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Conserved domains on  [gi|499299514|ref|WP_010990464|]
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site-specific integrase [Listeria innocua]

Protein Classification

site-specific integrase( domain architecture ID 10100340)

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
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 122-288 1.07e-47

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: 156.95  E-value: 1.07e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 122 EVQALLKELNLKEDiNWDWFILLIIKTGLRFSEALALTPSDFDFSKQKIIINKTWDY-KMVTGSFQPTKNESSNRKIQID 200
Cdd:cd01189    3 ELKKLLEALKKRGD-RYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLVRkKKGGYVIKPPKTKSSIRTIPLP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 201 WQLAMQFSQLIKMKDpdkpifvksrvfnstinnrlkvLCENANIPTITVHSLRHTHASLLLFAGVSIASVANRLGHSSMT 280
Cdd:cd01189   82 DELIELLKELKAFKK----------------------LLKKAGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDIS 139


                 ....*...
gi 499299514 281 TTQETYLH 288
Cdd:cd01189  140 TTLDVYAH 147
 
Name Accession Description Interval E-value
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 122-288 1.07e-47

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: 156.95  E-value: 1.07e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 122 EVQALLKELNLKEDiNWDWFILLIIKTGLRFSEALALTPSDFDFSKQKIIINKTWDY-KMVTGSFQPTKNESSNRKIQID 200
Cdd:cd01189    3 ELKKLLEALKKRGD-RYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLVRkKKGGYVIKPPKTKSSIRTIPLP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 201 WQLAMQFSQLIKMKDpdkpifvksrvfnstinnrlkvLCENANIPTITVHSLRHTHASLLLFAGVSIASVANRLGHSSMT 280
Cdd:cd01189   82 DELIELLKELKAFKK----------------------LLKKAGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDIS 139


                 ....*...
gi 499299514 281 TTQETYLH 288
Cdd:cd01189  140 TTLDVYAH 147
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
10-292 9.57e-42

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 145.91  E-value: 9.57e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  10 TFHEYFKEWVDLYKVGAIRSI-TLQKYYVTEQKIQELVPDLKIKDLDRYTYQQL---LNSYAVTHEKQTTMDFHH-HLKG 84
Cdd:COG4974    2 TLADLLEAFLEELKREKGLSPnTIKAYRRDLRRFLRFLEELGKIPLAEITPEDIrayLNYLRERGLSPSTINRYLaALRS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  85 AILDAVDEGVISQNPTRKIVIKgKTPRPKKaKFLNQFEVQALLKELNLKEDINWDW--FILLIIKTGLRFSEALALTPSD 162
Cdd:COG4974   82 FFRYAVREGLLEDNPAAKVKLP-KKPRKLP-RVLTEEEIEALLEALDTETPEGLRDraLLLLLYATGLRVSELLGLKWSD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 163 FDFSKQKIIINKTwdykmvtgsfqptKNeSSNRKIQIDWQLAMQFSQLIKMKDP--DKPIFVKSR---VFNSTINNRLKV 237
Cdd:COG4974  160 IDLDRGTIRVRRG-------------KG-GKERTVPLSPEALEALREYLEERRPrdSDYLFPTRRgrpLSRRAIRKILKR 225

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499299514 238 LCENANIP-TITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHIIQE 292
Cdd:COG4974  226 LAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQ-IYTHVSDE 280
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 117-289 4.47e-16

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: 74.28  E-value: 4.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  117 FLNQFEVQALLKELNLKEDINWDW-FILLIIKTGLRFSEALALTPSDFDFSKQKIIInktwdykmvtgsfQPTKNessNR 195
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKaLLELLYATGLRISELCSLRWSDIDFENGVIRV-------------HRGKG---NK 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  196 KIQIdwQLAMQFSQLIKM--------KDPDKPIFVK---SRVFNSTINNRLKVLCENANI-PTITVHSLRHTHASLLLFA 263
Cdd:pfam00589  65 ERTV--PLSDAALELLKEwlskrlleAPKSDYLFASkrgKPLSRQTVRKIFKRAGKEAGLeLPLHPHMLRHSFATHLLEA 142

