NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446728918|ref|WP_000806231|]
View 

MULTISPECIES: tyrosine-type recombinase/integrase [Bacillus]

Protein Classification

site-specific integrase( domain architecture ID 332)

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

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 6-175 8.76e-43

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


The actual alignment was detected with superfamily member cd01192:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 178  Bit Score: 140.51  E-value: 8.76e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918   6 QPIQNEKQLETIKNILLQSSKRDGLLFVLAVNSGLKVSEILQLKVSDV-IDEHENVRHSilfyneKVKKHKWFAVNEDLQ 84
Cdd:cd01192    4 EPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVtNKDKLSIKEQ------KTGKQKTFPLNPTLV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  85 HAIEDYMKERKTwKRNEPLLKS--QKGTKSITRQHAWYILNKAAKEVGLEG-ISSHTLRKTWGYCAYKSGVDIAFLQHFF 161
Cdd:cd01192   78 KALKEYIDDLDL-KRNDYLFKSlkQGPEKPISRKQAYKILKKAADDLGLNYnIGTHSLRKTFGYHVYKQGKDIELLMKLL 156

                        170
                 ....*....|....
gi 446728918 162 DHSTPSKTLKYIGI 175
Cdd:cd01192  157 NHSSPSITLRYLGI 170
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 6-175 8.76e-43

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: 140.51  E-value: 8.76e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918   6 QPIQNEKQLETIKNILLQSSKRDGLLFVLAVNSGLKVSEILQLKVSDV-IDEHENVRHSilfyneKVKKHKWFAVNEDLQ 84
Cdd:cd01192    4 EPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVtNKDKLSIKEQ------KTGKQKTFPLNPTLV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  85 HAIEDYMKERKTwKRNEPLLKS--QKGTKSITRQHAWYILNKAAKEVGLEG-ISSHTLRKTWGYCAYKSGVDIAFLQHFF 161
Cdd:cd01192   78 KALKEYIDDLDL-KRNDYLFKSlkQGPEKPISRKQAYKILKKAADDLGLNYnIGTHSLRKTFGYHVYKQGKDIELLMKLL 156

                        170
                 ....*....|....
gi 446728918 162 DHSTPSKTLKYIGI 175
Cdd:cd01192  157 NHSSPSITLRYLGI 170
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
27-172 4.35e-23

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 92.75  E-value: 4.35e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  27 RDGLLFVLAVNSGLKVSEILQLKVSDVIDEhenvRHSILFYNEKVKKHKWFAVNEDLQHAIEDYMKERKTwKRNEPLLKS 106
Cdd:COG4974  134 RDRALLLLLYATGLRVSELLGLKWSDIDLD----RGTIRVRRGKGGKERTVPLSPEALEALREYLEERRP-RDSDYLFPT 208

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446728918 107 QKGTKsITRQHAWYILNKAAKEVGLE-GISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTPSKTLKY 172
Cdd:COG4974  209 RRGRP-LSRRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIY 274
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 11-173 2.07e-20

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 82.75  E-value: 2.07e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918   11 EKQLETIKNIL--LQSSKRDGLLFVLAVNSGLKVSEILQLKVSDVideheNVRHSILFYNE-KVKKHKWFAVNEDLQHAI 87
Cdd:pfam00589   4 EDEVERLLDAAetGPLSIRDKALLELLYATGLRISELCSLRWSDI-----DFENGVIRVHRgKGNKERTVPLSDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918   88 EDYMKER-KTWKRNEPLLKSQKGtKSITRQHAWYILNKAAKEVGLEG-ISSHTLRKTWGYCAYKSGVDIAFLQHFFDHST 165
Cdd:pfam00589  79 KEWLSKRlLEAPKSDYLFASKRG-KPLSRQTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSS 157


                  ....*...
gi 446728918  166 PSKTLKYI 173
Cdd:pfam00589 158 ISTTQIYT 165
PRK09871 PRK09871
tyrosine recombinase; Provisional
 23-172 6.22e-12

