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Conserved domains on  [gi|2299336814|gb|UWO52715|]
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site-specific integrase [Catenibacterium mitsuokai]

Protein Classification

site-specific integrase( domain architecture ID 10315017)

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
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 125-309 2.47e-94

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: 278.01  E-value: 2.47e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 125 LTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNPTVKLHGKGSKIRIVPISKNMNQILEV 204
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 205 YISKFFSDIKLKN-EYLIKNKNNQQMSRDGIEYIVQKYATILKNNDPSFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFL 283
Cdd:cd01182    81 YLQEFHLTPDPKQlFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                         170       180
                  ....*....|....*....|....*.
gi 2299336814 284 GHEDISTTMIYARADSRKKNEAINNL 309
Cdd:cd01182   161 GHESVETTQIYAEADLEMKREALEKA 186
Phage_int_SAM_1 super family cl12235
Phage integrase, N-terminal SAM-like domain;
16-95 1.86e-09

Phage integrase, N-terminal SAM-like domain;


The actual alignment was detected with superfamily member pfam02899:

Pssm-ID: 472283 [Multi-domain]  Cd Length: 83  Bit Score: 53.80  E-value: 1.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  16 EYLPLHRNCSKNTISSYKDSLKLFILFLRDHKSmNINkfkmhQINRELILEFIEWLENRGNSPVTINHRLAGIKSFINFA 95
Cdd:pfam02899   6 EYLSLERGLSPHTLRAYRRDLLAFLKFLSEGGS-SLE-----QITTSDVRAFLAELRAQGLSASSLARRLSALRSFYQFL 79
 
Name Accession Description Interval E-value
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 125-309 2.47e-94

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: 278.01  E-value: 2.47e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 125 LTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNPTVKLHGKGSKIRIVPISKNMNQILEV 204
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 205 YISKFFSDIKLKN-EYLIKNKNNQQMSRDGIEYIVQKYATILKNNDPSFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFL 283
Cdd:cd01182    81 YLQEFHLTPDPKQlFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                         170       180
                  ....*....|....*....|....*.
gi 2299336814 284 GHEDISTTMIYARADSRKKNEAINNL 309
Cdd:cd01182   161 GHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-311 4.75e-79

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 242.98  E-value: 4.75e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814   4 TDFAVLVTKFLtEYLPLHRNCSKNTISSYKDSLKLFILFLRDHKSMNINkfkmhQINRELILEFIEWLENRGNSPVTINH 83
Cdd:COG4974     1 LTLADLLEAFL-EELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLA-----EITPEDIRAYLNYLRERGLSPSTINR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  84 RLAGIKSFINFAQYESV--ENLAylqtvLSVKSLKTTTRQVDYLTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARV 161
Cdd:COG4974    75 YLAALRSFFRYAVREGLleDNPA-----AKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 162 QELCDLKIEDINLGNNpTVKLH-GKGSKIRIVPISKNMNQILEVYISKFFSDiklKNEYLIKNKNNQQMSRDGIEYIVQK 240
Cdd:COG4974   150 SELLGLKWSDIDLDRG-TIRVRrGKGGKERTVPLSPEALEALREYLEERRPR---DSDYLFPTRRGRPLSRRAIRKILKR 225

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2299336814 241 YATILKnndpsFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIYARADSRKKNEAINNLAP 311
Cdd:COG4974   226 LAKRAG-----IPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 12-294 3.73e-57

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: 186.63  E-value: 3.73e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  12 KFLtEYLPLHRNCSKNTISSYKDSLKLFILFLrDHKSMNINKfkmhqINRELILEFIEWLENRGNSPVTINHRLAGIKSF 91
Cdd:TIGR02225   2 QFL-DYLWVERGLSQNTLEAYRRDLEKFLEFL-EERGIDLEE-----VDRGDIVDFLAELKEAGLSARSIARALSALRSF 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  92 INFAQYESV--ENLAYLqtvlsVKSLKTTTRQVDYLTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKI 169
Cdd:TIGR02225  75 YRFLLREGIreDDPSAL-----IEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRL 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 170 EDINLgNNPTVKLHGKGSKIRIVPISKNMNQILEVYISK---FFSDIKLKNE-YLIKNKNNQQMSRDGIEYIVQKYA--- 242
Cdd:TIGR02225 150 EDVNL-DEGFVRVRGKGNKERLVPLGEEAIEALERYLKEarpLLLKKKVKESdALFLNRRGGPLSRQGVWKILKEYAkra 228

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2299336814 243 TILKNndpsfpskVHPHMFRHSKAMHMLA--VDIPIVyiRDFLGHEDISTTMIY 294
Cdd:TIGR02225 229 GIEKP--------ISPHTLRHSFATHLLEngADLRVV--QELLGHADISTTQIY 272
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-294 1.92e-52

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 174.96  E-value: 1.92e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814   1 MTATDFAVLVTKFLtEYLPLHRNCSKNTISSYKDSLKLFILFLRDHKSMNINkfkmhQINRELILEFIEWLENRGNSPVT 80
Cdd:PRK00236    1 MADADLPAALEAFL-EYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQ-----DLDAADLRSFLARRRRQGLSARS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  81 INHRLAGIKSFINFAQYESV--ENLAylqtvLSVKSLKTTTRQVDYLTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTG 158
Cdd:PRK00236   75 LARRLSALRSFYRWLVRRGLlkANPA-----AGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSG 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 159 ARVQELCDLKIEDINLGNNpTVKLHGKGSKIRIVPISKNMNQILEVYIS---KFFSDiklkNEYLIKNKNNQQMSRDGIE 235
Cdd:PRK00236  150 LRLSELVGLDIDDLDLASG-TLRVLGKGNKERTVPLGRAAREALEAYLAlrpLFLPD----DDALFLGARGGRLSPRVVQ 224