                         170       180
                  ....*....|....*....|....*.
gi 499299514  264 GVSIASVANRLGHSSMTTTQeTYLHI 289
Cdd:pfam00589 143 GVDLRVVQKLLGHSSISTTQ-IYTHV 167
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 89-295 6.14e-14

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: 70.71  E-value: 6.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514   89 AVDEGVISQNPTRKIvikgKTPRPKKA--KFLNQFEVQALLKelnLKEDINWDWFIL-------LIIKTGLRFSEALALT 159
Cdd:TIGR02224  80 LLRRGLIDANPAAGV----RAPKQPKKlpKFLSEDEMEALLD---APEEDDEDWLALrdraileLLYSSGLRVSELVGLD 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  160 PSDFDFSKQKIIinktwdykmVTGsfqptKNeSSNRKIQI---------DWQLAMQFSQLikMKDPDKPIFVKS---RVF 227
Cdd:TIGR02224 153 LSDLDLDFGEVR---------VRG-----KG-NKERIVPFgpyardalqAYLEARRSPLL--ASEGQDALFLNRrggRLT 215

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  228 NSTINNRLKVLCENANIPT-ITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHI-IQELEN 295
Cdd:TIGR02224 216 PRGVQYRLQQLRAKAGLPKhVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQ-IYTHVdFQHLAK 284
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 89-289 6.29e-14

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 70.57  E-value: 6.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  89 AVDEGVISQNPTRKIvikgKTPRPKKA--KFLNQFEVQALLKELNLKedinwDWF-------ILLIIKTGLRFSEALALT 159
Cdd:PRK00236  89 LVRRGLLKANPAAGL----RAPKIPKRlpKPLDVDQAKRLLDAIDED-----DPLalrdraiLELLYGSGLRLSELVGLD 159

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 160 PSDFDFSKQKIII----NKTwdykmvtgsfqptknessnRKIQI---------DWqLAMqfsqLIKMKDPDKPIFVKS-- 224
Cdd:PRK00236 160 IDDLDLASGTLRVlgkgNKE-------------------RTVPLgraarealeAY-LAL----RPLFLPDDDALFLGArg 215

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499299514 225 -RVFNSTINNRLKVLCENANIP-TITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHI 289
Cdd:PRK00236 216 gRLSPRVVQRRVKKLGKKAGLPsHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQ-IYTHV 281
 
Name Accession Description Interval E-value
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 122-288 1.07e-47

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: 156.95  E-value: 1.07e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 122 EVQALLKELNLKEDiNWDWFILLIIKTGLRFSEALALTPSDFDFSKQKIIINKTWDY-KMVTGSFQPTKNESSNRKIQID 200
Cdd:cd01189    3 ELKKLLEALKKRGD-RYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLVRkKKGGYVIKPPKTKSSIRTIPLP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 201 WQLAMQFSQLIKMKDpdkpifvksrvfnstinnrlkvLCENANIPTITVHSLRHTHASLLLFAGVSIASVANRLGHSSMT 280
Cdd:cd01189   82 DELIELLKELKAFKK----------------------LLKKAGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDIS 139


                 ....*...
gi 499299514 281 TTQETYLH 288
Cdd:cd01189  140 TTLDVYAH 147
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
10-292 9.57e-42

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 145.91  E-value: 9.57e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  10 TFHEYFKEWVDLYKVGAIRSI-TLQKYYVTEQKIQELVPDLKIKDLDRYTYQQL---LNSYAVTHEKQTTMDFHH-HLKG 84
Cdd:COG4974    2 TLADLLEAFLEELKREKGLSPnTIKAYRRDLRRFLRFLEELGKIPLAEITPEDIrayLNYLRERGLSPSTINRYLaALRS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  85 AILDAVDEGVISQNPTRKIVIKgKTPRPKKaKFLNQFEVQALLKELNLKEDINWDW--FILLIIKTGLRFSEALALTPSD 162
Cdd:COG4974   82 FFRYAVREGLLEDNPAAKVKLP-KKPRKLP-RVLTEEEIEALLEALDTETPEGLRDraLLLLLYATGLRVSELLGLKWSD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 163 FDFSKQKIIINKTwdykmvtgsfqptKNeSSNRKIQIDWQLAMQFSQLIKMKDP--DKPIFVKSR---VFNSTINNRLKV 237
Cdd:COG4974  160 IDLDRGTIRVRRG-------------KG-GKERTVPLSPEALEALREYLEERRPrdSDYLFPTRRgrpLSRRAIRKILKR 225