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 61.15  E-value: 6.22e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  23 QSSKRDGLLFVLAVNSGLKVSEILQLKVSDvIDEHE---NVR---------HSILFynekvkkhkwfavneDLQHAIEDY 90
Cdd:PRK09871  23 ATGARDYCLILLAYRHGMRISELLDLHYQD-LDLNEgriNIRrlkngfstvHPLRF---------------DEREAVERW 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  91 MKERKTWK---RNEPLLKSQKGTKsITRQHAWYILNKAAKEVG-LEGISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTP 166
Cdd:PRK09871  87 TQERANWKgadRTDAIFISRRGSR-LSRQQAYRIIRDAGIEAGtVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNI 165


                 ....*.
gi 446728918 167 SKTLKY 172
Cdd:PRK09871 166 RHTVRY 171
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 6-175 8.76e-43

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: 140.51  E-value: 8.76e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918   6 QPIQNEKQLETIKNILLQSSKRDGLLFVLAVNSGLKVSEILQLKVSDV-IDEHENVRHSilfyneKVKKHKWFAVNEDLQ 84
Cdd:cd01192    4 EPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVtNKDKLSIKEQ------KTGKQKTFPLNPTLV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  85 HAIEDYMKERKTwKRNEPLLKS--QKGTKSITRQHAWYILNKAAKEVGLEG-ISSHTLRKTWGYCAYKSGVDIAFLQHFF 161
Cdd:cd01192   78 KALKEYIDDLDL-KRNDYLFKSlkQGPEKPISRKQAYKILKKAADDLGLNYnIGTHSLRKTFGYHVYKQGKDIELLMKLL 156

                        170
                 ....*....|....
gi 446728918 162 DHSTPSKTLKYIGI 175
Cdd:cd01192  157 NHSSPSITLRYLGI 170
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 11-173 5.50e-24

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: 92.16  E-value: 5.50e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  11 EKQLETIKNILLQSsKRDGLLFVLAVNSGLKVSEILQLKVSDvIDEHENVrhsILFYNEKVKKHK--WFAVNEDLQHAIE 88
Cdd:cd00397    3 EKLLDAIDEDKKID-LRDRAILLLLLETGLRISELLALKVKD-IDLDNGT---IRVRGKKTKGGKerTVPLPKELAEELK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  89 DYMKERKTWKR------NEPLLKSQKGTKSITRQHAWYILNKAAKEVGlEGISSHTLRKTWGYCAYKSGVDIAFLQHFFD 162
Cdd:cd00397   78 EYLKERRDKRGpllkslYLNKLFGTKLGERLSRRTLRRIFKKAGIEAG-RKITPHSLRHTFATNLLENGVDIKVVQKLLG 156

                        170
                 ....*....|.
gi 446728918 163 HSTPSKTLKYI 173
Cdd:cd00397  157 HSSISTTQRYL 167
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
27-172 4.35e-23

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 92.75  E-value: 4.35e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  27 RDGLLFVLAVNSGLKVSEILQLKVSDVIDEhenvRHSILFYNEKVKKHKWFAVNEDLQHAIEDYMKERKTwKRNEPLLKS 106
Cdd:COG4974  134 RDRALLLLLYATGLRVSELLGLKWSDIDLD----RGTIRVRRGKGGKERTVPLSPEALEALREYLEERRP-RDSDYLFPT 208

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446728918 107 QKGTKsITRQHAWYILNKAAKEVGLE-GISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTPSKTLKY 172
Cdd:COG4974  209 RRGRP-LSRRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIY 274
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 11-173 2.07e-20

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 82.75  E-value: 2.07e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918   11 EKQLETIKNIL--LQSSKRDGLLFVLAVNSGLKVSEILQLKVSDVideheNVRHSILFYNE-KVKKHKWFAVNEDLQHAI 87
Cdd:pfam00589   4 EDEVERLLDAAetGPLSIRDKALLELLYATGLRISELCSLRWSDI-----DFENGVIRVHRgKGNKERTVPLSDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918   88 EDYMKER-KTWKRNEPLLKSQKGtKSITRQHAWYILNKAAKEVGLEG-ISSHTLRKTWGYCAYKSGVDIAFLQHFFDHST 165
Cdd:pfam00589  79 KEWLSKRlLEAPKSDYLFASKRG-KPLSRQTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSS 157


                  ....*...
gi 446728918  166 PSKTLKYI 173
Cdd:pfam00589 158 ISTTQIYT 165
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 9-172 4.45e-16