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2299336814 236 YIVQKYATILknndpSFPSKVHPHMFRHSKAMHMLA--VDIPIVyiRDFLGHEDISTTMIY 294
Cdd:PRK00236  225 RRVKKLGKKA-----GLPSHITPHKLRHSFATHLLEsgGDLRAV--QELLGHASLSTTQIY 278
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 124-298 1.44e-38

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: 134.75  E-value: 1.44e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 124 YLTEEQMNNLINLPPTDtSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLgNNPTVKLH-GKGSKIRIVPISKNMNQIL 202
Cdd:pfam00589   1 RLTEDEVERLLDAAETG-PLSIRDKALLELLYATGLRISELCSLRWSDIDF-ENGVIRVHrGKGNKERTVPLSDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 203 EVYISKFfSDIKLKNEYLIKNKNNQQMSRDGIEYIVQKYATILKNNDPsfpskVHPHMFRHSKAMHMLAVDIPIVYIRDF 282
Cdd:pfam00589  79 KEWLSKR-LLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELP-----LHPHMLRHSFATHLLEAGVDLRVVQKL 152

                         170
                  ....*....|....*.
gi 2299336814 283 LGHEDISTTMIYARAD 298
Cdd:pfam00589 153 LGHSSISTTQIYTHVA 168
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
16-95 1.86e-09

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 53.80  E-value: 1.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  16 EYLPLHRNCSKNTISSYKDSLKLFILFLRDHKSmNINkfkmhQINRELILEFIEWLENRGNSPVTINHRLAGIKSFINFA 95
Cdd:pfam02899   6 EYLSLERGLSPHTLRAYRRDLLAFLKFLSEGGS-SLE-----QITTSDVRAFLAELRAQGLSASSLARRLSALRSFYQFL 79
 
Name Accession Description Interval E-value
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 125-309 2.47e-94

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: 278.01  E-value: 2.47e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 125 LTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNPTVKLHGKGSKIRIVPISKNMNQILEV 204
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 205 YISKFFSDIKLKN-EYLIKNKNNQQMSRDGIEYIVQKYATILKNNDPSFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFL 283
Cdd:cd01182    81 YLQEFHLTPDPKQlFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                         170       180
                  ....*....|....*....|....*.
gi 2299336814 284 GHEDISTTMIYARADSRKKNEAINNL 309
Cdd:cd01182   161 GHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-311 4.75e-79

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 242.98  E-value: 4.75e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814   4 TDFAVLVTKFLtEYLPLHRNCSKNTISSYKDSLKLFILFLRDHKSMNINkfkmhQINRELILEFIEWLENRGNSPVTINH 83
Cdd:COG4974     1 LTLADLLEAFL-EELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLA-----EITPEDIRAYLNYLRERGLSPSTINR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  84 RLAGIKSFINFAQYESV--ENLAylqtvLSVKSLKTTTRQVDYLTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARV 161
Cdd:COG4974    75 YLAALRSFFRYAVREGLleDNPA-----AKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 162 QELCDLKIEDINLGNNpTVKLH-GKGSKIRIVPISKNMNQILEVYISKFFSDiklKNEYLIKNKNNQQMSRDGIEYIVQK 240
Cdd:COG4974   150 SELLGLKWSDIDLDRG-TIRVRrGKGGKERTVPLSPEALEALREYLEERRPR---DSDYLFPTRRGRPLSRRAIRKILKR 225

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2299336814 241 YATILKnndpsFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIYARADSRKKNEAINNLAP 311
Cdd:COG4974   226 LAKRAG-----IPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 12-294 3.73e-57

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: 186.63  E-value: 3.73e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  12 KFLtEYLPLHRNCSKNTISSYKDSLKLFILFLrDHKSMNINKfkmhqINRELILEFIEWLENRGNSPVTINHRLAGIKSF 91
Cdd:TIGR02225   2 QFL-DYLWVERGLSQNTLEAYRRDLEKFLEFL-EERGIDLEE-----VDRGDIVDFLAELKEAGLSARSIARALSALRSF 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  92 INFAQYESV--ENLAYLqtvlsVKSLKTTTRQVDYLTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKI 169
Cdd:TIGR02225  75 YRFLLREGIreDDPSAL-----IEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRL 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 170 EDINLgNNPTVKLHGKGSKIRIVPISKNMNQILEVYISK---FFSDIKLKNE-YLIKNKNNQQMSRDGIEYIVQKYA--- 242
Cdd:TIGR02225 150 EDVNL-DEGFVRVRGKGNKERLVPLGEEAIEALERYLKEarpLLLKKKVKESdALFLNRRGGPLSRQGVWKILKEYAkra 228

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2299336814 243 TILKNndpsfpskVHPHMFRHSKAMHMLA--VDIPIVyiRDFLGHEDISTTMIY 294
Cdd:TIGR02225 229 GIEKP--------ISPHTLRHSFATHLLEngADLRVV--QELLGHADISTTQIY 272
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 11-298 5.71e-53

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


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 176.26  E-value: 5.71e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  11 TKFLtEYLPLHRNCSKNTISSYKDSLKLFILFLRdhKSMNINKFKmhQINRELILEFIEWLENRGNSPVTINHRLAGIKS 90
Cdd:TIGR02224   1 EAFL-EYLRLERNYSPHTVRAYRRDLEAFLEFLE--EEGGLASLA--EVTAADLRSFLAELHARGLSRRSLARKLSALRS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  91 FINFAQYEsveNLAYLQTVLSVKSLKTTTRQVDYLTEEQMNNLINLPPTDTS--TGIRHRIIMCLLYDTGARVQELCDLK 168
Cdd:TIGR02224  76 FYRFLLRR---GLIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEDDEdwLALRDRAILELLYSSGLRVSELVGLD 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 169 IEDINLGNNpTVKLHGKGSKIRIVPISKNMNQILEVYISKFFSDI--KLKNEYLIKNKNNQQMSRDGIEYIVQKYatILK 246
Cdd:TIGR02224 153 LSDLDLDFG-EVRVRGKGNKERIVPFGPYARDALQAYLEARRSPLlaSEGQDALFLNRRGGRLTPRGVQYRLQQL--RAK 229

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2299336814 247 NNDPSfpsKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIYARAD 298
Cdd:TIGR02224 230 AGLPK---HVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVD 278
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-294 1.92e-52

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 174.96  E-value: 1.92e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814   1 MTATDFAVLVTKFLtEYLPLHRNCSKNTISSYKDSLKLFILFLRDHKSMNINkfkmhQINRELILEFIEWLENRGNSPVT 80
Cdd:PRK00236    1 MADADLPAALEAFL-EYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQ-----DLDAADLRSFLARRRRQGLSARS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  81 INHRLAGIKSFINFAQYESV--ENLAylqtvLSVKSLKTTTRQVDYLTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTG 158
Cdd:PRK00236   75 LARRLSALRSFYRWLVRRGLlkANPA-----AGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSG 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 159 ARVQELCDLKIEDINLGNNpTVKLHGKGSKIRIVPISKNMNQILEVYIS---KFFSDiklkNEYLIKNKNNQQMSRDGIE 235
Cdd:PRK00236  150 LRLSELVGLDIDDLDLASG-TLRVLGKGNKERTVPLGRAAREALEAYLAlrpLFLPD----DDALFLGARGGRLSPRVVQ 224

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2299336814 236 YIVQKYATILknndpSFPSKVHPHMFRHSKAMHMLA--VDIPIVyiRDFLGHEDISTTMIY 294
Cdd:PRK00236  225 RRVKKLGKKA-----GLPSHITPHKLRHSFATHLLEsgGDLRAV--QELLGHASLSTTQIY 278
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
10-306 5.19e-52

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 173.22  E-value: 5.19e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  10 VTKFLTEYLPLH--RNCSKNTISSYKDSLKLFILFLRDHKSmninkfKMHQINRELILEFIEWLENRGNSPVTINHRLAG 87
Cdd:COG4973     4 LAEALEAYLEHLreRRLSPKTLEAYRRDLRRLIPLLGDADL------PLEELTPADVRRFLARLHRRGLSPRTLNRRLSA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  88 IKSFINFAQYESvenlaYLQT--VLSVKSLKTTTRQVDYLTEEQMNNLINLPPTDTsTGIRHRIIMCLLYDTGARVQELC 165
Cdd:COG4973    78 LRSFFNWAVREG-----LLEAnpAAGVKAPKAPRKLPRALTVDELAQLLDALADDP-LAVRDRAIVELLYSTGLRLGELV 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 166 DLKIEDINLgNNPTVKLHGKGSKIRIVPISKNMNQILEVYISKFFSDIKLKNEYLIKNKNNQQMSRDGIEYIVQKYATil 245
Cdd:COG4973   152 GLDWEDVDL-DAGEVRVRGKTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRLAK-- 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2299336814 246 knnDPSFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIYARADSRKKNEAI 306
Cdd:COG4973   229 ---KAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
xerD PRK00283
tyrosine recombinase;
1-294 4.53e-51

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 171.14  E-value: 4.53e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814   1 MTATDfAVLVTKFLtEYLPLHRNCSKNTISSYKDSLKLFILFLRDHKSmninkfKMHQINRELILEFIEWLENRGNSPVT 80
Cdd:PRK00283    1 MMMAD-RALIEQFL-DALWVERGLAENTLSSYRRDLELFAEWLAARGL------SLAEATRDDLQAFLAELAEGGYKATS 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  81 INHRLAGIKSFINFAqYEsvENLAYLQTVLSVKSLKTTTRQVDYLTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGAR 160
Cdd:PRK00283   73 SARRLSALRRFFQFL-LR--EGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLR 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 161 VQELCDLKIEDINLgNNPTVKLHGKGSKIRIVPISKNMNQILEVYISKFFSDI--KLKNEYLIKNKNNQQMSRDGIEYIV 238
Cdd:PRK00283  150 VSELVGLTLDDVSL-RQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGRPALlnGRSSDALFPSARGGQLTRQTFWHRI 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2299336814 239 QKYA---TILknndpsfPSKVHPHMFRHSKAMHMLA--VDIPIVyiRDFLGHEDISTTMIY 294
Cdd:PRK00283  229 KHYAkraGID-------PKKLSPHVLRHAFATHLLNhgADLRVV--QELLGHSDISTTQIY 280
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 127-294 1.14e-42

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: 145.35  E-value: 1.14e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 127 EEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLgNNPTVKLHGKGSKIRIVPISKNMNQILEVYI 206
Cdd:cd00798     1 VDEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDL-DEGLVRVTGKGNKERLVPFGSYAVEALEEYL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 207 SKF--FSDIKLKNEYLIKNKNNQQMSRDGIEYIVQKYATILknndpSFPSKVHPHMFRHSKAMHML--AVDIPivYIRDF 282
Cdd:cd00798    80 EERrpLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERA-----GLPKHVSPHTLRHSFATHLLegGADLR--VVQEL 152

                         170
                  ....*....|..
gi 2299336814 283 LGHEDISTTMIY 294
Cdd:cd00798   153 LGHASLSTTQIY 164
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 124-298 1.44e-38

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: 134.75  E-value: 1.44e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 124 YLTEEQMNNLINLPPTDtSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLgNNPTVKLH-GKGSKIRIVPISKNMNQIL 202
Cdd:pfam00589   1 RLTEDEVERLLDAAETG-PLSIRDKALLELLYATGLRISELCSLRWSDIDF-ENGVIRVHrGKGNKERTVPLSDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 203 EVYISKFfSDIKLKNEYLIKNKNNQQMSRDGIEYIVQKYATILKNNDPsfpskVHPHMFRHSKAMHMLAVDIPIVYIRDF 282
Cdd:pfam00589  79 KEWLSKR-LLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELP-----LHPHMLRHSFATHLLEAGVDLRVVQKL 152

                         170
                  ....*....|....*.
gi 2299336814 283 LGHEDISTTMIYARAD 298
Cdd:pfam00589 153 LGHSSISTTQIYTHVA 168
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 129-295 2.56e-33

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: 121.05  E-value: 2.56e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 129 QMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNpTVKLHGKG---SKIRIVPISKNMNQILEVY 205
Cdd:cd00397     1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNG-TIRVRGKKtkgGKERTVPLPKELAEELKEY 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 206 ISKFFSDIKLKNE-----YLIKNKNNQQMSRDGIEYIVQKYATILKNndpsfpsKVHPHMFRHSKAMHMLAVDIPIVYIR 280
Cdd:cd00397    80 LKERRDKRGPLLKslylnKLFGTKLGERLSRRTLRRIFKKAGIEAGR-------KITPHSLRHTFATNLLENGVDIKVVQ 152

                         170
                  ....*....|....*
gi 2299336814 281 DFLGHEDISTTMIYA 295
Cdd:cd00397   153 KLLGHSSISTTQRYL 167
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 125-294 3.11e-27

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: 105.05  E-value: 3.11e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 125 LTEEQMNNLINlpptdTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLgNNPTVKLH-GKGSKIRIVPISKNMNQILE 203
Cdd:cd01193     6 LSPDEVRRILG-----ALTELRHRLILSLLYGAGLRISELLRLRVKDIDF-ERGVIRVRqGKGGKDRVVPLPEKLLEPLR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 204 VYIS----KFFSDIKLKNEYLIKNKNNQQ----MSRDGIEYIVQKY---ATILKnndpsfpsKVHPHMFRHSKAMHMLAV 272
Cdd:cd01193    80 RYLKsarpKEELDPAEGRAGVLDPRTGVErrhhISETTVQRALKKAveqAGITK--------RVTPHTLRHSFATHLLEA 151

                         170       180
                  ....*....|....*....|..
gi 2299336814 273 DIPIVYIRDFLGHEDISTTMIY 294
Cdd:cd01193   152 GTDIRTIQELLGHSDLSTTMIY 173
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 125-296 1.37e-20

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: 87.43  E-value: 1.37e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 125 LTEEQMNNLINLPPTDTST-GIRHRIIMCLLYDTGARVQELCDLKIEDIN-LGNNPTVKLHGKG--SKIRIVPISKNMNQ 200
Cdd:cd01194     1 LTLEQARQLLASLPIDDSIiGLRDRAIISLMVTEGLRTVEIVRADVGDLRqEGEGTILYVQGKGktSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 201 ILEVYISK---------FFSDIKlkneyliKNKNNQQMSRDGIEYIVQKYatiLKNNDPSfPSKVHPHMFRHSKAMHMLA 271
Cdd:cd01194    81 ALQAYLKArgkldfeepLFTSLS-------NNSKGQRLTTRSIRRIIKKY---LRKAGLD-DDRLTAHSLRHTAGTLALK 149

                         170       180
                  ....*....|....*....|....*
gi 2299336814 272 VDIPIVYIRDFLGHEDISTTMIYAR 296
Cdd:cd01194   150 AGKSLREVQQLLRHSDPNTTMIYAH 174
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 126-298 2.00e-19

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: 84.22  E-value: 2.00e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 126 TEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNpTVKLHG-KGSKIRIVPISKNMNQILEV 204
Cdd:cd01188     1 SPDEVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSG-TITVRQkKTGRPVELPLTEPVGEALAD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 205 YI--SKFFSDIKlknEYLIKNKN--NQQMSRDGIEYIVQKYATILKNNdpsfPSKVHPHMFRHSKAMHMLAVDIPIVYIR 280
Cdd:cd01188    80 YLrdGRPRTDSR---EVFLRARApyRPLSSTSQISSIVRRYLRKAGIE----PSHRGTHSLRHSLATRMLRAGTSLKVIA 152

