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Conserved domains on  [gi|251764782|sp|Q38067|]
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RecName: Full=Putative integrase

Protein Classification

site-specific integrase( domain architecture ID 332)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 1-321 1.78e-123

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


The actual alignment was detected with superfamily member PHA02601:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 333  Bit Score: 357.50  E-value: 1.78e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782   1 MTVRK-DGKTWTADFYENGRSGRRIRKKgFATKSAAIRYEQDFFAVKGET---GRPLDDR-LSDLVKVWYDLHGCTLKDG 75
Cdd:PHA02601   1 MAVRKlKDGKWLCEIYPNGRDGKRIRKR-FATKGEALAFENYTMAEVDDKewvGEKEDRRrLSELLQIWWDLHGQTLEDG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  76 KQRLARCEALAKRLGNPLAFEFDSLAWARYRQRRL---------TEVKPETVNHEQRYLSAVFSELIRLGSWHKENPLGK 146
Cdd:PHA02601  80 KARLAKLLILCKGLGDPIASEFTAKDFADYRARRLsgefkvnkgRPIKPATVNRELAYLSAVFNELIKLGKWSGPNPLDG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 147 VRQIKTDQVELTFLSLDQVARLLEECKASTNNHTYPVALLCLATGARWEEAESLTRGAVHGGKVHYHRIKNRQSRSVPIP 226
Cdd:PHA02601 160 IRPFKEAEPELAFLTKEEIERLLDACDGSRSPDLGLIAKICLATGARWSEAETLKRSQISPYKITFVKTKGKKNRTVPIS 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 227 DELERLIFKvgmpGSGRLFMSCRAAFRCAYQRCGFQTP-GQMTHILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYA 305
Cdd:PHA02601 240 EELYKMLPK----RRGRLFKDAYESFERAVKRAGIDLPeGQATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYA 315

                        330
                 ....*....|....*.
gi 251764782 306 HLSPEHLASAMSLSPL 321
Cdd:PHA02601 316 HFAPDHLEDAVSLNPL 331
 
Name Accession Description Interval E-value
int PHA02601
integrase; Provisional
 1-321 1.78e-123

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 357.50  E-value: 1.78e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782   1 MTVRK-DGKTWTADFYENGRSGRRIRKKgFATKSAAIRYEQDFFAVKGET---GRPLDDR-LSDLVKVWYDLHGCTLKDG 75
Cdd:PHA02601   1 MAVRKlKDGKWLCEIYPNGRDGKRIRKR-FATKGEALAFENYTMAEVDDKewvGEKEDRRrLSELLQIWWDLHGQTLEDG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  76 KQRLARCEALAKRLGNPLAFEFDSLAWARYRQRRL---------TEVKPETVNHEQRYLSAVFSELIRLGSWHKENPLGK 146
Cdd:PHA02601  80 KARLAKLLILCKGLGDPIASEFTAKDFADYRARRLsgefkvnkgRPIKPATVNRELAYLSAVFNELIKLGKWSGPNPLDG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 147 VRQIKTDQVELTFLSLDQVARLLEECKASTNNHTYPVALLCLATGARWEEAESLTRGAVHGGKVHYHRIKNRQSRSVPIP 226
Cdd:PHA02601 160 IRPFKEAEPELAFLTKEEIERLLDACDGSRSPDLGLIAKICLATGARWSEAETLKRSQISPYKITFVKTKGKKNRTVPIS 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 227 DELERLIFKvgmpGSGRLFMSCRAAFRCAYQRCGFQTP-GQMTHILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYA 305
Cdd:PHA02601 240 EELYKMLPK----RRGRLFKDAYESFERAVKRAGIDLPeGQATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYA 315

                        330
                 ....*....|....*.
gi 251764782 306 HLSPEHLASAMSLSPL 321
Cdd:PHA02601 316 HFAPDHLEDAVSLNPL 331
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 156-306 5.88e-44

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: 148.24  E-value: 5.88e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 156 ELTFLSLDQVARLLEECKASTNNHTYPVALLCLATGARWEEAESLTRGAVH--GGKVHYHRIKNRQSRSVPIPDELERLI 233
Cdd:cd00796    1 RDRFLTEDEEARLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDleVGLIVLPETKNGKPRTVPLSDEAIAIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 234 FKV-------GMPGSGRLF----MSCRAAFRCAYQRCGFqtPGQMTHILRHTFASHYMMGGGDILTLQRILGHSSITMTM 302
Cdd:cd00796   81 KELkrkrgkdGFFVDGRFFgipiASLRRAFKKARKRAGL--EDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTM 158


                 ....
gi 251764782 303 RYAH 306
Cdd:cd00796  159 RYAH 162
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
57-317 7.87e-44

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 152.07  E-value: 7.87e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  57 LSDLVKVWYDLHGC-------TLKDGKQRLARCEALAKRLGNPLAFEFDSLAWARYRQRRLTE-VKPETVNHEQRYLSAV 128
Cdd:COG4974    3 LADLLEAFLEELKRekglspnTIKAYRRDLRRFLRFLEELGKIPLAEITPEDIRAYLNYLRERgLSPSTINRYLAALRSF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 129 FSELIRLGsWHKENPLGKVRQIKTDQVELTFLSLDQVARLLEECKASTNNHT--YPVALLCLATGARWEEAESLTRGAVH 206
Cdd:COG4974   83 FRYAVREG-LLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLrdRALLLLLYATGLRVSELLGLKWSDID 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 207 --GGKVHYHRIKNRQSRSVPIPDE----LERLIFKVGMPGSGRLFMSCRA----------AFRCAYQRCGFQ---TPgqm 267
Cdd:COG4974  162 ldRGTIRVRRGKGGKERTVPLSPEaleaLREYLEERRPRDSDYLFPTRRGrplsrrairkILKRLAKRAGIPkrvTP--- 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 251764782 268 tHILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHLASAMS 317
Cdd:COG4974  239 -HSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVE 287
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 159-309 3.69e-20

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: 85.83  E-value: 3.69e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  159 FLSLDQVARLLEECKASTNN-HTYPVALLCLATGARWEEAESLTRGAVH--GGKVHYHRIKNRQSRSVPIPDE----LER 231
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSiRDKALLELLYATGLRISELCSLRWSDIDfeNGVIRVHRGKGNKERTVPLSDAalelLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  232 LIFKVGMPGSGR--LFMSCR----------AAFRCAYQRCGFQTPgqMT-HILRHTFASHYMMGGGDILTLQRILGHSSI 298
Cdd:pfam00589  81 WLSKRLLEAPKSdyLFASKRgkplsrqtvrKIFKRAGKEAGLELP--LHpHMLRHSFATHLLEAGVDLRVVQKLLGHSSI 158

                         170
                  ....*....|.
gi 251764782  299 TMTMRYAHLSP 309
Cdd:pfam00589 159 STTQIYTHVAD 169
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 122-315 3.38e-13

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: 68.79  E-value: 3.38e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  122 QRYLSAV---FSELIRLGsWHKENPLGKVRQIKTDQVELTFLSLDQVARLLEECKASTN------NHtypvALLCL--AT 190
Cdd:TIGR02224  67 ARKLSALrsfYRFLLRRG-LIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEDDEdwlalrDR----AILELlySS 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  191 GARWEEAESLTRGA---------VHGgkvhyhriKNRQSRSVPIPDE--------LERLIFKVGMPGSGR-LFMSCRA-- 250
Cdd:TIGR02224 142 GLRVSELVGLDLSDldldfgevrVRG--------KGNKERIVPFGPYardalqayLEARRSPLLASEGQDaLFLNRRGgr 213

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 251764782  251 ----AFRCAYQRCGFQTPGQMT---HILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHLASA 315
Cdd:TIGR02224 214 ltprGVQYRLQQLRAKAGLPKHvhpHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKV 285
 
Name Accession Description Interval E-value
int PHA02601
integrase; Provisional
 1-321 1.78e-123

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 357.50  E-value: 1.78e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782   1 MTVRK-DGKTWTADFYENGRSGRRIRKKgFATKSAAIRYEQDFFAVKGET---GRPLDDR-LSDLVKVWYDLHGCTLKDG 75
Cdd:PHA02601   1 MAVRKlKDGKWLCEIYPNGRDGKRIRKR-FATKGEALAFENYTMAEVDDKewvGEKEDRRrLSELLQIWWDLHGQTLEDG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  76 KQRLARCEALAKRLGNPLAFEFDSLAWARYRQRRL---------TEVKPETVNHEQRYLSAVFSELIRLGSWHKENPLGK 146
Cdd:PHA02601  80 KARLAKLLILCKGLGDPIASEFTAKDFADYRARRLsgefkvnkgRPIKPATVNRELAYLSAVFNELIKLGKWSGPNPLDG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 147 VRQIKTDQVELTFLSLDQVARLLEECKASTNNHTYPVALLCLATGARWEEAESLTRGAVHGGKVHYHRIKNRQSRSVPIP 226
Cdd:PHA02601 160 IRPFKEAEPELAFLTKEEIERLLDACDGSRSPDLGLIAKICLATGARWSEAETLKRSQISPYKITFVKTKGKKNRTVPIS 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 227 DELERLIFKvgmpGSGRLFMSCRAAFRCAYQRCGFQTP-GQMTHILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYA 305
Cdd:PHA02601 240 EELYKMLPK----RRGRLFKDAYESFERAVKRAGIDLPeGQATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYA 315

                        330
                 ....*....|....*.
gi 251764782 306 HLSPEHLASAMSLSPL 321
Cdd:PHA02601 316 HFAPDHLEDAVSLNPL 331
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 156-306 5.88e-44

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: 148.24  E-value: 5.88e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 156 ELTFLSLDQVARLLEECKASTNNHTYPVALLCLATGARWEEAESLTRGAVH--GGKVHYHRIKNRQSRSVPIPDELERLI 233
Cdd:cd00796    1 RDRFLTEDEEARLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDleVGLIVLPETKNGKPRTVPLSDEAIAIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 234 FKV-------GMPGSGRLF----MSCRAAFRCAYQRCGFqtPGQMTHILRHTFASHYMMGGGDILTLQRILGHSSITMTM 302
Cdd:cd00796   81 KELkrkrgkdGFFVDGRFFgipiASLRRAFKKARKRAGL--EDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTM 158


                 ....
gi 251764782 303 RYAH 306
Cdd:cd00796  159 RYAH 162
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
57-317 7.87e-44

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 152.07  E-value: 7.87e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  57 LSDLVKVWYDLHGC-------TLKDGKQRLARCEALAKRLGNPLAFEFDSLAWARYRQRRLTE-VKPETVNHEQRYLSAV 128
Cdd:COG4974    3 LADLLEAFLEELKRekglspnTIKAYRRDLRRFLRFLEELGKIPLAEITPEDIRAYLNYLRERgLSPSTINRYLAALRSF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 129 FSELIRLGsWHKENPLGKVRQIKTDQVELTFLSLDQVARLLEECKASTNNHT--YPVALLCLATGARWEEAESLTRGAVH 206
Cdd:COG4974   83 FRYAVREG-LLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLrdRALLLLLYATGLRVSELLGLKWSDID 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 207 --GGKVHYHRIKNRQSRSVPIPDE----LERLIFKVGMPGSGRLFMSCRA----------AFRCAYQRCGFQ---TPgqm 267
Cdd:COG4974  162 ldRGTIRVRRGKGGKERTVPLSPEaleaLREYLEERRPRDSDYLFPTRRGrplsrrairkILKRLAKRAGIPkrvTP--- 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 251764782 268 tHILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHLASAMS 317
Cdd:COG4974  239 -HSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVE 287
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
56-316 7.20e-32

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 120.45  E-value: 7.20e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  56 RLSDLVKVWYDLHGC------TLKDGKQRLARCEALAKRLGNPLAfEFDSlAWAR--YRQRRLTEVKPETVNHEQRYLSA 127
Cdd:COG4973    3 TLAEALEAYLEHLRErrlspkTLEAYRRDLRRLIPLLGDADLPLE-ELTP-ADVRrfLARLHRRGLSPRTLNRRLSALRS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 128 VFSELIRLGSWHKeNPLGKVRQIKTDQVELTFLSLDQVARLLEECKASTNN-HTYPVALLCLATGARWEEAESLTRGAV- 205
Cdd:COG4973   81 FFNWAVREGLLEA-NPAAGVKAPKAPRKLPRALTVDELAQLLDALADDPLAvRDRAIVELLYSTGLRLGELVGLDWEDVd 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 206 -HGGKVHYHRiKNRQSRSVPIPDELERLI-------FKVGMPGSGRLFMSCR----------AAFRCAYQRCGFqtPGQM 267
Cdd:COG4973  160 lDAGEVRVRG-KTGKSRTVPLGPKALAALrewlavrPELAAPDEGALFPSRRgtrlsprnvqKRLRRLAKKAGL--PKHV 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 251764782 268 T-HILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHLASAM 316
Cdd:COG4973  237 HpHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 159-309 3.69e-20

