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Conserved domains on  [gi|1961400067|gb|QQX32772|]
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integrase, partial [Helicobacter phage COL 44-PUJ]

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; ...
 22-116 2.47e-24

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: 91.47  E-value: 2.47e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  22 LEEVKTLIENAP--SLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITINKSL----NELGKITSPKNKPSIRAVDL 95
Cdd:cd01189     1 PEELKKLLEALKkrGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLvrkkKGGYVIKPPKTKSSIRTIPL 80

                          90       100
                  ....*....|....*....|.
gi 1961400067  96 LEPVEKILKELKESEPASKKF 116
Cdd:cd01189    81 PDELIELLKELKAFKKLLKKA 101
 
Name Accession Description Interval E-value
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 22-116 2.47e-24

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: 91.47  E-value: 2.47e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  22 LEEVKTLIENAP--SLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITINKSL----NELGKITSPKNKPSIRAVDL 95
Cdd:cd01189     1 PEELKKLLEALKkrGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLvrkkKGGYVIKPPKTKSSIRTIPL 80

                          90       100
                  ....*....|....*....|.
gi 1961400067  96 LEPVEKILKELKESEPASKKF 116
Cdd:cd01189    81 PDELIELLKELKAFKKLLKKA 101
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
1-144 2.17e-17

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 76.19  E-value: 2.17e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067   1 NPYYSITLKNAlEAKEIEPFNLEEVKTLIENAP-----SLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITINKSl 75
Cdd:COG4974    95 NPAAKVKLPKK-PRKLPRVLTEEEIEALLEALDtetpeGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRG- 172

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1961400067  76 nelgkitspKNKpSIRAVDLLEPVEKILKE-LKESEPASKKFVFIDM---PKRSSIFQRHFKNLLKALNLKDR 144
Cdd:COG4974   173 ---------KGG-KERTVPLSPEALEALREyLEERRPRDSDYLFPTRrgrPLSRRAIRKILKRLAKRAGIPKR 235
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 23-144 3.35e-12

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: 60.41  E-value: 3.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  23 EEVKTLIENAP----SLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITInkslnELGKitspKNKPsiRAVDLLEP 98
Cdd:pfam00589   5 DEVERLLDAAEtgplSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRV-----HRGK----GNKE--RTVPLSDA 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1961400067  99 VEKILKEL--KESEPASK-KFVFI---DMPKRSSIFQRHFKNLLKALNLKDR 144
Cdd:pfam00589  74 ALELLKEWlsKRLLEAPKsDYLFAskrGKPLSRQTVRKIFKRAGKEAGLELP 125
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 19-144 2.06e-04

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 39.75  E-value: 2.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  19 PFNLEEVKTLIENAPS-----LRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITInkslneLGKitspKNKpsIRAV 93
Cdd:PRK00236  115 PLDVDQAKRLLDAIDEddplaLRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRV------LGK----GNK--ERTV 182

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1961400067  94 DLLEPVEKILK---ELKESEPASKKFVFID-----MPKRSsiFQRHFKNLLKALNLKDR 144
Cdd:PRK00236  183 PLGRAAREALEaylALRPLFLPDDDALFLGarggrLSPRV--VQRRVKKLGKKAGLPSH 239
 
Name Accession Description Interval E-value
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 22-116 2.47e-24

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: 91.47  E-value: 2.47e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  22 LEEVKTLIENAP--SLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITINKSL----NELGKITSPKNKPSIRAVDL 95
Cdd:cd01189     1 PEELKKLLEALKkrGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLvrkkKGGYVIKPPKTKSSIRTIPL 80

                          90       100
                  ....*....|....*....|.
gi 1961400067  96 LEPVEKILKELKESEPASKKF 116
Cdd:cd01189    81 PDELIELLKELKAFKKLLKKA 101
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
1-144 2.17e-17

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 76.19  E-value: 2.17e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067   1 NPYYSITLKNAlEAKEIEPFNLEEVKTLIENAP-----SLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITINKSl 75
Cdd:COG4974    95 NPAAKVKLPKK-PRKLPRVLTEEEIEALLEALDtetpeGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRG- 172

