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Conserved domains on  [gi|490419111|ref|WP_004291422|]
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MULTISPECIES: site-specific integrase [Bacteria]

Protein Classification

site-specific integrase( domain architecture ID 13879636)

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:  10047575|9278480|10577069
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 228-389 1.08e-54

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: 178.23  E-value: 1.08e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 228 DEIRLLMEGKLKN-AKQELYRDLYLFCAFTGLSFADMRNLTEENIRTyFDEHEWININRQKTGVVSNIRLLDIANRIIGK 306
Cdd:cd01185    1 EELKRLMALELSDtSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVE-ASGRTWIRYRRKKTGKPVTVPLLPVAREILEK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 307 YRGLCGDGRIFPVPHYNTCLAGIRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITK 386
Cdd:cd01185   80 YKDDRSEGKLFPVLSNQKINRYLKEIAKIAGIDKHLTFHVARHTFATLL-LLKGVDIETISKLLGHSSIKTTQIYAKIVD 158


                 ...
gi 490419111 387 EKL 389
Cdd:cd01185  159 SKK 161
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 108-215 2.03e-20

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: 85.35  E-value: 2.03e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111  108 TLMQVFRQHNEDYEKqveagMKAKGTLLKYRTVYKHMQEFLDiryhVKDIALKELTPAFISDFEMFLRTDKHCCTNTVWL 187
Cdd:pfam13102   1 DFLDYFKEYIEELKK-----KGSKGTARNYKSTLKHLKKFLK----KKDITFEEITVDFLEKFEEYLKKKKGLSENTISK 71

                          90       100
                  ....*....|....*....|....*...
gi 490419111  188 YVCPLRTMVFIAINNEWLTRDPFREYEI 215
Cdd:pfam13102  72 YFRTLRAVLNKAIKEGIIKKNPYPKYKI 99
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 9-96 9.79e-14

Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.


:

Pssm-ID: 465401  Cd Length: 87  Bit Score: 66.25  E-value: 9.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111    9 YYLKRQVVKKDGTVPVMGRITVDGSQTQFSCKLTVDPKLWDTKGGRVTGRSTAALETNRMLDKMRVRINRHYQEiMERDN 88
Cdd:pfam17293   1 VYLRKKKLNKNGEAPLYLRIYKNGKRKYESLGLYITPEPWDKKKQKVKRKHPNALELNEQIDQERSKLEDIILE-LEQKG 79


                  ....*...
gi 490419111   89 FVTAEKVK 96
Cdd:pfam17293  80 KLSAELLK 87
 
Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 228-389 1.08e-54

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: 178.23  E-value: 1.08e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 228 DEIRLLMEGKLKN-AKQELYRDLYLFCAFTGLSFADMRNLTEENIRTyFDEHEWININRQKTGVVSNIRLLDIANRIIGK 306
Cdd:cd01185    1 EELKRLMALELSDtSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVE-ASGRTWIRYRRKKTGKPVTVPLLPVAREILEK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 307 YRGLCGDGRIFPVPHYNTCLAGIRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITK 386
Cdd:cd01185   80 YKDDRSEGKLFPVLSNQKINRYLKEIAKIAGIDKHLTFHVARHTFATLL-LLKGVDIETISKLLGHSSIKTTQIYAKIVD 158


                 ...
gi 490419111 387 EKL 389
Cdd:cd01185  159 SKK 161
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
107-396 2.16e-46