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: 85.83  E-value: 3.69e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  159 FLSLDQVARLLEECKASTNN-HTYPVALLCLATGARWEEAESLTRGAVH--GGKVHYHRIKNRQSRSVPIPDE----LER 231
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSiRDKALLELLYATGLRISELCSLRWSDIDfeNGVIRVHRGKGNKERTVPLSDAalelLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  232 LIFKVGMPGSGR--LFMSCR----------AAFRCAYQRCGFQTPgqMT-HILRHTFASHYMMGGGDILTLQRILGHSSI 298
Cdd:pfam00589  81 WLSKRLLEAPKSdyLFASKRgkplsrqtvrKIFKRAGKEAGLELP--LHpHMLRHSFATHLLEAGVDLRVVQKLLGHSSI 158

                         170
                  ....*....|.
gi 251764782  299 TMTMRYAHLSP 309
Cdd:pfam00589 159 STTQIYTHVAD 169
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 164-305 3.47e-18

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: 80.60  E-value: 3.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 164 QVARLLEECKASTNNHTYPVALLCLA--TGARWEEAESLTRGAVHGG----KVHYHRIKNRQSRSVPIPDELERLI---- 233
Cdd:cd00397    1 ELEKLLDAIDEDKKIDLRDRAILLLLleTGLRISELLALKVKDIDLDngtiRVRGKKTKGGKERTVPLPKELAEELkeyl 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 234 --------------FKVGMPGSGRLFMSCRAAFRCAYQRCGFQTPGQMT-HILRHTFASHYMMGGGDILTLQRILGHSSI 298
Cdd:cd00397   81 kerrdkrgpllkslYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRKITpHSLRHTFATNLLENGVDIKVVQKLLGHSSI 160


                 ....*..
gi 251764782 299 TMTMRYA 305
Cdd:cd00397  161 STTQRYL 167
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 185-310 1.31e-16

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: 76.15  E-value: 1.31e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 185 LLCLATGARWEEAESLTR----GAVHGGKVHYHRIKNRQSRSVPIPDELERLIFKVGM-PGSGRLFMscrAAFRCAYQR- 258
Cdd:cd01185   25 LFSCYTGLRFSDLKNLTWknivEASGRTWIRYRRKKTGKPVTVPLLPVAREILEKYKDdRSEGKLFP---VLSNQKINRy 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 251764782 259 -------CGFQTPGQmTHILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPE 310
Cdd:cd01185  102 lkeiakiAGIDKHLT-FHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVDS 159
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 162-306 2.05e-16

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: 74.90  E-value: 2.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 162 LDQVARLLEECKASTNNHtYPVALLCLATGARWEEAESLT-------------RGAVHGGKVHYHRI---KNRQS-RSVP 224
Cdd:cd01189    1 PEELKKLLEALKKRGDRY-YLLFLLALLTGLRRGELLALTwsdidfengtiriNRTLVRKKKGGYVIkppKTKSSiRTIP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 225 IPDELERLIFKvgmpgsgrlfmscRAAFRCAYQRCGFQTPGqmTHILRHTFASHYMMGGGDILTLQRILGHSSITMTMR- 303
Cdd:cd01189   80 LPDELIELLKE-------------LKAFKKLLKKAGLPRIT--PHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDv 144


                 ...
gi 251764782 304 YAH 306
Cdd:cd01189  145 YAH 147
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 57-306 6.38e-14

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 71.99  E-value: 6.38e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  57 LSDLVKVWYDLHGCTLKDG--KQRLARCEA-LAKRLGN-PLAfEFDSLAWARYRQRRLTEVKPETVNHEQRYLSAVFSEL 132
Cdd:COG0582   99 FEEVAEEWLEEKKPEWKEKtaAQVRRTLEKhIFPVLGDrPIA-EITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYA 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 133 IRLGsWHKENPLGKVRQ--IKTDQVELTFLSLDQVARLLEECKASTNNHTYPVAL-LCLATGARWEEAESLTRGAVHGGK 209
Cdd:COG0582  178 VARG-LIERNPAADLKGalPKPKVKHHPALTPEELPELLRALDAYRGSPVTRLALrLLLLTGVRPGELRGARWSEIDLEA 256

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 210 ----VHYHRIKNRQSRSVPIPDE----LERLifKVGMPGSGRLFMSCR--------AAFRCAYQRCGFqtpGQMT-HILR 272
Cdd:COG0582  257 alwtIPAERMKTRRPHIVPLSRQaleiLKEL--KPLTGDSEYVFPSRRgpkkpmseNTLNKALRRMGY---GRFTpHGFR 331

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 251764782 273 HTFASHYMMGGGDILTLQRILGHSSITMTMR-YAH 306
Cdd:COG0582  332 HTASTLLNEAGFPPDVIERQLAHKDGNKVRAaYNR 366
xerD PRK00283
tyrosine recombinase;
160-312 8.87e-14

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 70.61  E-value: 8.87e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 160 LSLDQVARLLEECKASTnnhtyPV-----ALLCL--ATGARWEEAESLTRGAVH--GGKVhyhRI--KNRQSRSVPIPDE 228
Cdd:PRK00283 114 LSEAQVEALLDAPDIDT-----PLglrdrAMLELlyATGLRVSELVGLTLDDVSlrQGVV---RVtgKGNKERLVPLGEE 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 229 ----LERLI-----FKVGMPGSGRLFMSCRAafrcayqrcgfqtpGQMT------------------------HILRHTF 275
Cdd:PRK00283 186 avyaIERYLergrpALLNGRSSDALFPSARG--------------GQLTrqtfwhrikhyakragidpkklspHVLRHAF 251

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 251764782 276 ASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHL 312
Cdd:PRK00283 252 ATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERL 288
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 158-307 1.05e-13

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: 68.07  E-value: 1.05e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 158 TFLSLDQVARLLEeckASTNNHTYPVALLCLATGARWEEAESLTRGAV--HGGKVHYHRIKNRQSRSVPIPDEL-ERL-- 232
Cdd:cd01193    4 VVLSPDEVRRILG---ALTELRHRLILSLLYGAGLRISELLRLRVKDIdfERGVIRVRQGKGGKDRVVPLPEKLlEPLrr 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 233 ----------------IFKVGMPGSGRL---FMSCRA---AFRCAYQRCGFQ---TPgqmtHILRHTFASHYMMGGGDIL 287
Cdd:cd01193   81 ylksarpkeeldpaegRAGVLDPRTGVErrhHISETTvqrALKKAVEQAGITkrvTP----HTLRHSFATHLLEAGTDIR 156

                        170       180
                 ....*....|....*....|
gi 251764782 288 TLQRILGHSSITMTMRYAHL 307
Cdd:cd01193  157 TIQELLGHSDLSTTMIYTHV 176
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 122-315 3.38e-13

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: 68.79  E-value: 3.38e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  122 QRYLSAV---FSELIRLGsWHKENPLGKVRQIKTDQVELTFLSLDQVARLLEECKASTN------NHtypvALLCL--AT 190
Cdd:TIGR02224  67 ARKLSALrsfYRFLLRRG-LIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEDDEdwlalrDR----AILELlySS 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  191 GARWEEAESLTRGA---------VHGgkvhyhriKNRQSRSVPIPDE--------LERLIFKVGMPGSGR-LFMSCRA-- 250
Cdd:TIGR02224 142 GLRVSELVGLDLSDldldfgevrVRG--------KGNKERIVPFGPYardalqayLEARRSPLLASEGQDaLFLNRRGgr 213

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 251764782  251 ----AFRCAYQRCGFQTPGQMT---HILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHLASA 315
Cdd:TIGR02224 214 ltprGVQYRLQQLRAKAGLPKHvhpHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKV 285
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 269-315 6.78e-13

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 67.87  E-value: 6.78e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 251764782 269 HILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHLASA 315
Cdd:PRK00236 243 HKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEV 289
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 269-312 7.26e-13

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: 65.61  E-value: 7.26e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 251764782 269 HILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHL 312
Cdd:cd00798  129 HTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIYTHVSFERL 172
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 160-313 6.59e-12

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: 64.91  E-value: 6.59e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  160 LSLDQVARLLEECKASTnnhTYPV---ALLCL--ATGARWEEAESLTRGAVH--GGKVHYHRIKNRQsRSVPIPDE---- 228
Cdd:TIGR02225 105 LTVEEVEALLAAPDVDT---PLGLrdrAMLELlyATGLRVSELVGLRLEDVNldEGFVRVRGKGNKE-RLVPLGEEaiea 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782  229 LER-------LIFKVGMPGSGRLF-------MSCRAAFRC--AY-QRCGFQ---TPgqmtHILRHTFASHYMMGGGDILT 288
Cdd:TIGR02225 181 LERylkearpLLLKKKVKESDALFlnrrggpLSRQGVWKIlkEYaKRAGIEkpiSP----HTLRHSFATHLLENGADLRV 256

                         170       180
                  ....*....|....*....|....*
gi 251764782  289 LQRILGHSSITMTMRYAHLSPEHLA 313
Cdd:TIGR02225 257 VQELLGHADISTTQIYTHVARERLK 281
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 161-305 9.67e-11

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: 59.95  E-value: 9.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 161 SLDQVARLLEECKASTNNHT--YPVALLCLATGARWEEAESLTRGAVH--GGKVHYHRIKNRQSRSVPIPDEL-ERLI-- 233
Cdd:cd01188    1 SPDEVRRLLAAIDRLTPVGLrdYAILLLLARLGLRAGDVAGLRLDDIDwrSGTITVRQKKTGRPVELPLTEPVgEALAdy 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 234 FKVGMP--GSGRLFMSCRA-------------AFRCAYQRCGFQTPGQMTHILRHTFASHYMMGGGDILTLQRILGHSSI 298
Cdd:cd01188   81 LRDGRPrtDSREVFLRARApyrplsstsqissIVRRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSI 160


                 ....*..
gi 251764782 299 TMTMRYA 305
Cdd:cd01188  161 ETTAIYA 167
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 182-306 1.28e-10

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


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 58.60  E-value: 1.28e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 182 PVALLCLATGARWEEAESLT----RGAVHGGKVHYH----RIKNRQSRSVPIPDELERLIFKVGmpgsGRLFmscraAFR 253
Cdd:cd01187   17 PVVQAAVFTGARASELATLKfgclHAQTSDDGTFLYwlkwENKGGKQLDIPISKKVAELIKTIN----WTLN-----ELS 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 251764782 254 CAYQRCGFQTPGQM--THILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAH 306
Cdd:cd01187   88 ELKNISDDHGERFRfhTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 268-304 1.54e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 53.45  E-value: 1.54e-08
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 251764782 268 THILRHTFASHYMMGGGDILTLQRILGHSSITMTMRY 304
Cdd:cd01192  131 THSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 251-321 1.21e-07

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: 52.40  E-value: 1.21e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 251764782  251 AFRCAYQRCGFQTPGQmTHILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHLASAmsLSPL 321
Cdd:TIGR02249 245 AVRRAVERAGIEKPVT-CHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVLNRGASGV--LSPL 312
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 184-308 1.72e-07

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


Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 50.74  E-value: 1.72e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 184 ALLCLA--TGARWEEAESLTRGAVHGGKVHYHRI--KNRQSRSVPIPDELERLIFK-VGMPGSGRLFMSCRAAFRCAY-- 256
Cdd:cd01182   25 ALLLLLydTGARVQELADLTIRDLRLDDPATVRLhgKGRKERTVPLWKETVAALKAyLQEFHLTPDPKQLFPLFPNRRgq 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 251764782 257 --QRCGFQ----------------TPGQMT-HILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLS 308
Cdd:cd01182  105 plTRDGVAyilnkyvalasnrcpsLPKRITpHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYAEAD 175
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 269-316 1.80e-06

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 49.15  E-value: 1.80e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 251764782 269 HILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHLSPEHLASAM 316
Cdd:PRK05084 306 HKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKEAL 353
PRK15417 PRK15417
integron integrase;
251-307 3.25e-06

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 48.12  E-value: 3.25e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 251764782 251 AFRCAYQRCGFQTPGQmTHILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAHL 307
Cdd:PRK15417 260 AFKRAVEQAGITKPAT-PHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 315
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 160-312 4.53e-06

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 47.82  E-value: 4.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 160 LSLDQVARLLEECKASTNNHTYPVALLCL--ATGARWEEAESLTRGAVHGGK--VHYHRIKNRQSRSVPIPDE----LER 231
Cdd:PRK01287 137 LSEAETEQVLASPDLTTLQGLRDRALLELlwSTGIRRGELARLDLYDVDASRgvVTVRQGKGNKDRVVPVGERalawLQR 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 232 LIFKV-----GMPGSGRLFMSCR----------AAFRCAYQRCGFQTPGQmTHILRHTFASHYMMGGGDILTLQRILGHS 296
Cdd:PRK01287 217 YLQDVrpqlaVRPDSGALFVAMDgdglarntltNMVGRYIRAAGIEKAGA-CHLFRHAMATQMLENGADTRHIQAILGHA 295

                        170
                 ....*....|....*.
gi 251764782 297 SITMTMRYAHLSPEHL 312
Cdd:PRK01287 296 KLETTQIYTRVSIGHL 311
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 160-317 1.83e-05

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: 44.99  E-value: 1.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 160 LSLDQVARLLEECKASTNNH-----TYPVALLCLA-TGARWEEAESLTRGAVH--GGKVHYHRIKNRQSRSVPIP----D 227
Cdd:cd00797    1 YTDAEIRRLLAAADQLPPESplrplTYATLFGLLYaTGLRVGEALRLRLEDVDldSGILTIRQTKFGKSRLVPLHpstvG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 228 ELERLIFKVG----MPGSGRLFMSCRA----------AFRCAYQRCGFQTPGQ----MTHILRHTFASHYMM----GGGD 285
Cdd:cd00797   81 ALRDYLARRDrllpSPSSSYFFVSQQGgrltgggvyrVFRRLLRRIGLRGAGDgrgpRLHDLRHTFAVNRLTrwyrEGAD 160

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 251764782 286 ILT----LQRILGHSSITMTMRYAHLSPEHLASAMS 317
Cdd:cd00797  161 VERklpvLSTYLGHVNVTDTYWYLTATPELMELASL 196
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 214-310 3.84e-05

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: 43.56  E-value: 3.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 214 RIKNRQSRSVPIPDELERL-----IFKVGMPG--SGRLFMSCRA-----AFRCAYQRCGFQTPGQMT------HILRHTF 275
Cdd:cd01186   64 RAKSMRERRIPVSQDLIDLyadylTYIYCEEAefSITVFVNVKGgnqgkAMNYSDVYDLVRRLKKRTgidftpHMFRHTH 143

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 251764782 276 ASHYMMGGGDILTLQRILGHSSITMTMR-YAHLSPE 310
Cdd:cd01186  144 ATALIRAGWSIEVVARRLGHAHVQTTLNtYGHLSEE 179
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 255-306 8.06e-05

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: 42.75  E-value: 8.06e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 251764782 255 AYQRCGFQTPGQMTHILRHTFASHYMMGGGDILTLQRILGHSSITMTMRYAH 306
Cdd:cd01194  123 YLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIYAH 174
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 165-304 2.04e-04

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: 41.52  E-value: 2.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 165 VARLLEECKASTNNHTYPVALLCL--ATGARWEE-----AESLTRGAVHGGKVHYHRIKNRQS---RSVPIPDELERL-- 232
Cdd:cd00799    1 LKAMLATLDDTTLRGLRDRALLLLgfAGALRRSElvalrVEDLTRFVDGGLLIRLRRSKTDQDgegEIKALPYGPETCpv 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 233 ----------------IF----KVGMPGSGRLF-MSCRAAFRCAYQRCGFQTPGQMTHILRHTFASHYMMGGGDILTLQR 291
Cdd:cd00799   81 ralrawleaagipsgpLFrrirRGGSVGTTRLSdRSVARIVKRRAALAGLDPGDFSGHSLRRGFATEAARAGASLPEIMA 160

                        170
                 ....*....|...
gi 251764782 292 ILGHSSITMTMRY 304
Cdd:cd00799  161 QGGHKSVATVMRY 173
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 161-296 8.26e-03

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: 36.86  E-value: 8.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 251764782 161 SLDQVARLLEECKASTNNHTYPVAL-LCLATGARWEEAESLTRGAVHGGK----VHYHRIKNRQSRSVPIPDELERLI-- 233
Cdd:cd00801    1 SPDELPELWRALDTANLSPPTKLALrLLLLTGQRIGELARARWSEIDLEEktwtIPAERTKNKRPHRVPLSDQALEILee 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 251764782 234 FKVGMPGSGRLF--------MSCRAAFRCAYQRCGFQTPGQMTHILRHTFASHymMG--GGDILTLQRILGHS 296
Cdd:cd00801   81 LKEFTGDSGYLFpsrrkkkkPISENTINKALKRLGYKGKEFTPHDLRRTFSTL--LNelGIDPEVIERLLNHV 151
 
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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