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: 71.64  E-value: 4.45e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918   9 QNEKQLETIKNILLQSSKRDGLLFVLAVNSGLKVSEILQLKVSDVIDEHENVrhsILFYNEKVKKHK--WFAVNEDLQHA 86
Cdd:cd01194    5 QARQLLASLPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGT---ILYVQGKGKTSKddFVYLRPDVLKA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  87 IEDYMKERKTWKRNEPL---LKSQKGTKSITRQHAWYILNKAAKEVGL--EGISSHTLRKTWGYCAYKSGVDIAFLQHFF 161
Cdd:cd01194   82 LQAYLKARGKLDFEEPLftsLSNNSKGQRLTTRSIRRIIKKYLRKAGLddDRLTAHSLRHTAGTLALKAGKSLREVQQLL 161

                        170
                 ....*....|.
gi 446728918 162 DHSTPSKTLKY 172
Cdd:cd01194  162 RHSDPNTTMIY 172
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
25-172 4.43e-14

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 68.06  E-value: 4.43e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  25 SKRDGLLFVLAVNSGLKVSEILQLKVSDVideheNVRHSILFYNEKVKKHKWFAVNEDLQHAIEDYMKERKTWKR--NEP 102
Cdd:COG4973  130 AVRDRAIVELLYSTGLRLGELVGLDWEDV-----DLDAGEVRVRGKTGKSRTVPLGPKALAALREWLAVRPELAApdEGA 204

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446728918 103 LLKSQKGTkSITRQHAWYILNKAAKEVGLEG-ISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTPSKTLKY 172
Cdd:COG4973  205 LFPSRRGT-RLSPRNVQKRLRRLAKKAGLPKhVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIY 274
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 17-172 5.47e-14

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 65.81  E-value: 5.47e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  17 IKNILLQSSKRDGLLFVLAVNSGLKVSEILQLKVSDVIDEHenvrHSILFYNEKVKKHKWFAVNEDLQHAIEDYMKERKT 96
Cdd:cd00796   14 LAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEV----GLIVLPETKNGKPRTVPLSDEAIAILKELKRKRGK 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446728918  97 WKRNEPllKSQKGTKSITRQHAWyilNKAAKEVGLEGISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTPSKTLKY 172
Cdd:cd00796   90 DGFFVD--GRFFGIPIASLRRAF---KKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRY 160
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 13-173 3.14e-13

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: 64.22  E-value: 3.14e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  13 QLETIKNILLQ------SSKRDGLLFVLAVNSGLKVSEILQLKVSDVIDehENVRHSILFynEKVKKHK----WFAVNED 82
Cdd:cd01182    2 TREEMKALLAApdrntsLGRRDHALLLLLYDTGARVQELADLTIRDLRL--DDPATVRLH--GKGRKERtvplWKETVAA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  83 LQHaiedYMKER---KTWKRNEPLLKSQKGTKsITRQHAWYILNKAAKEV-----GLEG-ISSHTLRKTwgyCA---YKS 150
Cdd:cd01182   78 LKA----YLQEFhltPDPKQLFPLFPNRRGQP-LTRDGVAYILNKYVALAsnrcpSLPKrITPHTLRHT---KAmhlLQA 149

                        170       180
                 ....*....|....*....|...
gi 446728918 151 GVDIAFLQHFFDHSTPSKTLKYI 173
Cdd:cd01182  150 GVDLTVIRDWLGHESVETTQIYA 172
PRK09871 PRK09871
tyrosine recombinase; Provisional
 23-172 6.22e-12

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 61.15  E-value: 6.22e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  23 QSSKRDGLLFVLAVNSGLKVSEILQLKVSDvIDEHE---NVR---------HSILFynekvkkhkwfavneDLQHAIEDY 90
Cdd:PRK09871  23 ATGARDYCLILLAYRHGMRISELLDLHYQD-LDLNEgriNIRrlkngfstvHPLRF---------------DEREAVERW 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  91 MKERKTWK---RNEPLLKSQKGTKsITRQHAWYILNKAAKEVG-LEGISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTP 166
Cdd:PRK09871  87 TQERANWKgadRTDAIFISRRGSR-LSRQQAYRIIRDAGIEAGtVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNI 165