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1961400067  76 nelgkitspKNKpSIRAVDLLEPVEKILKE-LKESEPASKKFVFIDM---PKRSSIFQRHFKNLLKALNLKDR 144
Cdd:COG4974   173 ---------KGG-KERTVPLSPEALEALREyLEERRPRDSDYLFPTRrgrPLSRRAIRKILKRLAKRAGIPKR 235
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 20-147 4.04e-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: 65.43  E-value: 4.04e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  20 FNLEEVKTLIENAPSL---RLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITInkslnelgKITspKNKPSiRAVDLL 96
Cdd:cd00796     5 LTEDEEARLLAALEEStnpHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVL--------PET--KNGKP-RTVPLS 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1961400067  97 EPVEKILKELKESEPASKKFVFIDMPKRSSI-FQRHFKNLLKALNLKDRKLY 147
Cdd:cd00796    74 DEAIAILKELKRKRGKDGFFVDGRFFGIPIAsLRRAFKKARKRAGLEDLRFH 125
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
15-144 2.45e-13

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 64.98  E-value: 2.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  15 KEIEPFNLEEVKTLIENAP----SLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITINkslnelgkitsPKNKpSI 90
Cdd:COG4973   107 KLPRALTVDELAQLLDALAddplAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVR-----------GKTG-KS 174

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1961400067  91 RAVDLLEPVEKILKELKESEPASK----KFVFIDM---PKRSSIFQRHFKNLLKALNLKDR 144
Cdd:COG4973   175 RTVPLGPKALAALREWLAVRPELAapdeGALFPSRrgtRLSPRNVQKRLRRLAKKAGLPKH 235
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 23-144 3.35e-12

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: 60.41  E-value: 3.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  23 EEVKTLIENAP----SLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITInkslnELGKitspKNKPsiRAVDLLEP 98
Cdd:pfam00589   5 DEVERLLDAAEtgplSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRV-----HRGK----GNKE--RTVPLSDA 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1961400067  99 VEKILKEL--KESEPASK-KFVFI---DMPKRSSIFQRHFKNLLKALNLKDR 144
Cdd:pfam00589  74 ALELLKEWlsKRLLEAPKsDYLFAskrGKPLSRQTVRKIFKRAGKEAGLELP 125
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 11-118 2.18e-10

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 57.36  E-value: 2.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  11 ALEAKEIEPFnleeVKTLIENAPSLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITINKslnelgkiTSPKNKpSI 90
Cdd:COG0582   205 ALTPEELPEL----LRALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPA--------ERMKTR-RP 271

                          90       100
                  ....*....|....*....|....*...
gi 1961400067  91 RAVDLLEPVEKILKELKESEPASkKFVF 118
Cdd:COG0582   272 HIVPLSRQALEILKELKPLTGDS-EYVF 298
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 22-139 7.27e-10

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: 54.58  E-value: 7.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  22 LEEVKTLIENAPSLRL----KAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITINKSLNelgkitspKNKPSIRaVDLLE 97
Cdd:cd00801     2 PDELPELWRALDTANLspptKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERT--------KNKRPHR-VPLSD 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1961400067  98 PVEKILKELKESEPASkKFVFIdmPKRSSIFQRHFKNLLKAL 139
Cdd:cd00801    73 QALEILEELKEFTGDS-GYLFP--SRRKKKKPISENTINKAL 111
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 24-145 2.17e-09

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: 52.87  E-value: 2.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  24 EVKTLIENA-----PSLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITINKslnelGKITSPKNkpsiRAV----D 94
Cdd:cd00397     1 ELEKLLDAIdedkkIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRG-----KKTKGGKE----RTVplpkE 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1961400067  95 LLEPVEKILKELKESEPASKKFVFIDMPK----RSSIFQRHFKNLLKALNLKDRK 145
Cdd:cd00397    72 LAEELKEYLKERRDKRGPLLKSLYLNKLFgtklGERLSRRTLRRIFKKAGIEAGR 126
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 23-71 5.28e-07

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: 46.64  E-value: 5.28e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1961400067  23 EEVKTLIENAPSLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITI 71
Cdd:cd01186     5 REVQELINACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIEL 53
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 23-144 5.37e-06

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: 43.80  E-value: 5.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  23 EEVKTLIENAPSLRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITInkslnELGKitSPKNKPSIRAVDLLEPVEKI 102
Cdd:cd01193     9 DEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRV-----RQGK--GGKDRVVPLPEKLLEPLRRY 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1961400067 103 LKELKESE---PASKKFVFIDM--------PKRSSIFQRHFKNLLKALNLKDR 144
Cdd:cd01193    82 LKSARPKEeldPAEGRAGVLDPrtgverrhHISETTVQRALKKAVEQAGITKR 134
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 19-144 2.06e-04

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 39.75  E-value: 2.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  19 PFNLEEVKTLIENAPS-----LRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITInkslneLGKitspKNKpsIRAV 93
Cdd:PRK00236  115 PLDVDQAKRLLDAIDEddplaLRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRV------LGK----GNK--ERTV 182

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1961400067  94 DLLEPVEKILK---ELKESEPASKKFVFID-----MPKRSsiFQRHFKNLLKALNLKDR 144
Cdd:PRK00236  183 PLGRAAREALEaylALRPLFLPDDDALFLGarggrLSPRV--VQRRVKKLGKKAGLPSH 239
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 22-146 2.92e-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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 38.89  E-value: 2.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  22 LEEVKTLIENAP------SLRLKAFLVVAFFTGMRTGEQLALLWEDIDfkekTITINKSLNELGKITSPKNKPSIRAVDL 95
Cdd:cd01194     3 LEQARQLLASLPiddsiiGLRDRAIISLMVTEGLRTVEIVRADVGDLR----QEGEGTILYVQGKGKTSKDDFVYLRPDV 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1961400067  96 LEPVEKILK---ELKESEPaskkfVFIDMPKRS--------SIfQRHFKNLLKALNLKDRKL 146
Cdd:cd01194    79 LKALQAYLKargKLDFEEP-----LFTSLSNNSkgqrlttrSI-RRIIKKYLRKAGLDDDRL 134
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 43-145 6.66e-04

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


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 38.06  E-value: 6.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  43 VAFFTGMRTGE--QLALlwEDIDFKEKTITINksLNELGKITSPKNKPSIRAVdllePVEKILKEL--------KESEPA 112
Cdd:cd01184    31 IGLYTGARLNEicQLRV--DDIKEEDGIWCID--INDDAEGRRLKTKASRRLV----PIHPRLIELgfldyveaLRADGK 102

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1961400067 113 SKKFVFIDMP--KRSSIFQRHFKNLLKALNLKDRK 145
Cdd:cd01184   103 LFLFPEKRDKdgKYSKAASKWFNRLLRKLGIKDDE 137
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 23-115 4.58e-03

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: 35.56  E-value: 4.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1961400067  23 EEVKTLIENAPS-----LRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEKTITInkslneLGKitspKNKPsiRAVDLLE 97
Cdd:cd00798     2 DEVERLLDAPDTdtplgLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRV------TGK----GNKE--RLVPFGS 69

                          90
                  ....*....|....*....
gi 1961400067  98 PVEKILKE-LKESEPASKK 115
Cdd:cd00798    70 YAVEALEEyLEERRPLLLK 88
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 25-74 6.03e-03

C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.


Pssm-ID: 271180  Cd Length: 188  Bit Score: 35.35  E-value: 6.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1961400067  25 VKTLIENAPS-LRLKAFLVVAFFTGMRTGEQLALLWEDIDFKEK---TITINKS 74
Cdd:cd00799     5 LATLDDTTLRgLRDRALLLLGFAGALRRSELVALRVEDLTRFVDgglLIRLRRS 58
 
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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