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 160.93  E-value: 2.16e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 107 HTLMQVFRQHNEDYEKQVEagmKAKGTLLKYRTVYKHMQEFLDiryHVKDIALKELTPAFISDFEMFLRtDKHCCTNTVW 186
Cdd:COG4974    1 LTLADLLEAFLEELKREKG---LSPNTIKAYRRDLRRFLRFLE---ELGKIPLAEITPEDIRAYLNYLR-ERGLSPSTIN 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 187 LYVCPLRTMVFIAINNEWLTRDPFREYEIKKEETTR-SFLTKDEIRLLMEgKLKNAKQELYRD--LYLFCAFTGLSFADM 263
Cdd:COG4974   74 RYLAALRSFFRYAVREGLLEDNPAAKVKLPKKPRKLpRVLTEEEIEALLE-ALDTETPEGLRDraLLLLLYATGLRVSEL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 264 RNLTEENIRTyfdEHEWININRQKTGVVSNIRLLDIANRIIGKY---RGLCGDGRIFPVP-----HYNTCLAGIRAVAKR 335
Cdd:COG4974  153 LGLKWSDIDL---DRGTIRVRRGKGGKERTVPLSPEALEALREYleeRRPRDSDYLFPTRrgrplSRRAIRKILKRLAKR 229

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490419111 336 CGITKHITWHQSRHTAATtIFLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKLNQDMENL 396
Cdd:COG4974  230 AGIPKRVTPHSLRHTFAT-HLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 108-215 2.03e-20

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: 85.35  E-value: 2.03e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111  108 TLMQVFRQHNEDYEKqveagMKAKGTLLKYRTVYKHMQEFLDiryhVKDIALKELTPAFISDFEMFLRTDKHCCTNTVWL 187
Cdd:pfam13102   1 DFLDYFKEYIEELKK-----KGSKGTARNYKSTLKHLKKFLK----KKDITFEEITVDFLEKFEEYLKKKKGLSENTISK 71

                          90       100
                  ....*....|....*....|....*...
gi 490419111  188 YVCPLRTMVFIAINNEWLTRDPFREYEI 215
Cdd:pfam13102  72 YFRTLRAVLNKAIKEGIIKKNPYPKYKI 99
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 224-386 1.23e-14

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: 71.20  E-value: 1.23e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111  224 FLTKDEIRLLMEgKLKNAKQELYRDLYL-FCAFTGLSFADMRNLTEENIRTyfdEHEWININRQKTGVVSNIRLLDIANR 302
Cdd:pfam00589   1 RLTEDEVERLLD-AAETGPLSIRDKALLeLLYATGLRISELCSLRWSDIDF---ENGVIRVHRGKGNKERTVPLSDAALE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111  303 IIGKYRGLCGDGR-----IFPVPH-----YNTCLAGIRAVAKRCGITKHITWHQSRHTAATtIFLSNGVPIETVSSMLGH 372
Cdd:pfam00589  77 LLKEWLSKRLLEApksdyLFASKRgkplsRQTVRKIFKRAGKEAGLELPLHPHMLRHSFAT-HLLEAGVDLRVVQKLLGH 155

                         170
                  ....*....|....
gi 490419111  373 KSIKTTQIYAKITK 386
Cdd:pfam00589 156 SSISTTQIYTHVAD 169
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 9-96 9.79e-14

Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.


Pssm-ID: 465401  Cd Length: 87  Bit Score: 66.25  E-value: 9.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111    9 YYLKRQVVKKDGTVPVMGRITVDGSQTQFSCKLTVDPKLWDTKGGRVTGRSTAALETNRMLDKMRVRINRHYQEiMERDN 88
Cdd:pfam17293   1 VYLRKKKLNKNGEAPLYLRIYKNGKRKYESLGLYITPEPWDKKKQKVKRKHPNALELNEQIDQERSKLEDIILE-LEQKG 79


                  ....*...
gi 490419111   89 FVTAEKVK 96
Cdd:pfam17293  80 KLSAELLK 87
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 329-390 2.47e-11

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: 64.14  E-value: 2.47e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490419111  329 IRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKLN 390
Cdd:TIGR02225 221 LKEYAKRAGIEKPISPHTLRHSFATHL-LENGADLRVVQELLGHADISTTQIYTHVARERLK 281
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 329-389 7.45e-09

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 56.70  E-value: 7.45e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490419111 329 IRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKL 389
Cdd:PRK00236 227 VKKLGKKAGLPSHITPHKLRHSFATHL-LESGGDLRAVQELLGHASLSTTQIYTHVDFQHL 286
 
Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 228-389 1.08e-54

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: 178.23  E-value: 1.08e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 228 DEIRLLMEGKLKN-AKQELYRDLYLFCAFTGLSFADMRNLTEENIRTyFDEHEWININRQKTGVVSNIRLLDIANRIIGK 306
Cdd:cd01185    1 EELKRLMALELSDtSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVE-ASGRTWIRYRRKKTGKPVTVPLLPVAREILEK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 307 YRGLCGDGRIFPVPHYNTCLAGIRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITK 386
Cdd:cd01185   80 YKDDRSEGKLFPVLSNQKINRYLKEIAKIAGIDKHLTFHVARHTFATLL-LLKGVDIETISKLLGHSSIKTTQIYAKIVD 158


                 ...
gi 490419111 387 EKL 389
Cdd:cd01185  159 SKK 161
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
107-396 2.16e-46

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 160.93  E-value: 2.16e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 107 HTLMQVFRQHNEDYEKQVEagmKAKGTLLKYRTVYKHMQEFLDiryHVKDIALKELTPAFISDFEMFLRtDKHCCTNTVW 186
Cdd:COG4974    1 LTLADLLEAFLEELKREKG---LSPNTIKAYRRDLRRFLRFLE---ELGKIPLAEITPEDIRAYLNYLR-ERGLSPSTIN 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 187 LYVCPLRTMVFIAINNEWLTRDPFREYEIKKEETTR-SFLTKDEIRLLMEgKLKNAKQELYRD--LYLFCAFTGLSFADM 263
Cdd:COG4974   74 RYLAALRSFFRYAVREGLLEDNPAAKVKLPKKPRKLpRVLTEEEIEALLE-ALDTETPEGLRDraLLLLLYATGLRVSEL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 264 RNLTEENIRTyfdEHEWININRQKTGVVSNIRLLDIANRIIGKY---RGLCGDGRIFPVP-----HYNTCLAGIRAVAKR 335
Cdd:COG4974  153 LGLKWSDIDL---DRGTIRVRRGKGGKERTVPLSPEALEALREYleeRRPRDSDYLFPTRrgrplSRRAIRKILKRLAKR 229

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490419111 336 CGITKHITWHQSRHTAATtIFLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKLNQDMENL 396
Cdd:COG4974  230 AGIPKRVTPHSLRHTFAT-HLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
120-389 6.81e-25

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 103.12  E-value: 6.81e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 120 YEKQVEAGMKAKgTLLKYRTVYKHMQEFLDiryhVKDIALKELTPAFISDFEMFLRTDKHCcTNTVWLYVCPLRTMVFIA 199
Cdd:COG4973   12 LEHLRERRLSPK-TLEAYRRDLRRLIPLLG----DADLPLEELTPADVRRFLARLHRRGLS-PRTLNRRLSALRSFFNWA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 200 INNEWLTRDPFREYEI-KKEETTRSFLTKDEIRLLMEGKLKNAKQELYRDLYLFCAFTGLSFADMRNLTEENIRTyfdEH 278
Cdd:COG4973   86 VREGLLEANPAAGVKApKAPRKLPRALTVDELAQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDL---DA 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 279 EWINInRQKTGVVSNIRLLDIANRIIGKYRGLC------GDGRIFPVP-----HYNTCLAGIRAVAKRCGITKHITWHQS 347
Cdd:COG4973  163 GEVRV-RGKTGKSRTVPLGPKALAALREWLAVRpelaapDEGALFPSRrgtrlSPRNVQKRLRRLAKKAGLPKHVHPHDL 241

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 490419111 348 RHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKL 389
Cdd:COG4973  242 RHSFATHL-LESGGDLRAVQELLGHASISTTQIYTHLDFQHL 282
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 108-215 2.03e-20

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: 85.35  E-value: 2.03e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111  108 TLMQVFRQHNEDYEKqveagMKAKGTLLKYRTVYKHMQEFLDiryhVKDIALKELTPAFISDFEMFLRTDKHCCTNTVWL 187
Cdd:pfam13102   1 DFLDYFKEYIEELKK-----KGSKGTARNYKSTLKHLKKFLK----KKDITFEEITVDFLEKFEEYLKKKKGLSENTISK 71

                          90       100
                  ....*....|....*....|....*...
gi 490419111  188 YVCPLRTMVFIAINNEWLTRDPFREYEI 215
Cdd:pfam13102  72 YFRTLRAVLNKAIKEGIIKKNPYPKYKI 99
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 224-382 8.34e-18

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: 80.06  E-value: 8.34e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 224 FLTKDEIRLLMEGkLKNAKQELYRDLYLFCAFTGLSFADMRNLTEENIRTyfdEHEWININRQKTGVVSNIRLLDIANRI 303
Cdd:cd00796    4 FLTEDEEARLLAA-LEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDL---EVGLIVLPETKNGKPRTVPLSDEAIAI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 304 IGKY-RGLCGDGRIFPVP----HYNTCLAGIRAVAKRCGITKhITWHQSRHTAATtIFLSNGVPIETVSSMLGHKSIKTT 378
Cdd:cd00796   80 LKELkRKRGKDGFFVDGRffgiPIASLRRAFKKARKRAGLED-LRFHDLRHTFAS-RLVQAGVPIKTVAKILGHSSIKMT 157


                 ....
gi 490419111 379 QIYA 382
Cdd:cd00796  158 MRYA 161
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 229-382 1.90e-15

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: 73.67  E-value: 1.90e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 229 EIRLLMEGKLKNAKQELYRDLYLFCAF-TGLSFADMRNLTEENIRTyfdEHEWININRQKTG------VVSNIRLLDIAN 301
Cdd:cd00397    1 ELEKLLDAIDEDKKIDLRDRAILLLLLeTGLRISELLALKVKDIDL---DNGTIRVRGKKTKggkertVPLPKELAEELK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 302 RIIGKYRGLCGDGRIFPVPH--------YNTCLAGIRAVAKRCGIT--KHITWHQSRHTAATTiFLSNGVPIETVSSMLG 371
Cdd:cd00397   78 EYLKERRDKRGPLLKSLYLNklfgtklgERLSRRTLRRIFKKAGIEagRKITPHSLRHTFATN-LLENGVDIKVVQKLLG 156

                        170
                 ....*....|.
gi 490419111 372 HKSIKTTQIYA 382
Cdd:cd00397  157 HSSISTTQRYL 167
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 226-391 5.57e-15

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: 72.66  E-value: 5.57e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 226 TKDEIRLLMEG--KLKNAKQelyRDLYLF-CAFT-GLSFADMRNLTEENIrtyfdehEW----ININRQKTGVVSNIRLL 297
Cdd:cd01188    1 SPDEVRRLLAAidRLTPVGL---RDYAILlLLARlGLRAGDVAGLRLDDI-------DWrsgtITVRQKKTGRPVELPLT 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 298 DIANRIIGKY----RGLCGDGRIF-----PVPHY--NTCLAGI-RAVAKRCGITKHIT-WHQSRHTAATTIfLSNGVPIE 364
Cdd:cd01188   71 EPVGEALADYlrdgRPRTDSREVFlraraPYRPLssTSQISSIvRRYLRKAGIEPSHRgTHSLRHSLATRM-LRAGTSLK 149

                        170       180
                 ....*....|....*....|....*..
gi 490419111 365 TVSSMLGHKSIKTTQIYAKITKEKLNQ 391
Cdd:cd01188  150 VIADLLGHRSIETTAIYAKIDVDDLRE 176
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 224-386 1.23e-14

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: 71.20  E-value: 1.23e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111  224 FLTKDEIRLLMEgKLKNAKQELYRDLYL-FCAFTGLSFADMRNLTEENIRTyfdEHEWININRQKTGVVSNIRLLDIANR 302
Cdd:pfam00589   1 RLTEDEVERLLD-AAETGPLSIRDKALLeLLYATGLRISELCSLRWSDIDF---ENGVIRVHRGKGNKERTVPLSDAALE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111  303 IIGKYRGLCGDGR-----IFPVPH-----YNTCLAGIRAVAKRCGITKHITWHQSRHTAATtIFLSNGVPIETVSSMLGH 372
Cdd:pfam00589  77 LLKEWLSKRLLEApksdyLFASKRgkplsRQTVRKIFKRAGKEAGLELPLHPHMLRHSFAT-HLLEAGVDLRVVQKLLGH 155

                         170
                  ....*....|....
gi 490419111  373 KSIKTTQIYAKITK 386
Cdd:pfam00589 156 SSISTTQIYTHVAD 169
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 329-389 2.37e-14

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: 70.62  E-value: 2.37e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490419111 329 IRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKL 389
Cdd:cd00798  113 LKKYAERAGLPKHVSPHTLRHSFATHL-LEGGADLRVVQELLGHASLSTTQIYTHVSFERL 172
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 9-96 9.79e-14

Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.


Pssm-ID: 465401  Cd Length: 87  Bit Score: 66.25  E-value: 9.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111    9 YYLKRQVVKKDGTVPVMGRITVDGSQTQFSCKLTVDPKLWDTKGGRVTGRSTAALETNRMLDKMRVRINRHYQEiMERDN 88
Cdd:pfam17293   1 VYLRKKKLNKNGEAPLYLRIYKNGKRKYESLGLYITPEPWDKKKQKVKRKHPNALELNEQIDQERSKLEDIILE-LEQKG 79


                  ....*...
gi 490419111   89 FVTAEKVK 96
Cdd:pfam17293  80 KLSAELLK 87
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 227-383 2.18e-13

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: 67.20  E-value: 2.18e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 227 KDEIRLLMEGKLKnaKQELYRDLYLFCAFTGLSFADMRNLTEENIrtyFDEHEWININRQ--------------KTGvvS 292
Cdd:cd01189    1 PEELKKLLEALKK--RGDRYYLLFLLALLTGLRRGELLALTWSDI---DFENGTIRINRTlvrkkkggyvikppKTK--S 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 293 NIRLLDIANRIIGKYRGLcgdgRIFpvphyntclagiRAVAKRCGItKHITWHQSRHTAATtIFLSNGVPIETVSSMLGH 372
Cdd:cd01189   74 SIRTIPLPDELIELLKEL----KAF------------KKLLKKAGL-PRITPHDLRHTFAS-LLLEAGVPLKVIAERLGH 135

                        170
                 ....*....|..
gi 490419111 373 KSIKTT-QIYAK 383
Cdd:cd01189  136 SDISTTlDVYAH 147
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 199-383 3.50e-13

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 70.45  E-value: 3.50e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 199 AINNEWLTRDPF---REYEIKKEETTRSFLTKDEIRLLMEgKLKNAK-QELYRDLYLFCAFTGLSFADMRNLTEENIRty 274
Cdd:COG0582  177 AVARGLIERNPAadlKGALPKPKVKHHPALTPEELPELLR-ALDAYRgSPVTRLALRLLLLTGVRPGELRGARWSEID-- 253

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 275 FDEHEW-ININRQKTGVVSNIRLLDIANRIIGKYRGLCGDGR-IFPVPH-------YNTclagIRAVAKRCGItKHITWH 345
Cdd:COG0582  254 LEAALWtIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEyVFPSRRgpkkpmsENT----LNKALRRMGY-GRFTPH 328

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 490419111 346 QSRHTAAtTIFLSNGVPIETVSSMLGHKSI-KTTQIYAK 383
Cdd:COG0582  329 GFRHTAS-TLLNEAGFPPDVIERQLAHKDGnKVRAAYNR 366
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 224-384 1.57e-11

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 62.68  E-value: 1.57e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 224 FLTKDEIRLLMEgklkNAKQELYRDLYLFCAFTGLSFADMRNLTEENIRTyfdEHEWININRQKTG----------VVSN 293
Cdd:cd01193    5 VLSPDEVRRILG----ALTELRHRLILSLLYGAGLRISELLRLRVKDIDF---ERGVIRVRQGKGGkdrvvplpekLLEP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 294 IR-LLDIANRIIGKYRGLCGDGRIFPVP------HYNTCLAG--IRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIE 364
Cdd:cd01193   78 LRrYLKSARPKEELDPAEGRAGVLDPRTgverrhHISETTVQraLKKAVEQAGITKRVTPHTLRHSFATHL-LEAGTDIR 156

                        170       180
                 ....*....|....*....|
gi 490419111 365 TVSSMLGHKSIKTTQIYAKI 384
Cdd:cd01193  157 TIQELLGHSDLSTTMIYTHV 176
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 329-390 2.47e-11

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: 64.14  E-value: 2.47e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490419111  329 IRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKLN 390
Cdd:TIGR02225 221 LKEYAKRAGIEKPISPHTLRHSFATHL-LENGADLRVVQELLGHADISTTQIYTHVARERLK 281
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 332-396 6.60e-10

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: 58.06  E-value: 6.60e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490419111 332 VAKRC-GITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKLNQDMENL 396
Cdd:cd01182  122 ASNRCpSLPKRITPHTLRHTKAMHL-LQAGVDLTVIRDWLGHESVETTQIYAEADLEMKREALEKA 186
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 329-381 2.13e-09

integron integrase; Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 58.56  E-value: 2.13e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 490419111  329 IRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIY 381
Cdd:TIGR02249 246 VRRAVERAGIEKPVTCHTLRHSFATHL-LESGADIRTVQELLGHSDVKTTQIY 297
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 329-389 7.45e-09

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 56.70  E-value: 7.45e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490419111 329 IRAVAKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKL 389
Cdd:PRK00236 227 VKKLGKKAGLPSHITPHKLRHSFATHL-LESGGDLRAVQELLGHASLSTTQIYTHVDFQHL 286
xerD PRK00283
tyrosine recombinase;
329-389 1.58e-07

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 52.50  E-value: 1.58e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490419111 329 IRAVAKRCGI-TKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITKEKL 389
Cdd:PRK00283 228 IKHYAKRAGIdPKKLSPHVLRHAFATHL-LNHGADLRVVQELLGHSDISTTQIYTHVATERL 288
int PHA02601
integrase; Provisional
 203-401 4.19e-07

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 51.27  E-value: 4.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 203 EWLTRDPFREYE-IKKEETTRSFLTKDEIRLLMEgKLKNAKQELYRDLYLFCAFTGLSFADMRNLTEENIRTYFDEHEWI 281
Cdd:PHA02601 150 KWSGPNPLDGIRpFKEAEPELAFLTKEEIERLLD-ACDGSRSPDLGLIAKICLATGARWSEAETLKRSQISPYKITFVKT 228

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 282 NINRQKTGVVSNiRLLDIANRiigkyrglcGDGRIFPvphynTCLAGIRAVAKRCGI--TKHITWHQSRHTAATTiFLSN 359
Cdd:PHA02601 229 KGKKNRTVPISE-ELYKMLPK---------RRGRLFK-----DAYESFERAVKRAGIdlPEGQATHVLRHTFASH-FMMN 292

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 490419111 360 GVPIETVSSMLGHKSIKTTQIYAKITKEKLNQdmenlAARLN 401
Cdd:PHA02601 293 GGNILVLQRILGHATIEMTMAYAHFAPDHLED-----AVSLN 329
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 322-378 1.26e-06

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


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 48.57  E-value: 1.26e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 490419111 322 YNTCLAGIRAVAKRCGItkHITWHQSRHTAAtTIFLSNGVPIETVSSMLGHKSIKTT 378
Cdd:cd01186  116 YSDVYDLVRRLKKRTGI--DFTPHMFRHTHA-TALIRAGWSIEVVARRLGHAHVQTT 169
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 225-382 1.31e-06

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


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 48.14  E-value: 1.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 225 LTKDEIRLLMEGKLKNAKQELYRD--LYLFCAFTGLSFADMRNLTEENIRTYfDEHEWININ-RQKTGVVSNIRLLDIAN 301
Cdd:cd01194    1 LTLEQARQLLASLPIDDSIIGLRDraIISLMVTEGLRTVEIVRADVGDLRQE-GEGTILYVQgKGKTSKDDFVYLRPDVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 302 RIIGKY---RGLCGDGRIFPVPHYNTCLA------GIRAVAK----RCGITKH-ITWHQSRHTAATtIFLSNGVPIETVS 367
Cdd:cd01194   80 KALQAYlkaRGKLDFEEPLFTSLSNNSKGqrlttrSIRRIIKkylrKAGLDDDrLTAHSLRHTAGT-LALKAGKSLREVQ 158

                        170
                 ....*....|....*
gi 490419111 368 SMLGHKSIKTTQIYA 382
Cdd:cd01194  159 QLLRHSDPNTTMIYA 173
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 329-381 1.56e-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: 271196  Cd Length: 183  Bit Score: 45.16  E-value: 1.56e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 490419111 329 IRAVAKRCGITKHITWHQSRHTAATTiFLSNGVPIETVSSMLGHKSIKTTQIY 381
Cdd:cd01196  120 VRRRAIAADIPTAIGNHSFRATGITA-YLKNGGTLEDAQNMANHASTRTTQLY 171
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 296-391 2.30e-05

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 46.28  E-value: 2.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 296 LLDIANRIIGKYrglcGDGRIFpVPHYNTCLA--GIRAVAKRC----GITKHITWHQSRHTAATTIfLSNGVPIETVSSM 369
Cdd:PRK01287 218 LQDVRPQLAVRP----DSGALF-VAMDGDGLArnTLTNMVGRYiraaGIEKAGACHLFRHAMATQM-LENGADTRHIQAI 291

                         90       100
                 ....*....|....*....|..
gi 490419111 370 LGHKSIKTTQIYAKITKEKLNQ 391
Cdd:PRK01287 292 LGHAKLETTQIYTRVSIGHLQA 313
PRK15417 PRK15417
integron integrase;
330-386 7.07e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 44.65  E-value: 7.07e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 490419111 330 RAVaKRCGITKHITWHQSRHTAATTIfLSNGVPIETVSSMLGHKSIKTTQIYAKITK 386
Cdd:PRK15417 263 RAV-EQAGITKPATPHTLRHSFATAL-LRSGYDIRTVQDLLGHSDVSTTMIYTHVLK 317
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 226-373 1.27e-04

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 42.64  E-value: 1.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419111 226 TKDEIRLLMEGKLKNAKQELYRDLYLFCAFTGLSFADMRNLTEENIRtyFDEHEW-ININRQKTGVVSNIRLLDIANRII 304
Cdd:cd00801    1 SPDELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEID--LEEKTWtIPAERTKNKRPHRVPLSDQALEIL 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490419111 305 GKYRGLCGDGR-IFP---VPHYNTCLAGIRAVAKR-CGITKHITWHQSRHTAAtTIFLSNGVPIETVSSMLGHK 373
Cdd:cd00801   79 EELKEFTGDSGyLFPsrrKKKKPISENTINKALKRlGYKGKEFTPHDLRRTFS-TLLNELGIDPEVIERLLNHV 151
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 326-383 8.73e-03

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


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 36.64  E-value: 8.73e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 490419111 326 LAGIRAVAKRCGITKHITWHQSRHTAAtTIFLSNGVPIETVSSMLGHKSIKTTQIYAK 383
Cdd:cd01187   86 LSELKNISDDHGERFRFHTHRFRHTVA-TRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
 
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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