                 ....*.
gi 446728918 167 SKTLKY 172
Cdd:PRK09871 166 RHTVRY 171
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 27-140 7.26e-12

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: 60.22  E-value: 7.26e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  27 RDGLLFVLAVNSGLKVSEILQLKVSDVIDEHENVR-------HSILFYNEKVKKhkwfavnedlqhAIEDYMKERKTW-- 97
Cdd:cd00798   20 RDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRvtgkgnkERLVPFGSYAVE------------ALEEYLEERRPLll 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446728918  98 --KRNEPLLKSQKGTKsITRQHAWYILNKAAKEVGL-EGISSHTLR 140
Cdd:cd00798   88 kkKPPDALFLNKRGKR-LSRRGVWRILKKYAERAGLpKHVSPHTLR 132
xerD PRK00283
tyrosine recombinase;
38-140 9.55e-11

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 59.05  E-value: 9.55e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  38 SGLKVSEILQLKVSDVideheNVRHSILFYNEKVKKHKWFAVNEDLQHAIEDYMKERKTW---KRNEP-LLKSQKGTKsI 113
Cdd:PRK00283 146 TGLRVSELVGLTLDDV-----SLRQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGRPAllnGRSSDaLFPSARGGQ-L 219

                         90       100
                 ....*....|....*....|....*....
gi 446728918 114 TRQHAWYILNKAAKEVGL--EGISSHTLR 140
Cdd:PRK00283 220 TRQTFWHRIKHYAKRAGIdpKKLSPHVLR 248
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 13-176 2.83e-09

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: 53.40  E-value: 2.83e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  13 QLETIKNILLQSS---KRDGLLFVLAVNSGLKVSEILQLKVSDVidehENVRHSILFYNEKVKKHKWFAVNEDLQHAIED 89
Cdd:cd01188    4 EVRRLLAAIDRLTpvgLRDYAILLLLARLGLRAGDVAGLRLDDI----DWRSGTITVRQKKTGRPVELPLTEPVGEALAD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  90 YMKERKTwKRNEPL--LKSQKGTKSITRQHAWY-ILNKAAKEVGLEGI--SSHTLRKTWGYCAYKSGVDIAFLQHFFDHS 164
Cdd:cd01188   80 YLRDGRP-RTDSREvfLRARAPYRPLSSTSQISsIVRRYLRKAGIEPShrGTHSLRHSLATRMLRAGTSLKVIADLLGHR 158

                        170
                 ....*....|..
gi 446728918 165 TPSKTLKYIGIA 176
Cdd:cd01188  159 SIETTAIYAKID 170
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 11-172 4.86e-09

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: 52.18  E-value: 4.86e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  11 EKQLETIKNILLQSSKRDGLLFVLAVNSGLKVSEILQLKVSDVIDEHE--NVRHSIlfynEKVKKHKWfavnedlqhaie 88
Cdd:cd01189    1 PEELKKLLEALKKRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGtiRINRTL----VRKKKGGY------------ 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  89 dYMKERKT--WKRNEPLLKSqkgTKSITRQHAWYilNKAAKEVGLEGISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTP 166
Cdd:cd01189   65 -VIKPPKTksSIRTIPLPDE---LIELLKELKAF--KKLLKKAGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDI 138


                 ....*.
gi 446728918 167 SKTLKY 172
Cdd:cd01189  139 STTLDV 144
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 31-175 4.31e-08

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: 49.96  E-value: 4.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  31 LFVLAVNSGLKVSEILQLKVSDVIDEHENVRhsILFYNEKVKKHkwfaVNEDLQHAIEDYMKERKTWKRNEPLLKSqkgt 110
Cdd:cd01185   23 MFLFSCYTGLRFSDLKNLTWKNIVEASGRTW--IRYRRKKTGKP----VTVPLLPVAREILEKYKDDRSEGKLFPV---- 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446728918 111 ksITRQHAWYILNKAAKEVGLE-GISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTPSKTLKYIGI 175
Cdd:cd01185   93 --LSNQKINRYLKEIAKIAGIDkHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKI 156
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 27-172 7.17e-08