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499299514 238 LCENANIP-TITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHIIQE 292
Cdd:COG4974  226 LAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQ-IYTHVSDE 280
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
9-293 2.04e-33

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 123.92  E-value: 2.04e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514   9 QTFHEYFKEWVDLYKVGAIRSITLQKYyvtEQKIQELVP-----DLKIKDLDRYTYQQLLNSYAVTHEKQTTM-DFHHHL 82
Cdd:COG4973    2 LTLAEALEAYLEHLRERRLSPKTLEAY---RRDLRRLIPllgdaDLPLEELTPADVRRFLARLHRRGLSPRTLnRRLSAL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  83 KGAILDAVDEGVISQNPTRKIvikgKTPRPKKA--KFLNQFEVQALLkELNLKEDINWDW--FILLIIKTGLRFSEALAL 158
Cdd:COG4973   79 RSFFNWAVREGLLEANPAAGV----KAPKAPRKlpRALTVDELAQLL-DALADDPLAVRDraIVELLYSTGLRLGELVGL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 159 TPSDFDFSKQKIiinktwdykMVTGsfqptKNESSnRKIQIDWQLAMQFSQLIKMKD-----PDKPIFVKS---RVFNST 230
Cdd:COG4973  154 DWEDVDLDAGEV---------RVRG-----KTGKS-RTVPLGPKALAALREWLAVRPelaapDEGALFPSRrgtRLSPRN 218

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499299514 231 INNRLKVLCENANIPT-ITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHI-IQEL 293
Cdd:COG4973  219 VQKRLRRLAKKAGLPKhVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQ-IYTHLdFQHL 282
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 115-288 1.23e-24

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: 97.40  E-value: 1.23e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 115 AKFLNQFEVQALLKELNLKEDINWDWFILLIIKTGLRFSEALALTPSDFDFSKQKIiinktwdykmvtgSFQPTKNESSn 194
Cdd:cd00796    2 DRFLTEDEEARLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLI-------------VLPETKNGKP- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 195 RKIQIDWQlAMQFSQLIKMKDPDKPIFVKSRVFN---STINNRLKVLCENANIPTITVHSLRHTHASLLLFAGVSIASVA 271
Cdd:cd00796   68 RTVPLSDE-AIAILKELKRKRGKDGFFVDGRFFGipiASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVA 146

                        170
                 ....*....|....*..
gi 499299514 272 NRLGHSSMTTTQeTYLH 288
Cdd:cd00796  147 KILGHSSIKMTM-RYAH 162
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 122-283 9.83e-23

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: 92.54  E-value: 9.83e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 122 EVQALLKELNLKEDINW-DWFILLII-KTGLRFSEALALTPSDFDFSKQKIIINKTWDYKmvtgsfqptkneSSNRKIQI 199
Cdd:cd00397    1 ELEKLLDAIDEDKKIDLrDRAILLLLlETGLRISELLALKVKDIDLDNGTIRVRGKKTKG------------GKERTVPL 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 200 DWQLAMQFSQLIKM---------KDPDKPIFVKSRVFNSTINNRLKVLCENANIPT---ITVHSLRHTHASLLLFAGVSI 267
Cdd:cd00397   69 PKELAEELKEYLKErrdkrgpllKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAgrkITPHSLRHTFATNLLENGVDI 148

                        170
                 ....*....|....*.
gi 499299514 268 ASVANRLGHSSMTTTQ 283
Cdd:cd00397  149 KVVQKLLGHSSISTTQ 164
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 2-288 4.36e-22

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 95.11  E-value: 4.36e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514   2 KARKRKEQTFHEYFKEWVDLYKVGaIRSITLQKYYVT-EQKIQELVPDLKIKDLDRYTYQQLLNSYavthEKQTTMDFHH 80
Cdd:COG0582   90 AAAAAAANTFEEVAEEWLEEKKPE-WKEKTAAQVRRTlEKHIFPVLGDRPIAEITPPDLLAVLRPI----EARGAPETAR 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  81 HLKG---AILD-AVDEGVISQNPTRKIVIKGKTPRPKKAKFLNQFEVQALLKELNlKEDINWD--WFILLIIKTGLRFSE 154
Cdd:COG0582  165 RVRQrlrQVFRyAVARGLIERNPAADLKGALPKPKVKHHPALTPEELPELLRALD-AYRGSPVtrLALRLLLLTGVRPGE 243

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 155 ALALTPSDFDFSKQKIIINKTwdyKMVTGSfqptknessNRKIQIDWQLAMQFSQLIKMKDPDKPIFVKSRVFNSTI-NN 233
Cdd:COG0582  244 LRGARWSEIDLEAALWTIPAE---RMKTRR---------PHIVPLSRQALEILKELKPLTGDSEYVFPSRRGPKKPMsEN 311

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 499299514 234 RLKVLCENANIPTITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQETYLH 288
Cdd:COG0582  312 TLNKALRRMGYGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNR 366
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 117-289 4.47e-16

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: 74.28  E-value: 4.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  117 FLNQFEVQALLKELNLKEDINWDW-FILLIIKTGLRFSEALALTPSDFDFSKQKIIInktwdykmvtgsfQPTKNessNR 195
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKaLLELLYATGLRISELCSLRWSDIDFENGVIRV-------------HRGKG---NK 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  196 KIQIdwQLAMQFSQLIKM--------KDPDKPIFVK---SRVFNSTINNRLKVLCENANI-PTITVHSLRHTHASLLLFA 263
Cdd:pfam00589  65 ERTV--PLSDAALELLKEwlskrlleAPKSDYLFASkrgKPLSRQTVRKIFKRAGKEAGLeLPLHPHMLRHSFATHLLEA 142

                         170       180
                  ....*....|....*....|....*.
gi 499299514  264 GVSIASVANRLGHSSMTTTQeTYLHI 289
Cdd:pfam00589 143 GVDLRVVQKLLGHSSISTTQ-IYTHV 167
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 122-292 7.08e-15

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: 71.29  E-value: 7.08e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 122 EVQALLKELNLKEDinwDWFILLIIKTGLRFSEALALTPSDFDFSKQKIIINKTWDykmvtGSFQPTKNESSNRKIQIDW 201
Cdd:cd01186    6 EVQELINACNNLRD---KFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPRED-----NTNEARAKSMRERRIPVSQ 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 202 QLAMQFSQLIKMKDPDKPIF-------VKSRVFN-----STINNRLKVLCENANIpTITVHSLRHTHASLLLFAGVSIAS 269
Cdd:cd01186   78 DLIDLYADYLTYIYCEEAEFsitvfvnVKGGNQGkamnySDVYDLVRRLKKRTGI-DFTPHMFRHTHATALIRAGWSIEV 156

                        170       180
                 ....*....|....*....|...
gi 499299514 270 VANRLGHSSMTTTQETYLHIIQE 292
Cdd:cd01186  157 VARRLGHAHVQTTLNTYGHLSEE 179
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 139-290 2.71e-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: 69.22  E-value: 2.71e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 139 DWFILLIIkTGLRFSEALALTPSDFDFSKQKIIInktwdykmvtgSFQPTKNESsnrKIQIDW-QLAMQFSQLIKMKDPD 217
Cdd:cd01185   22 DMFLFSCY-TGLRFSDLKNLTWKNIVEASGRTWI-----------RYRRKKTGK---PVTVPLlPVAREILEKYKDDRSE 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499299514 218 KPIF-VKSrvfNSTINNRLKVLCENANI-PTITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQEtYLHII 290
Cdd:cd01185   87 GKLFpVLS---NQKINRYLKEIAKIAGIdKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQI-YAKIV 157
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 89-295 6.14e-14

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: 70.71  E-value: 6.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514   89 AVDEGVISQNPTRKIvikgKTPRPKKA--KFLNQFEVQALLKelnLKEDINWDWFIL-------LIIKTGLRFSEALALT 159
Cdd:TIGR02224  80 LLRRGLIDANPAAGV----RAPKQPKKlpKFLSEDEMEALLD---APEEDDEDWLALrdraileLLYSSGLRVSELVGLD 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  160 PSDFDFSKQKIIinktwdykmVTGsfqptKNeSSNRKIQI---------DWQLAMQFSQLikMKDPDKPIFVKS---RVF 227
Cdd:TIGR02224 153 LSDLDLDFGEVR---------VRG-----KG-NKERIVPFgpyardalqAYLEARRSPLL--ASEGQDALFLNRrggRLT 215

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  228 NSTINNRLKVLCENANIPT-ITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHI-IQELEN 295
Cdd:TIGR02224 216 PRGVQYRLQQLRAKAGLPKhVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQ-IYTHVdFQHLAK 284
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 89-289 6.29e-14

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 70.57  E-value: 6.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  89 AVDEGVISQNPTRKIvikgKTPRPKKA--KFLNQFEVQALLKELNLKedinwDWF-------ILLIIKTGLRFSEALALT 159
Cdd:PRK00236  89 LVRRGLLKANPAAGL----RAPKIPKRlpKPLDVDQAKRLLDAIDED-----DPLalrdraiLELLYGSGLRLSELVGLD 159

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 160 PSDFDFSKQKIII----NKTwdykmvtgsfqptknessnRKIQI---------DWqLAMqfsqLIKMKDPDKPIFVKS-- 224
Cdd:PRK00236 160 IDDLDLASGTLRVlgkgNKE-------------------RTVPLgraarealeAY-LAL----RPLFLPDDDALFLGArg 215

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499299514 225 -RVFNSTINNRLKVLCENANIP-TITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHI 289
Cdd:PRK00236 216 gRLSPRVVQRRVKKLGKKAGLPsHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQ-IYTHV 281
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 116-289 1.60e-12

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: 64.60  E-value: 1.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 116 KFLNQFEVQALLKEL-NLKEDInwdwFILLIIKTGLRFSEALALTPSDFDFSKQKIII-----NKtwdYKMVTGSfqptk 189
Cdd:cd01193    4 VVLSPDEVRRILGALtELRHRL----ILSLLYGAGLRISELLRLRVKDIDFERGVIRVrqgkgGK---DRVVPLP----- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 190 nESSNRKIQIDWQLA----MQFSQLIKMKDPDKPIFVKSRV--FNSTINNRLKVLCENANI-PTITVHSLRHTHASLLLF 262
Cdd:cd01193   72 -EKLLEPLRRYLKSArpkeELDPAEGRAGVLDPRTGVERRHhiSETTVQRALKKAVEQAGItKRVTPHTLRHSFATHLLE 150

                        170       180
                 ....*....|....*....|....*..
gi 499299514 263 AGVSIASVANRLGHSSMTTTQeTYLHI 289
Cdd:cd01193  151 AGTDIRTIQELLGHSDLSTTM-IYTHV 176
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 148-289 1.26e-10

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: 59.06  E-value: 1.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 148 TGLRFSEALALTPSDFDFSKQKIiinktwdykMVTGsfqptKNeSSNRKIQIDwQLAMQ--------FSQLIKMKDPDKP 219
Cdd:cd00798   31 SGLRVSELVGLDLSDVDLDEGLV---------RVTG-----KG-NKERLVPFG-SYAVEaleeyleeRRPLLLKKKPPDA 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499299514 220 IFV---KSRVFNSTINNRLKVLCENANIP-TITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHI 289
Cdd:cd00798   95 LFLnkrGKRLSRRGVWRILKKYAERAGLPkHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQ-IYTHV 167
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 142-289 2.64e-10

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: 58.41  E-value: 2.64e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 142 ILLIIKTGLRFSEALALTPSDFDFSKQKIIINKtwdYKmvTGSFQ--PTKNESSNRkiQIDWqlamqfsqlIKMKDP--- 216
Cdd:cd01188   26 LLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQ---KK--TGRPVelPLTEPVGEA--LADY---------LRDGRPrtd 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 217 DKPIFVKSR------VFNSTINNRLKVLCENANIPTITV--HSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLH 288
Cdd:cd01188   90 SREVFLRARapyrplSSTSQISSIVRRYLRKAGIEPSHRgtHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTA-IYAK 168


                 .
gi 499299514 289 I 289
Cdd:cd01188  169 I 169
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 78-292 3.30e-10

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: 59.90  E-value: 3.30e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514   78 FHHHLkgaildaVDEGVISQNPTRKIvikgKTPRPKKA--KFLNQFEVQALL------KELNLKedinwDWFILLII-KT 148
Cdd:TIGR02225  74 FYRFL-------LREGIREDDPSALI----EPPKVARKlpKVLTVEEVEALLaapdvdTPLGLR-----DRAMLELLyAT 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  149 GLRFSEALALTPSDFDFSKQKIII----NKTwdyKMVtgsfqPTkNESSNRKIQIdWQLAMQFSQLIKMKDPDKPIFVK- 223
Cdd:TIGR02225 138 GLRVSELVGLRLEDVNLDEGFVRVrgkgNKE---RLV-----PL-GEEAIEALER-YLKEARPLLLKKKVKESDALFLNr 207

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499299514  224 -----SRVfnsTINNRLKVLCENANI-PTITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHIIQE 292
Cdd:TIGR02225 208 rggplSRQ---GVWKILKEYAKRAGIeKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQ-IYTHVARE 278
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 104-291 2.86e-09

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


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 57.02  E-value: 2.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  104 VIKGKTPRpKKAKFLNQFEVQALLKELNLKEDInwdwFILLIIKTGLRFSEALALTPSDFDFSKQKIIInktWDYK---- 179
Cdd:TIGR02249  89 FVRAKRPR-KLPVVLTREEVRRLLEHLEGKYRL----IAKLLYGSGMRLMECLRLRIQDIDFDYGEIRI---RQGKggkd 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  180 -MVT-----------------------------GSFQPT--KNESSNRKIQIDWQLAmqFSQLIKMKDPDKPIFVKSRVF 227
Cdd:TIGR02249 161 rTVTlpkelipplreqielarayheadlaegygGVYLPHalARKYPNAPKEWGWQYL--FPSHRLSRDPESGVIRRHHIN 238

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499299514  228 NSTINNRLKVLCENANIP-TITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHIIQ 291
Cdd:TIGR02249 239 ETTIQRAVRRAVERAGIEkPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQ-IYTHVLN 302
PRK15417 PRK15417
integron integrase;
141-291 3.07e-09

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 57.36  E-value: 3.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 141 FILLIIKTGLRFSEALALTPSDFDFSKQKIIINKTWDYK----MVTGSFQPTKNESSNR------KIQID---------- 200
Cdd:PRK15417 136 FAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKdralMLPESLAPSLREQLSRarawwlKDQAEgrsgvalpda 215

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 201 -----------WQLAMQFSQLIKMKDPDKPIFVKSRVFNSTINNRLKVLCENANIPT-ITVHSLRHTHASLLLFAGVSIA 268
Cdd:PRK15417 216 lerkypraghsWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGITKpATPHTLRHSFATALLRSGYDIR 295

                        170       180
                 ....*....|....*....|...
gi 499299514 269 SVANRLGHSSMTTTQeTYLHIIQ 291
Cdd:PRK15417 296 TVQDLLGHSDVSTTM-IYTHVLK 317
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 122-283 3.68e-09

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: 55.36  E-value: 3.68e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 122 EVQALLKELNLKEDINW-DWFILLII-KTGLRFSEALALTPSDFDFSKQKIIInktwdykmVTGsfqptKNESSnRKIQI 199
Cdd:cd01182    5 EMKALLAAPDRNTSLGRrDHALLLLLyDTGARVQELADLTIRDLRLDDPATVR--------LHG-----KGRKE-RTVPL 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 200 DWQLAMQFSQLIKMKDPDKPIFVKSRVFNSTINNRL-----KVLCEN------ANIPT----ITVHSLRHTHASLLLFAG 264
Cdd:cd01182   71 WKETVAALKAYLQEFHLTPDPKQLFPLFPNRRGQPLtrdgvAYILNKyvalasNRCPSlpkrITPHTLRHTKAMHLLQAG 150

                        170
                 ....*....|....*....
gi 499299514 265 VSIASVANRLGHSSMTTTQ 283
Cdd:cd01182  151 VDLTVIRDWLGHESVETTQ 169
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 142-292 2.00e-07

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 51.84  E-value: 2.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 142 ILLIIKTGLRFSEALALTPSDFDFSKQKI-IINKtwdykmvtGSFQPTKNESSNRKIQIDWQLAMQfSQLIKMKDPDKPI 220
Cdd:PRK05084 201 IALILGSGLRVSELVNLDLSDLNLKQMTIdVTRK--------GGKRDSVNIAPFALPYLEEYLKIR-ASRYKAEKQEKAL 271

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499299514 221 FVK------SRVFNSTINNRLKVLCENANIPtITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTqETYLHIIQE 292
Cdd:PRK05084 272 FLTkyrgkpNRISARAIEKMVAKYSEAFGVR-LTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETT-DLYTHIVND 347
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 215-288 4.08e-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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 49.29  E-value: 4.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 215 DPDKPIFVK-------SRVFNSTINNRLKVLCENANIPT--ITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTqET 285
Cdd:cd01194   93 DFEEPLFTSlsnnskgQRLTTRSIRRIIKKYLRKAGLDDdrLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTT-MI 171


                 ...
gi 499299514 286 YLH 288
Cdd:cd01194  172 YAH 174
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 122-288 6.12e-07

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: 48.84  E-value: 6.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 122 EVQALLK-ELNLKEDIN--WDWFILLI-IKTGLRFSEALALTPSDFdfskqkIIINKTWDYKMV-TGSFQPTKNESSNRK 196
Cdd:cd01184    5 ELAKIFSsPLYTGCKKKdpALYWLPLIgLYTGARLNEICQLRVDDI------KEEDGIWCIDINdDAEGRRLKTKASRRL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 197 IQIDwqlamqfSQLIKM----------KDPDKPIFVK------------SRVFNSTINNRLKVLCENaniptITVHSLRH 254
Cdd:cd01184   79 VPIH-------PRLIELgfldyvealrADGKLFLFPEkrdkdgkyskaaSKWFNRLLRKLGIKDDER-----KSFHSFRH 146

                        170       180       190
                 ....*....|....*....|....*....|....
gi 499299514 255 THASLLLFAGVSIASVANRLGHSSMTTTQETYLH 288
Cdd:cd01184  147 TFITALKRAGVPEELIAQIVGHSRGGVTHDTYGK 180
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 113-282 1.57e-05

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: 44.81  E-value: 1.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 113 KKAKFLNQFEVQALLKELNLKEDINWDW-FILLIIKTGLRFSEALALTPSDFDFSKQKIIINKtwdYKMVTGSFQPTKNE 191
Cdd:cd01197    2 KQRKYLTGKEVQALLQAACRGRTPARDYcLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRR---LKNGFSTTHPLRFD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 192 SsnRKIQIDWqlaMQFSQLIKMKDPDKpIFV---KSRVFNSTINNRLKVLCENANIPTIT-VHSLRHTHASLLLFAGVSI 267
Cdd:cd01197   79 E--REALEAW---LKERANWKGADTDW-IFLsrrGGPLSRQQAYRIIRDLGKEAGTVTQThPHMLRHACGYALADRGADT 152

                        170
                 ....*....|....*
gi 499299514 268 ASVANRLGHSSMTTT 282
Cdd:cd01197  153 RLIQDYLGHRNIRHT 167
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 122-288 2.36e-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: 41.10  E-value: 2.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 122 EVQALLKELNlkeDINWD----WFILLIIKTGLRFSEALALTPSDFDFSKQKIIInktwdykmvtgsfqP---TKNESSN 194
Cdd:cd00801    4 ELPELWRALD---TANLSpptkLALRLLLLTGQRIGELARARWSEIDLEEKTWTI--------------PaerTKNKRPH 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 195 RkIQIDWQLAMQFSQLIKMKDPDKPIFVKSRVFN-----STINNRLKVLCENAniPTITVHSLRHTHASLLLFAGVSiAS 269
Cdd:cd00801   67 R-VPLSDQALEILEELKEFTGDSGYLFPSRRKKKkpiseNTINKALKRLGYKG--KEFTPHDLRRTFSTLLNELGID-PE 142

                        170       180
                 ....*....|....*....|
gi 499299514 270 VANR-LGHSSMTTTQETYLH 288
Cdd:cd00801  143 VIERlLNHVLGGVVRAAYNR 162
xerD PRK00283
tyrosine recombinase;
78-289 2.75e-04

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 41.72  E-value: 2.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514  78 FHHHLkgaildaVDEGVISQNPTRKIvikgKTPRPKKA--KFLNQFEVQALLK--ELNLKEDINwDWFIL-LIIKTGLRF 152
Cdd:PRK00283  83 FFQFL-------LREGLREDDPSALL----DSPKLPRRlpKTLSEAQVEALLDapDIDTPLGLR-DRAMLeLLYATGLRV 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 153 SEALALTPSDFDFSKQKIII----NKTwdyKMVtgsfqPTkneSSNRKIQIDWQLAMQFSQLIKmKDPDKPIFVKSR--- 225
Cdd:PRK00283 151 SELVGLTLDDVSLRQGVVRVtgkgNKE---RLV-----PL---GEEAVYAIERYLERGRPALLN-GRSSDALFPSARggq 218

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 226 ----VFNstinNRLKVLCENANIPT--ITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQeTYLHI 289
Cdd:PRK00283 219 ltrqTFW----HRIKHYAKRAGIDPkkLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQ-IYTHV 283
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 130-292 5.40e-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: 39.97  E-value: 5.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 130 LNLKEDINWDWFILLI-IKTGLRFSEALALTPSDFDF-SKQKIIINKTWDYKMVtgsfqPTKNESSNRKIQIDWQLAMQF 207
Cdd:cd01192   17 LYLKKANPRNYLLFIVgINTGLRISDLLSLKVEDVTNkDKLSIKEQKTGKQKTF-----PLNPTLVKALKEYIDDLDLKR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 208 SQLIKMKDPDKPIFVKSRVFNSTINNRLKVLCENANipTITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQEtYL 287
Cdd:cd01192   92 NDYLFKSLKQGPEKPISRKQAYKILKKAADDLGLNY--NIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLR-YL 168


                 ....*
gi 499299514 288 HIIQE 292
Cdd:cd01192  169 GIDQE 173
INT_StrepXerD_C_like cd01190
Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; ...
 142-286 3.82e-03

Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; This family includes a putative XerD recombinase in Streptococcus pneumonia and similar tyrosine recombinases. However, the members of this family contain unusual active site motifs from the XerD from Escherichia coli. E. coli XerD and homologous enzymes show four conserved amino acids R-H-R-H that are spaced along the C-terminal domain. The putative S. pneumoniae XerD contains three unique replacements at the conserved positions resulting in L-Q-R-L. Severe growth defects in a loss-of-function xerD mutant demonstrate an important in vivo function of the S. pneumoniae XerD protein. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271190  Cd Length: 150  Bit Score: 37.33  E-value: 3.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 142 ILLIIKTGLRFSEALALTPSDFDfskqkiiinktWDYKMVTgsfqpTKNESSNRKIQIDWQLAMQFSQLIKMKDP--DKP 219
Cdd:cd01190   23 ALLILELGLTPSEIANLKWADFD-----------LDFQVLT-----IEKGGIKRVLPLPKKLLPFLEQHIKADYLefDHE 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499299514 220 IFVKSRVFnstINNRLKVLCENANIPTITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTTQETY 286
Cdd:cd01190   87 GKAYSRQW---LFNQLKKFLNSIGLSGLTAQKLREQYILKQKEAGKSIYELAKLLGLKSPVTLEKYY 150
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 142-282 4.33e-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: 37.02  E-value: 4.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499299514 142 ILLIIKTGLRFSEALAL--------TPSDFDFSKQKIIINKTWDYkmvtgsfqptknessnRKIQIDWQLAmqfsQLIKm 213
Cdd:cd01187   19 VQAAVFTGARASELATLkfgclhaqTSDDGTFLYWLKWENKGGKQ----------------LDIPISKKVA----ELIK- 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499299514 214 kdpdkpifvksrvfnsTINNRLKVLCENANIPT-------ITVHSLRHTHASLLLFAGVSIASVANRLGHSSMTTT 282
Cdd:cd01187   78 ----------------TINWTLNELSELKNISDdhgerfrFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMT 137
 
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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