                         170
                  ....*....|....*...
gi 2299336814 281 DFLGHEDISTTMIYARAD 298
Cdd:cd01188   153 DLLGHRSIETTAIYAKID 170
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 22-294 6.18e-18

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: 82.83  E-value: 6.18e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  22 RNCSKNTISSYKDSLKLFIlflRDHKSMNINKfkMHQINRELileFIEWLENRGN-SPVTINHRLAGIkSFInfaqYESV 100
Cdd:TIGR02249  12 RHYAKRTEEAYLHWIKRFI---RFHNKRHPST--MGDTEVEA---FLSDLAVDGKvAASTQNQALNAL-LFL----YKEI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 101 enlayLQTVLS-----VKSLKTTTRQVdYLTEEQMNNLINLPPTDtstgirHRIIMCLLYDTGARVQELCDLKIEDINLG 175
Cdd:TIGR02249  79 -----LKTPLSlmerfVRAKRPRKLPV-VLTREEVRRLLEHLEGK------YRLIAKLLYGSGMRLMECLRLRIQDIDFD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 176 NNPTVKLHGKGSKIRIVPISKNMNQILEVYISK----FFSDIK-----------LKNEY-----------------LIKN 223
Cdd:TIGR02249 147 YGEIRIRQGKGGKDRTVTLPKELIPPLREQIELarayHEADLAegyggvylphaLARKYpnapkewgwqylfpshrLSRD 226

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2299336814 224 KNNQQMSRDGI-EYIVQKY-------ATILKNndpsfpskVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIY 294
Cdd:TIGR02249 227 PESGVIRRHHInETTIQRAvrraverAGIEKP--------VTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 157-309 9.08e-18

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


Pssm-ID: 271191  Cd Length: 176  Bit Score: 79.78  E-value: 9.08e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 157 TGARVQELCDLKIEDINLGnnpTVKLHGKGSKIRIVPISKNMNQILEvyisKFFSDIKLKNEYLIKNKNNQQMSRDGIEY 236
Cdd:cd01191    32 TGARVSELIKIKVEHVELG---YFDIYSKGGKLRRLYIPKKLRNEAL----EWLKSTNRKSGYIFLNRFGERITTRGIAQ 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2299336814 237 IVQKYATILKNNdpsfPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIYARADSRKKNEAINNL 309
Cdd:cd01191   105 QLKNYARKYGLN----PKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRKTASEQQEIVDKI 173
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 120-296 1.09e-17

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 82.87  E-value: 1.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 120 RQVdyLTEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNPTVKLHGKGSKIRIVPISKNMN 199
Cdd:PRK01287  134 RQI--LSEAETEQVLASPDLTTLQGLRDRALLELLWSTGIRRGELARLDLYDVDASRGVVTVRQGKGNKDRVVPVGERAL 211

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 200 QILEVYISKFFSDI--KLKNEYLIKNKNNQQMSRDGIEYIVQKY--ATILKNNDPSfpskvhpHMFRHSKAMHMLAVDIP 275
Cdd:PRK01287  212 AWLQRYLQDVRPQLavRPDSGALFVAMDGDGLARNTLTNMVGRYirAAGIEKAGAC-------HLFRHAMATQMLENGAD 284

                         170       180
                  ....*....|....*....|.
gi 2299336814 276 IVYIRDFLGHEDISTTMIYAR 296
Cdd:PRK01287  285 TRHIQAILGHAKLETTQIYTR 305
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 124-296 2.41e-17

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: 78.14  E-value: 2.41e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 124 YLTEEQMNNLINLPPTDTSTGIRhRIIMcLLYDTGARVQELCDLKIEDINLGNNPTVKLHGKGSKIRIVPIS-------K 196
Cdd:cd00796     4 FLTEDEEARLLAALEESTNPHLR-LIVL-LALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSdeaiailK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 197 NMNQILEVYISKFFSDIKLKNEYLIKNKNNQQMSRDGIEyivqkyatilknndpsfpsKVHPHMFRHSKAMHMLAVDIPI 276
Cdd:cd00796    82 ELKRKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLE-------------------DLRFHDLRHTFASRLVQAGVPI 142

                         170       180
                  ....*....|....*....|
gi 2299336814 277 VYIRDFLGHEDISTTMIYAR 296
Cdd:cd00796   143 KTVAKILGHSSIKMTMRYAH 162
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 33-309 1.63e-15

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 76.50  E-value: 1.63e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  33 KDSLKLFILFLRDHKSMNinkfkmhqinrelilefiEWLENRGNSPVTINHRLAGIKSFINF----AQYESVENLAYLQT 108
Cdd:PRK05084   76 KKDVEAFILYLRERPLLN------------------GHSTKKGNSQTTINRTLSALKSLFKYlteeAENEDGEPYFYRNV 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 109 VLSVKSLKTT----TRQ--------VDYLTEEQMNNLINLPPTDTSTG---------IRHRIIMCLLYDTGARVQELCDL 167
Cdd:PRK05084  138 MKKIELKKKKetlaARAhnlkqklfLGDEDYEFLDFIDNEYEQKLSNRalssfkknkERDLAIIALILGSGLRVSELVNL 217

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 168 KIEDINLgNNPTVKLHGKGSKIRIVPISKNMNQILEVYI----SKFFSDIKLKNEYLIKNKNN-QQMSRDGIEYIVQKYA 242
Cdd:PRK05084  218 DLSDLNL-KQMTIDVTRKGGKRDSVNIAPFALPYLEEYLkiraSRYKAEKQEKALFLTKYRGKpNRISARAIEKMVAKYS 296

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2299336814 243 TilknndpSFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIYARADSRKKNEAINNL 309
Cdd:PRK05084  297 E-------AFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKEALDRL 356
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 133-302 1.18e-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: 70.37  E-value: 1.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 133 LINLPPTDTSTGIRHR---IIMCLlydTGARVQELCDLKIEDI-NLGNNPTVKLH-GKGSKIRIVPISKNMNQILEVYIS 207
Cdd:cd01185     6 LMALELSDTSRLELVRdmfLFSCY---TGLRFSDLKNLTWKNIvEASGRTWIRYRrKKTGKPVTVPLLPVAREILEKYKD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 208 KFfsdiklKNEYLIKNKNNQQMSRdgieYI--VQKYATILKNndpsfpskVHPHMFRHSKAMHMLAVDIPIVYIRDFLGH 285
Cdd:cd01185    83 DR------SEGKLFPVLSNQKINR----YLkeIAKIAGIDKH--------LTFHVARHTFATLLLLKGVDIETISKLLGH 144

                         170
                  ....*....|....*..
gi 2299336814 286 EDISTTMIYARADSRKK 302
Cdd:cd01185   145 SSIKTTQIYAKIVDSKK 161
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 127-295 3.00e-14

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: 69.12  E-value: 3.00e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 127 EEQMNNLINLPPTDtstGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNpTVKLHG----KGSKIRIVPISKNMNQIL 202
Cdd:cd01189     1 PEELKKLLEALKKR---GDRYYLLFLLALLTGLRRGELLALTWSDIDFENG-TIRINRtlvrKKKGGYVIKPPKTKSSIR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 203 EVYISKFFSDIkLKneyliknknnqqmsrdgiEYIvqKYATILKNNDPSfpsKVHPHMFRHSKAMHMLAVDIPIVYIRDF 282
Cdd:cd01189    77 TIPLPDELIEL-LK------------------ELK--AFKKLLKKAGLP---RITPHDLRHTFASLLLEAGVPLKVIAER 132

                         170
                  ....*....|....
gi 2299336814 283 LGHEDISTTM-IYA 295
Cdd:cd01189   133 LGHSDISTTLdVYA 146
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 125-292 1.23e-12

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


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 65.52  E-value: 1.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 125 LTEEQMNNLINlpptdTSTGIRHRIIMCLLYDTGARVQELCDLKIEDI-------------NLGNNPTVKLhgkgSKIRI 191
Cdd:cd01186     2 LTPREVQELIN-----ACNNLRDKFLLALLYETGLRIGEALGLRIEDIdmadnqielvpreDNTNEARAKS----MRERR 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 192 VPISKNMNQILEVYISKFFSD---------IKLKNEYLIKNKNNQqmsrdgieYIVQKYATILKNNDPSFpskvHPHMFR 262
Cdd:cd01186    73 IPVSQDLIDLYADYLTYIYCEeaefsitvfVNVKGGNQGKAMNYS--------DVYDLVRRLKKRTGIDF----TPHMFR 140

                         170       180       190
                  ....*....|....*....|....*....|
gi 2299336814 263 HSKAMHMLAVDIPIVYIRDFLGHEDISTTM 292
Cdd:cd01186   141 HTHATALIRAGWSIEVVARRLGHAHVQTTL 170
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 6-298 3.45e-12

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 66.60  E-value: 3.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814   6 FAVLVTKFLTEYLPlhrNCSKNTISSYKDSLKLFIL-FLRDhksmninkFKMHQINRELILEFIEWLENRGnSPVTINHR 84
Cdd:COG0582    99 FEEVAEEWLEEKKP---EWKEKTAAQVRRTLEKHIFpVLGD--------RPIAEITPPDLLAVLRPIEARG-APETARRV 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  85 LAGIKSFINFAqyesvENLAYLQT--VLSVKSL--KTTTRQVDYLTEEQMNNLINLPPTDTSTGIRHRIIMCLLYdTGAR 160
Cdd:COG0582   167 RQRLRQVFRYA-----VARGLIERnpAADLKGAlpKPKVKHHPALTPEELPELLRALDAYRGSPVTRLALRLLLL-TGVR 240

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 161 VQELCDLKIEDINLGNNpTVKLHG---KGSKIRIVPISKNMNQILEVYI-----SKF-FSDIKLKNEYLIKNKNNQQMSR 231
Cdd:COG0582   241 PGELRGARWSEIDLEAA-LWTIPAermKTRRPHIVPLSRQALEILKELKpltgdSEYvFPSRRGPKKPMSENTLNKALRR 319

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2299336814 232 DGIEYIVqkyatilknndpsfpskvhPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTM-IYARAD 298
Cdd:COG0582   320 MGYGRFT-------------------PHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaAYNRAD 368
int PHA02601
integrase; Provisional
 73-295 1.11e-11