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: 49.58  E-value: 7.17e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  27 RDGLLFVLAVNSGLKVSEILQLKVSDvIDEHenvRHSILFYNEKVKKHKWFAVNEDLQHAIEDYMKERKTW------KRN 100
Cdd:cd01193   22 RHRLILSLLYGAGLRISELLRLRVKD-IDFE---RGVIRVRQGKGGKDRVVPLPEKLLEPLRRYLKSARPKeeldpaEGR 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446728918 101 EPLLKSQKGTKS---ITRQHAWYILNKAAKEVGLEG-ISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTPSKTLKY 172
Cdd:cd01193   98 AGVLDPRTGVERrhhISETTVQRALKKAVEQAGITKrVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIY 173
PRK09870 PRK09870
tyrosine recombinase; Provisional
 27-172 3.33e-07

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 48.01  E-value: 3.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  27 RDGLLFVLAVNSGLKVSEILQLKVSDvIDEHENVrhsilFYNEKVKKHkwFAVNEDLQ----HAIEDYMKERKTWKRNEP 102
Cdd:PRK09870  33 RNYCLTLLCFIHGFRASEICRLRISD-IDLKAKC-----IYIHRLKKG--FSTTHPLLnkeiQALKNWLSIRTSYPHAES 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446728918 103 --LLKSQKGTkSITRQHAWYILNKAAKEVGLE-GISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTPSKTLKY 172
Cdd:PRK09870 105 ewVFLSRKGN-PLSRQQFYHIISTSGGNAGLSlEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWY 176
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 12-173 4.91e-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: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 44.38  E-value: 4.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  12 KQLETIKNILLQSSKRDGLLFVLAVNSGLKVSEILQLKVSDVidEHENVRHSILfynEKVKKHKWFA-VNEDLQHAIEDY 90
Cdd:cd01195    6 RQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDL--EKEHRRLRIL---GKGKKQREVVtLPPTTREALAAW 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  91 MKERKtwKRNEPL---LKSQKGTKSITRQHAWYILNKAAKEVGL-EGISSHTLRKTWGYCAY-KSGVDIAFLQHFFDHST 165
Cdd:cd01195   81 LAARG--EAEGPLfvsLDRASRGRRLSPQAVYRIVRRLAERIGLgKRLSPHGLRHSAITLALdAGAGLIRKVQDFSRHAD 158


                 ....*...
gi 446728918 166 PSKTLKYI 173
Cdd:cd01195  159 LRTLQVYD 166
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 32-173 4.20e-04

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: 38.57  E-value: 4.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  32 FVLAVNSGLKVSEILQLKVSDVI-DEHENVRHSILFYNEKV--KKHKWfavnedlqhAIEDYMKER-KTWKRnepllksq 107
Cdd:cd01187   19 VQAAVFTGARASELATLKFGCLHaQTSDDGTFLYWLKWENKggKQLDI---------PISKKVAELiKTINW-------- 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446728918 108 kgtksiTRQHAWYILNKAAKEVGLEGISSHTLRKTWGYCAYKSGVDIAFLQHFFDHSTPSKTLKYI 173
Cdd:cd01187   82 ------TLNELSELKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYA 141
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 30-173 9.70e-04

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


Pssm-ID: 271178 [Multi-domain]  Cd Length: 198  Bit Score: 38.06  E-value: 9.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918  30 LLFVLAVNSGLKVSEILQLKVSDVidehENVRHSILFYNEKVKKHKWFAVNEDLQHAIEDYMKERK---TWKRNEPLLKS 106
Cdd:cd00797   29 TLFGLLYATGLRVGEALRLRLEDV----DLDSGILTIRQTKFGKSRLVPLHPSTVGALRDYLARRDrllPSPSSSYFFVS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446728918 107 QKGTKsITRQHAWYILNKAAKEVGLEGISS------HTLRKTWGYCA----YKSGVDIA----FLQHFFDHSTPSKTLKY 172
Cdd:cd00797  105 QQGGR-LTGGGVYRVFRRLLRRIGLRGAGDgrgprlHDLRHTFAVNRltrwYREGADVErklpVLSTYLGHVNVTDTYWY 183


                 .
gi 446728918 173 I 173
Cdd:cd00797  184 L 184
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH