSPRWVGTLCAEA-----LPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATT 276
Cdd:cd00798    82 RRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYaeragLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTT 161


                  ....*..
gi 2047447479 277 QRYTAVD 283
Cdd:cd00798   162 QIYTHVS 168
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 31-285 2.48e-26

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: 104.97  E-value: 2.48e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  31 FLRHLRAA-GQPNTTINTRRQQIERMARALEG---EPSEVTRDAITDYHAAQTwaletRRGHRNAAV--------SFFAW 98
Cdd:TIGR02225   3 FLDYLWVErGLSQNTLEAYRRDLEKFLEFLEErgiDLEEVDRGDIVDFLAELK-----EAGLSARSIaralsalrSFYRF 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  99 AHSCGHIPENPAQHLPIVKSSVPAPRPAPDRVVNVALKTPEKRIQLMLRLSCEL------GLRRAEVAVVSTTDV--EDG 170
Cdd:TIGR02225  78 LLREGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLellyatGLRVSELVGLRLEDVnlDEG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 171 VggamLRVHGKGGKIRVIPISDELALRIEDGAAGHTPG-----APRTGYLFPGNDGGHLSP----RWVGTLCAEALPG-G 240
Cdd:TIGR02225 158 F----VRVRGKGNKERLVPLGEEAIEALERYLKEARPLllkkkVKESDALFLNRRGGPLSRqgvwKILKEYAKRAGIEkP 233

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2047447479 241 WTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDED 285
Cdd:TIGR02225 234 ISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARE 278
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 141-284 4.79e-25

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: 98.16  E-value: 4.79e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 141 RIQLMLRLSCELGLRRAEVAVVSTTDVEDGVGgaMLRVH-GKGGKIRVIPISDELALRIEDGAAGHTPGAPRTGYLFPGN 219
Cdd:pfam00589  22 RDKALLELLYATGLRISELCSLRWSDIDFENG--VIRVHrGKGNKERTVPLSDAALELLKEWLSKRLLEAPKSDYLFASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 220 DGGHLSPR----WVGTLCAEA-LPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDE 284
Cdd:pfam00589 100 RGKPLSRQtvrkIFKRAGKEAgLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVAD 169
xerD PRK00283
tyrosine recombinase;
25-285 1.51e-23

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 97.57  E-value: 1.51e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  25 QPLIAGFLRHL---RAAGQpnTTINTRRQQIERMARALEGE---PSEVTRDAITDYhaaqtwaLETRRGHRNAAVS---- 94
Cdd:PRK00283    6 RALIEQFLDALwveRGLAE--NTLSSYRRDLELFAEWLAARglsLAEATRDDLQAF-------LAELAEGGYKATSsarr 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  95 ------FFAWAHSCGHIPENPAQHLpivksSVPA-PRPAPDRV----VNVALKTPEKRIQLMLRLSC--EL----GLRRA 157
Cdd:PRK00283   77 lsalrrFFQFLLREGLREDDPSALL-----DSPKlPRRLPKTLseaqVEALLDAPDIDTPLGLRDRAmlELlyatGLRVS 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 158 EVAVVSTTDV--EDGVggamLRVHGKGGKIRVIPISDE--LALR--IEDGAAGHTPGAPrTGYLFPGNDGGHLSpR---W 228
Cdd:PRK00283  152 ELVGLTLDDVslRQGV----VRVTGKGNKERLVPLGEEavYAIEryLERGRPALLNGRS-SDALFPSARGGQLT-RqtfW 225

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2047447479 229 --------VGTLCAEALpggwTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDED 285
Cdd:PRK00283  226 hrikhyakRAGIDPKKL----SPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATE 286
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 113-282 4.37e-20

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: 85.40  E-value: 4.37e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 113 LPIVKSsvpaprpaPDRVVNVALKTPEKRIQLMLRLSCELGLRRAEVAVVSTTDV--EDGVggamLRVH-GKGGKIRVIP 189
Cdd:cd01193     2 LPVVLS--------PDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIdfERGV----IRVRqGKGGKDRVVP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 190 ISDELALRIEDGAAGHTPgaprTGYLFPGNDGG-------------HLSPRWVGTLCAEAL-------PGgwTMHTLRHR 249
Cdd:cd01193    70 LPEKLLEPLRRYLKSARP----KEELDPAEGRAgvldprtgverrhHISETTVQRALKKAVeqagitkRV--TPHTLRHS 143