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 64.75  E-value: 1.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  73 NRGNSPVTINHRLAGIKS-FINFAQYE--SVENlaylqTVLSVKSLKTTTRQVDYLTEEQMNNLINLPPTDTSTGIRHRI 149
Cdd:PHA02601  123 GRPIKPATVNRELAYLSAvFNELIKLGkwSGPN-----PLDGIRPFKEAEPELAFLTKEEIERLLDACDGSRSPDLGLIA 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 150 IMCLlyDTGARVQELCDLKIEdiNLGNNPTVKLHGKGSKIRIVPISKNMNQILEVYISKFFSDiklkneyliknknnqqm 229
Cdd:PHA02601  198 KICL--ATGARWSEAETLKRS--QISPYKITFVKTKGKKNRTVPISEELYKMLPKRRGRLFKD----------------- 256

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2299336814 230 srdgiEYivQKYATILKNNDPSFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIYA 295
Cdd:PHA02601  257 -----AY--ESFERAVKRAGIDLPEGQATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYA 315
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 126-297 1.17e-11

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: 62.49  E-value: 1.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 126 TEEQMNNLINLPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNpTVKLHGKGSKIR-IVPISKNMNQILEV 204
Cdd:cd01195     1 SREEARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHR-RLRILGKGKKQReVVTLPPTTREALAA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 205 YISKFFSdiklKNEYLI----KNKNNQQMSRDGIEYIVQKYATILKNNDpsfpsKVHPHMFRHSKAmhMLAVDIP---IV 277
Cdd:cd01195    80 WLAARGE----AEGPLFvsldRASRGRRLSPQAVYRIVRRLAERIGLGK-----RLSPHGLRHSAI--TLALDAGaglIR 148

                         170       180
                  ....*....|....*....|
gi 2299336814 278 YIRDFLGHEDISTTMIYARA 297
Cdd:cd01195   149 KVQDFSRHADLRTLQVYDDQ 168
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 120-301 5.41e-10

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


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 57.90  E-value: 5.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 120 RQVDYLTEEQMNNLINlPPTDTSTGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNPTVKLHGKGSKIRIVPISKNMN 199
Cdd:cd01197     2 KQRKYLTGKEVQALLQ-AACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDER 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 200 QILEVYISKFFSDIKLKNEYLIKNKNNQQMSRDGIEYIVQKYATilknnDPSFPSKVHPHMFRHS--KAMHMLAVDIPIv 277
Cdd:cd01197    81 EALEAWLKERANWKGADTDWIFLSRRGGPLSRQQAYRIIRDLGK-----EAGTVTQTHPHMLRHAcgYALADRGADTRL- 154

                         170       180
                  ....*....|....*....|....
gi 2299336814 278 yIRDFLGHEDISTTMIYARADSRK 301
Cdd:cd01197   155 -IQDYLGHRNIRHTVIYTASNAAR 177
PRK09870 PRK09870
tyrosine recombinase; Provisional
 123-299 7.61e-10

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 57.64  E-value: 7.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 123 DYLTEEQMNNLINLPPTDTStGIRHRIIMCLLYDTGARVQELCDLKIEDINLGNNPTVKLHGKGSKIRIVPISKNMNQIL 202
Cdd:PRK09870   11 NFLTHSEIESLLKAANTGPH-AARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEIQAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 203 EVYISKFFSDIKLKNEYLIKNKNNQQMSRDgieyivQKYATILKNNDPS-FPSKVHPHMFRHSKAMHMLAVDIPIVYIRD 281
Cdd:PRK09870   90 KNWLSIRTSYPHAESEWVFLSRKGNPLSRQ------QFYHIISTSGGNAgLSLEIHPHMLRHSCGFALANMGIDTRLIQD 163

                         170
                  ....*....|....*...
gi 2299336814 282 FLGHEDISTTMIYARADS 299
Cdd:PRK09870  164 YLGHRNIRHTVWYTASNA 181
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
16-95 1.86e-09

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 53.80  E-value: 1.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  16 EYLPLHRNCSKNTISSYKDSLKLFILFLRDHKSmNINkfkmhQINRELILEFIEWLENRGNSPVTINHRLAGIKSFINFA 95
Cdd:pfam02899   6 EYLSLERGLSPHTLRAYRRDLLAFLKFLSEGGS-SLE-----QITTSDVRAFLAELRAQGLSASSLARRLSALRSFYQFL 79
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 150-296 2.24e-09

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: 55.13  E-value: 2.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 150 IMCLLYDTGARVQELCDLKIEDINLGN------NPTVKLHGKGSKIRIVPISKNMNQILEVYiskffsdiklkNEYLIKn 223
Cdd:cd01187    18 VVQAAVFTGARASELATLKFGCLHAQTsddgtfLYWLKWENKGGKQLDIPISKKVAELIKTI-----------NWTLNE- 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2299336814 224 knnqqMSRdgieyivqkyaTILKNNDPSFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIYAR 296
Cdd:cd01187    86 -----LSE-----------LKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
PRK15417 PRK15417
integron integrase;
67-296 2.57e-08

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 54.67  E-value: 2.57e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814  67 FIEWLENRGNSPVTiNHRLAgIKSFINFAQYESVENLAYLQtvlSVKSLKTTTRQVDYLTEEQMNNLINLPPTDtstgir 146
Cdd:PRK15417   64 FLSWLANERKVSVS-THRQA-LAALLFFYGKVLCTDLPWLQ---EIGRPRPSRRLPVVLTPDEVVRILGFLEGE------ 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 147 HRIIMCLLYDTGARVQELCDLKIEDINLGNNPTVKLHGKGSKIRIVPISKNMNQILEVYISKffsdiklKNEYLIKNknn 226
Cdd:PRK15417  133 HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLREQLSR-------ARAWWLKD--- 202