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2047447479 250 FATRAYRGSRNLRAVQVLLGHASLATTQRYTAV 282
Cdd:cd01193   144 FATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 136-280 7.00e-20

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: 84.45  E-value: 7.00e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 136 KTPEKRIQLMLRLSCELGLRRAEVAVVSTTDVEDGvgGAMLRVHGKG---GKIRVIPISDELALRIED------GAAGHT 206
Cdd:cd00397    13 KKIDLRDRAILLLLLETGLRISELLALKVKDIDLD--NGTIRVRGKKtkgGKERTVPLPKELAEELKEylkerrDKRGPL 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2047447479 207 PGAPRTGYLFPGNDGGHLSPRWVGTLC---AEALPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYT 280
Cdd:cd00397    91 LKSLYLNKLFGTKLGERLSRRTLRRIFkkaGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 21-282 3.91e-17

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 80.56  E-value: 3.91e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  21 PASWQPLIAGFLRHLRAAGQPNTTINTRRQQIERMA-----RALEgEPSEVTRDAITDYHA---------AQTWALETRR 86
Cdd:PRK01287   18 PKTLRQLLERFLAWLQERNWSERTLKVYTEHLYPFIlwceeRGLY-YAADVTLPVLERYQRylygyrkanGEPLSTRTQR 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  87 GHRNAAVSFFAWAHSCGHIPENPAQHLPIVKssvpAPRPAPDRVVNVA----------LKTPEK-RIQLMLRLSCELGLR 155
Cdd:PRK01287   97 TQLSPLRVWFRWLLKRHHILYNPAEDLELPK----EEKRLPRQILSEAeteqvlaspdLTTLQGlRDRALLELLWSTGIR 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 156 RAEVAVVSTTDVEDGVGGAMLRvHGKGGKIRVIPISdELAL----RIEDGAAGHTPGAPRTGYLFPGNDGGHLSPRWV-- 229
Cdd:PRK01287  173 RGELARLDLYDVDASRGVVTVR-QGKGNKDRVVPVG-ERALawlqRYLQDVRPQLAVRPDSGALFVAMDGDGLARNTLtn 250

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2047447479 230 ---GTLCAEALPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAV 282
Cdd:PRK01287  251 mvgRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRV 306
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 140-294 1.05e-16

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: 76.16  E-value: 1.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 140 KRIQLMLRLSCELGLRRAEVAVVSTTDVEDGVGgAMLRVHGKGGKIRVIPISDELALRIEDGAAGH--TPGAPRTGYLFP 217
Cdd:cd01182    21 RRDHALLLLLYDTGARVQELADLTIRDLRLDDP-ATVRLHGKGRKERTVPLWKETVAALKAYLQEFhlTPDPKQLFPLFP 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 218 GNDGGHLSPRWVGTLCA----------EALPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEV 287
Cdd:cd01182   100 NRRGQPLTRDGVAYILNkyvalasnrcPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYAEADLEMK 179


                  ....*..
gi 2047447479 288 RAAMNSA 294
Cdd:cd01182   180 REALEKA 186
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 129-280 3.30e-14

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: 68.89  E-value: 3.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 129 RVVNVALKTPEKRIQLMLRLSCELGLRRAEVAVVSTTDVEDGVGGAMLRvHGKGGKIRVIPISDELALRIEDGAAGHTPG 208
Cdd:cd00796    12 RLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLP-ETKNGKPRTVPLSDEAIAILKELKRKRGKD 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2047447479 209 APRTGYLFPGNDGGHLSPRWvGTLCAEALPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYT 280
Cdd:cd00796    91 GFFVDGRFFGIPIASLRRAF-KKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRYA 161
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 138-287 8.58e-14

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: 67.67  E-value: 8.58e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 138 PEKRIQLMLRL---SCELGLRRAEVAVVSTTDVEDGVGGAMLRVH-GKGGKIRVIPISDElALRIedgaAGHTPGAPRTG 213
Cdd:cd01185    13 DTSRLELVRDMflfSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRrKKTGKPVTVPLLPV-AREI----LEKYKDDRSEG 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2047447479 214 YLFPGNDGGHLSpRWVGTLCAEA-LPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEV 287
Cdd:cd01185    88 KLFPVLSNQKIN-RYLKEIAKIAgIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVDSKK 161
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 145-289 1.00e-12

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: 65.34  E-value: 1.00e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 145 MLRLSCELGLRRAEVAVVSTTDVEDGVGGAMLRvHGKGGKIRVIPISDELALRIEDGAAGHTPgAPRTGYLFPGND---G 221
Cdd:cd01188    25 ILLLLARLGLRAGDVAGLRLDDIDWRSGTITVR-QKKTGRPVELPLTEPVGEALADYLRDGRP-RTDSREVFLRARapyR 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2047447479 222 GHLSPRWVGTLCAEAL------PGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRA 289
Cdd:cd01188   103 PLSSTSQISSIVRRYLrkagiePSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAKIDVDDLRE 176
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 142-279 5.24e-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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 63.16  E-value: 5.24e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 142 IQLMLRLscelGLRRAEVAVVSTTDVEDGVGGAMLRVHGKG--GKIRVIPISDEL--ALRIEDGAAGHT-PGAPRTGYLF 216
Cdd:cd01194    28 ISLMVTE----GLRTVEIVRADVGDLRQEGEGTILYVQGKGktSKDDFVYLRPDVlkALQAYLKARGKLdFEEPLFTSLS 103

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2047447479 217 PGNDGGHLSPRWVGTLCAEAL------PGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRY 279
Cdd:cd01194   104 NNSKGQRLTTRSIRRIIKKYLrkagldDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIY 172
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 140-290 5.41e-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: 63.08  E-value: 5.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 140 KRIQLMLRLSCELGLRRAEVAVVSTTDVedgVGGAMLRVH-GKGGKIRVIPISD----ELALRIEDgaAGHTPgapRTGY 214
Cdd:cd01192    24 PRNYLLFIVGINTGLRISDLLSLKVEDV---TNKDKLSIKeQKTGKQKTFPLNPtlvkALKEYIDD--LDLKR---NDYL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 215 LFPGNDG--GHLSPRWVGTLCAEA-----LPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEV 287
Cdd:cd01192    96 FKSLKQGpeKPISRKQAYKILKKAaddlgLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYLGIDQEDV 175


                  ...
gi 2047447479 288 RAA 290
Cdd:cd01192   176 DKA 178
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 64-292 2.79e-11

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 63.52  E-value: 2.79e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479  64 SEVTRDAITDYHA--AQTWALETRRGHRNAAVSFFAWAHSCGHIPENPAQHLpivKSSVPAPRPAPDRVVN--------V 133
Cdd:COG0582   140 AEITPPDLLAVLRpiEARGAPETARRVRQRLRQVFRYAVARGLIERNPAADL---KGALPKPKVKHHPALTpeelpellR 216

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 134 ALKTPEKRIQ--LMLRLSCELGLRRAEV--AVVSTTDVEDGVggamLRVHG---KGGKIRVIPISDElALRIEDGAAGHT 206
Cdd:COG0582   217 ALDAYRGSPVtrLALRLLLLTGVRPGELrgARWSEIDLEAAL----WTIPAermKTRRPHIVPLSRQ-ALEILKELKPLT 291

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 207 PGaprTGYLFPG--NDGGHLSPRWVGTLCAEALPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQR-YTAVD 283
Cdd:COG0582   292 GD---SEYVFPSrrGPKKPMSENTLNKALRRMGYGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAaYNRAD 368

                         250
                  ....*....|
gi 2047447479 284 -EDEVRAAMN 292
Cdd:COG0582   369 yLEERREMMQ 378
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 153-293 1.27e-09

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 58.39  E-value: 1.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 153 GLRRAEVAVVSTTDV--EDGvggaMLRVHGKGGKIRVIPISDE--------LALRIEDGAAGHTPGAprtgyLF---PGN 219
Cdd:PRK05084  208 GLRVSELVNLDLSDLnlKQM----TIDVTRKGGKRDSVNIAPFalpyleeyLKIRASRYKAEKQEKA-----LFltkYRG 278

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2047447479 220 DGGHLSPRWVGTLCA---EALPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAVDEDEVRAAMNS 293
Cdd:PRK05084  279 KPNRISARAIEKMVAkysEAFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKEALDR 355
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 108-282 1.71e-09

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: 57.79  E-value: 1.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 108 NPAQHLPIVKSsvpaprpaPDRVVNVaLKTPEKRIQLMLRLSCELGLRRAEVAVVSTTDVEDGVGGAMLRvHGKGGKIRV 187
Cdd:TIGR02249  93 KRPRKLPVVLT--------REEVRRL-LEHLEGKYRLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIR-QGKGGKDRT 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 188 IPISDELALRIE---------------DGAAG---------HTPGAPRT---GYLFPGN-------DGG----HLSPRWV 229
Cdd:TIGR02249 163 VTLPKELIPPLReqielarayheadlaEGYGGvylphalarKYPNAPKEwgwQYLFPSHrlsrdpeSGVirrhHINETTI 242

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2047447479 230 GTLCAEA-----LPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAV 282
Cdd:TIGR02249 243 QRAVRRAveragIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHV 300
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 140-279 7.22e-09

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: 54.01  E-value: 7.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 140 KRIQLMLRLSCELGLRRAEVAVVSTTDVEDGVGgaMLRVHGKGGKIR-VIPISDELALRIEDG-AAGHTPGAPRTGYLFP 217
Cdd:cd01195    20 KRDEALVRLLLDNALRRSEAVALDVEDLEKEHR--RLRILGKGKKQReVVTLPPTTREALAAWlAARGEAEGPLFVSLDR 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2047447479 218 GNDGGHLSPRWVGTLC---AEALPGGWTM--HTLRHRFATRAYRGSR-NLRAVQVLLGHASLATTQRY 279
Cdd:cd01195    98 ASRGRRLSPQAVYRIVrrlAERIGLGKRLspHGLRHSAITLALDAGAgLIRKVQDFSRHADLRTLQVY 165
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 134-279 4.52e-07

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: 48.32  E-value: 4.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 134 ALKTPEKRIQLMLRLSCELGLRRAEVAVVSTTDV--EDG---VGGAMLRVHGKGGKI---------RVIPISDELALRIE 199
Cdd:cd01189    10 ALKKRGDRYYLLFLLALLTGLRRGELLALTWSDIdfENGtirINRTLVRKKKGGYVIkppktkssiRTIPLPDELIELLK 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 200 DgaaghtpgaprtgylfpgndggHlspRWVGTLCAEALPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRY 279
Cdd:cd01189    90 E----------------------L---KAFKKLLKKAGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDV 144
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 153-279 9.17e-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: 48.46  E-value: 9.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 153 GLRRAEVAVVSTTDVEDGVGgaMLRV-HGKGGKIRVIPISDELALRIEDGAA--GHTPGAPRTGYLFPGNDGGHLSPRWV 229
Cdd:cd00797    38 GLRVGEALRLRLEDVDLDSG--ILTIrQTKFGKSRLVPLHPSTVGALRDYLArrDRLLPSPSSSYFFVSQQGGRLTGGGV 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2047447479 230 GTLCAEAL-------PGGWT---MHTLRHRFATRA----YRGSRNL-RAVQVL---LGHASLATTQRY 279
Cdd:cd00797   116 YRVFRRLLrriglrgAGDGRgprLHDLRHTFAVNRltrwYREGADVeRKLPVLstyLGHVNVTDTYWY 183
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 146-288 1.26e-06

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: 47.80  E-value: 1.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 146 LRLSCELGLRRAEVA----VVSTTDVEDGVGGAMLrvhgKGGKIRVIPISDELA-LRIEDGAAGHTPGAPRTGYLF---- 216
Cdd:cd01186    31 LRIGEALGLRIEDIDmadnQIELVPREDNTNEARA----KSMRERRIPVSQDLIdLYADYLTYIYCEEAEFSITVFvnvk 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2047447479 217 PGNDGGHLSPRWVGTLcAEAL----PGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATT-QRYTAVDEDEVR 288
Cdd:cd01186   107 GGNQGKAMNYSDVYDL-VRRLkkrtGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTlNTYGHLSEEDIR 182
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 139-280 6.27e-06

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: 45.41  E-value: 6.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 139 EKRIQLMLRLSCELGLRRAEVAVVSTTDVEDGVggaMLRVHGKGGKIRVIPISDELALRIEDgaaghTPGAPRTG--YLF 216
Cdd:cd00800    11 PPLLRLAMELALLTGQRQGDLLRLKWSDITDGG---LLVEQSKTGKKLLIPWTPSLRALVDR-----IRALPRKRseYLI 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2047447479 217 PGNDGGHLS-----PRW---VGTLCAEALPGGWTMHTLRHRFATRaYRGSRNLRAVQVLLGHASLATTQRYT 280
Cdd:cd00800    83 NSRKGGPLSydtlkSAWrraRKAAGLKGETEGFTFHDLRAKAATD-YAEQGGSTDAQALLGHKSDAMTERYT 153
int PHA02601
integrase; Provisional
 181-279 7.29e-06

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 46.64  E-value: 7.29e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 181 KGGKIRVIPISDELALRIEDgaaghtpgapRTGYLFPGNdgghlSPRWVGTLCAEA--LPGGWTMHTLRHRFATRAYRGS 258
Cdd:PHA02601  229 KGKKNRTVPISEELYKMLPK----------RRGRLFKDA-----YESFERAVKRAGidLPEGQATHVLRHTFASHFMMNG 293

                          90       100
                  ....*....|....*....|.
gi 2047447479 259 RNLRAVQVLLGHASLATTQRY 279
Cdd:PHA02601  294 GNILVLQRILGHATIEMTMAY 314
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 140-295 8.02e-06

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: 45.37  E-value: 8.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 140 KRIQLMLRLSCELGLRRAEVAVVSTTDVEDGVGGAML--------RVHGKGgkiRVIPISDELAL----RIED--GAAGH 205
Cdd:cd00799    16 LRDRALLLLGFAGALRRSELVALRVEDLTRFVDGGLLirlrrsktDQDGEG---EIKALPYGPETcpvrALRAwlEAAGI 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 206 TpgaprTGYLF---PGND---GGHLSPRWVGTLCAEA------LPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASL 273
Cdd:cd00799    93 P-----SGPLFrriRRGGsvgTTRLSDRSVARIVKRRaalaglDPGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSV 167

                         170       180
                  ....*....|....*....|..
gi 2047447479 274 ATTQRYTavdeDEVRAAMNSAA 295
Cdd:cd00799   168 ATVMRYI----READRFKDNAA 185
PRK15417 PRK15417
integron integrase;
242-282 2.11e-04

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 42.34  E-value: 2.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2047447479 242 TMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRYTAV 282
Cdd:PRK15417  275 TPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 315
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 153-280 6.03e-04

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: 39.98  E-value: 6.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 153 GLRRAEVAVVSTTDV--EDGVGGAMLRVHGKGGK------IRVIPISDELalrIEDG---------AAGHTPGAPrtgyL 215
Cdd:cd01184    36 GARLNEICQLRVDDIkeEDGIWCIDINDDAEGRRlktkasRRLVPIHPRL---IELGfldyvealrADGKLFLFP----E 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2047447479 216 FPGNDGGHLSP--RWVGTLCAEALPGGW---TMHTLRHRFATRAYRGSRNLRAVQVLLGHA-SLATTQRYT 280
Cdd:cd01184   109 KRDKDGKYSKAasKWFNRLLRKLGIKDDerkSFHSFRHTFITALKRAGVPEELIAQIVGHSrGGVTHDTYG 179
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 142-271 6.25e-04

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: 39.95  E-value: 6.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 142 IQLMLRLSCELGLRRAEV--AVVSTTDVEDGVggamLRV---HGKGGKIRVIPISDELALRIEDgaagHTPGAPRTGYLF 216
Cdd:cd00801    21 TKLALRLLLLTGQRIGELarARWSEIDLEEKT----WTIpaeRTKNKRPHRVPLSDQALEILEE----LKEFTGDSGYLF 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 217 PGNDGGHlSPRWVGTLCAE-----ALPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHA 271
Cdd:cd00801    93 PSRRKKK-KPISENTINKAlkrlgYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHV 151
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 145-279 5.69e-03

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: 36.64  E-value: 5.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 145 MLRLSCELGLRRAEVAVVSTTDV-----EDGVGGAMLRVHGKGGKIRVIPISDELALRIEDgaaghtpgapRTGYLFpgn 219
Cdd:cd01187    18 VVQAAVFTGARASELATLKFGCLhaqtsDDGTFLYWLKWENKGGKQLDIPISKKVAELIKT----------INWTLN--- 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047447479 220 dggHLSPRWVGTLcAEALPGGWTMHTLRHRFATRAYRGSRNLRAVQVLLGHASLATTQRY 279
Cdd:cd01187    85 ---ELSELKNISD-DHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRY 140
 
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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