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 227 QQMSRDGI---EYIVQKY-------------ATILKNNDP-----------------SFPSKVH---------PHMFRHS 264
Cdd:PRK15417  203 QAEGRSGValpDALERKYpraghswpwfwvfAQHTHSTDPrsgvvrrhhmydqtfqrAFKRAVEqagitkpatPHTLRHS 282

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2299336814 265 KAMHMLAVDIPIVYIRDFLGHEDISTTMIYAR 296
Cdd:PRK15417  283 FATALLRSGYDIRTVQDLLGHSDVSTTMIYTH 314
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 141-304 4.52e-07

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


Pssm-ID: 271196  Cd Length: 183  Bit Score: 49.40  E-value: 4.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 141 TSTGIRHRIIMCLLYDTGARVQELCDLKIEDI-NLGNNPTVKLHGKGSKIRIVPISKNMNQILEVYISKFFSDIKLKNEY 219
Cdd:cd01196    16 HPVGLRDRALIALMVYSFARIGAVLAMRVEDVyDQGRRLWVRLAEKGGKQHEMPCHHDLEEYLRAYLEAAEIEEDPKGPL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 220 L------IKNKNNQQMSRDGIEYIVQKYATilknnDPSFPSKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMI 293
Cdd:cd01196    96 FrttrggTRKLTHNPLTQANAYRMVRRRAI-----AADIPTAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQL 170

                         170
                  ....*....|..
gi 2299336814 294 YAR-ADSRKKNE 304
Cdd:cd01196   171 YDRrSDKITLDE 182
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 20-95 1.52e-06

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 46.06  E-value: 1.52e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2299336814  20 LHRNCSKNTISSYKDSLKLFILFLRDhksmniNKFKMHQINRELILEFIEWL-ENRGNSPVTINHRLAGIKSFINFA 95
Cdd:pfam13102  13 LKKKGSKGTARNYKSTLKHLKKFLKK------KDITFEEITVDFLEKFEEYLkKKKGLSENTISKYFRTLRAVLNKA 83
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 125-294 7.40e-06

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: 46.15  E-value: 7.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 125 LTEEQMNNLIN----LPPTDtstGIRHRIIMC---LLYDTGARVQELCDLKIEDINLGNNP-TVKlHGKGSKIRIVPISK 196
Cdd:cd00797     1 YTDAEIRRLLAaadqLPPES---PLRPLTYATlfgLLYATGLRVGEALRLRLEDVDLDSGIlTIR-QTKFGKSRLVPLHP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 197 NMNQILEVYISK----FFSDiklKNEYLIKNKNNQQMSRDGIEyivQKYATILKNNDPSFPSKVH---PHMFRHSKAMHM 269
Cdd:cd00797    77 STVGALRDYLARrdrlLPSP---SSSYFFVSQQGGRLTGGGVY---RVFRRLLRRIGLRGAGDGRgprLHDLRHTFAVNR 150

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2299336814 270 LA--------VDIPIVYIRDFLGHEDISTTMIY 294
Cdd:cd00797   151 LTrwyregadVERKLPVLSTYLGHVNVTDTYWY 183
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
21-91 1.45e-04

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 39.90  E-value: 1.45e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2299336814  21 HRNCSKNTISSYKDSLKLFILFLrDHKSMNinkfkmhQINRELILEFIEWLENRGN-SPVTINHRLAGIKSF 91
Cdd:pfam13495  11 LRGYAERTIKAYLRWIRRFLRFH-DKKHPE-------ELTEEDIEAYLSHLANERNvSASTQNQALNALSFF 74
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 157-294 2.37e-04

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


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 41.12  E-value: 2.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 157 TGARVQELCDLKIEDINLGNNPTVKLHgKGSKIRIVPISKNMNQILEVYISKFFSDIKLKNEYLIKNKNNQQMSRDGIEY 236
Cdd:cd01192    36 TGLRISDLLSLKVEDVTNKDKLSIKEQ-KTGKQKTFPLNPTLVKALKEYIDDLDLKRNDYLFKSLKQGPEKPISRKQAYK 114

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2299336814 237 IVQKYATILKNNDpsfpsKVHPHMFRHSKAMHMLAVDIPIVYIRDFLGHEDISTTMIY 294
Cdd:cd01192   115 ILKKAADDLGLNY-----NIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 125-287 5.74e-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: 40.37  E-value: 5.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 125 LTEEQMNNLINLPPTDTSTGIR-HR--IIMCLLYdTGARVQELCDLKIEDINLGNN----------PTVKLHGKGSKiRI 191
Cdd:cd01184     1 FTPEELAKIFSSPLYTGCKKKDpALywLPLIGLY-TGARLNEICQLRVDDIKEEDGiwcidinddaEGRRLKTKASR-RL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2299336814 192 VPISKNMNQI-LEVYISKFFSDIKLKNEYLIKNKNNqqmsrDGIEYIVQKYATILKNNDPSFPSKVHPHMFRHSKAMHML 270
Cdd:cd01184    79 VPIHPRLIELgFLDYVEALRADGKLFLFPEKRDKDG-----KYSKAASKWFNRLLRKLGIKDDERKSFHSFRHTFITALK 153

                         170
                  ....*....|....*..
gi 2299336814 271 AVDIPIVYIRDFLGHED 287
Cdd:cd01184   154 RAGVPEELIAQIVGHSR 170
 
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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