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Conserved domains on  [gi|759449498|ref|WP_043171237|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Aeromonas]

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

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List of domain hits

 Name Accession Description Interval E-value
XerD super family cl44177
Site-specific recombinase XerD [Replication, recombination and repair];
502-705 3.64e-14

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


The actual alignment was detected with superfamily member COG4974:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 74.26  E-value: 3.64e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  502 SQKNAVSYMAARLTSLHS---YAVASYHLAPLPEELVPRERqRPHVRATYLSEPLFRQLLRGMERMTHTSSSYReclsAL 578
Cdd:COG4974    64 ERGLSPSTINRYLAALRSffrYAVREGLLEDNPAAKVKLPK-KPRKLPRVLTEEEIEALLEALDTETPEGLRDR----AL 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  579 YIVAYRAGLRLSEIQKLRLKDIERSpECWLYIRdtrldDGKSDSAtRKIPLGvlltPEERTRLDAYLSGLWPRKaknaNA 658
Cdd:COG4974   139 LLLLYATGLRVSELLGLKWSDIDLD-RGTIRVR-----RGKGGKE-RTVPLS----PEALEALREYLEERRPRD----SD 203

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 759449498  659 LAFPSQSGWliPMSDEEIRGPLTSILRQVG-GKYYTFHHLRHTALSRL 705
Cdd:COG4974   204 YLFPTRRGR--PLSRRAIRKILKRLAKRAGiPKRVTPHSLRHTFATHL 249
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
502-705 3.64e-14

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 74.26  E-value: 3.64e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  502 SQKNAVSYMAARLTSLHS---YAVASYHLAPLPEELVPRERqRPHVRATYLSEPLFRQLLRGMERMTHTSSSYReclsAL 578
Cdd:COG4974    64 ERGLSPSTINRYLAALRSffrYAVREGLLEDNPAAKVKLPK-KPRKLPRVLTEEEIEALLEALDTETPEGLRDR----AL 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  579 YIVAYRAGLRLSEIQKLRLKDIERSpECWLYIRdtrldDGKSDSAtRKIPLGvlltPEERTRLDAYLSGLWPRKaknaNA 658
Cdd:COG4974   139 LLLLYATGLRVSELLGLKWSDIDLD-RGTIRVR-----RGKGGKE-RTVPLS----PEALEALREYLEERRPRD----SD 203

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 759449498  659 LAFPSQSGWliPMSDEEIRGPLTSILRQVG-GKYYTFHHLRHTALSRL 705
Cdd:COG4974   204 YLFPTRRGR--PLSRRAIRKILKRLAKRAGiPKRVTPHSLRHTFATHL 249
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 545-705 5.39e-08

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: 53.48  E-value: 5.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  545 RATYLSEPLFRQLLRGMERMThtsssyRECLSALYIVAYRAGLRLSEIQKLRLKDIerspecWLYIRDTRLDDGKSDSAt 624
Cdd:cd00796     1 RDRFLTEDEEARLLAALEEST------NPHLRLIVLLALYTGARRGEILSLRWDDI------DLEVGLIVLPETKNGKP- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  625 RKIPLgvllTPEERTRLDAylsglwpRKAKNANALAFPSQSGWLIPmsDEEIRGPLTSILRQVGGKYYTFHHLRHTALSR 704
Cdd:cd00796    68 RTVPL----SDEAIAILKE-------LKRKRGKDGFFVDGRFFGIP--IASLRRAFKKARKRAGLEDLRFHDLRHTFASR 134


                  .
gi 759449498  705 L 705
Cdd:cd00796   135 L 135
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 581-705 8.31e-07

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: 50.01  E-value: 8.31e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498   581 VAYRAGLRLSEIQKLRLKDIErspecwLYIRDTRLDDGKSdSATRKIPLGVlltpEERTRLDAYLSGLWPRKAKNaNALa 660
Cdd:pfam00589   29 LLYATGLRISELCSLRWSDID------FENGVIRVHRGKG-NKERTVPLSD----AALELLKEWLSKRLLEAPKS-DYL- 95

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 759449498   661 FPSQSGWliPMSDEEIRGPLTSILRQVGGKYY-TFHHLRHTALSRL 705
Cdd:pfam00589   96 FASKRGK--PLSRQTVRKIFKRAGKEAGLELPlHPHMLRHSFATHL 139
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
502-705 3.64e-14

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 74.26  E-value: 3.64e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  502 SQKNAVSYMAARLTSLHS---YAVASYHLAPLPEELVPRERqRPHVRATYLSEPLFRQLLRGMERMTHTSSSYReclsAL 578
Cdd:COG4974    64 ERGLSPSTINRYLAALRSffrYAVREGLLEDNPAAKVKLPK-KPRKLPRVLTEEEIEALLEALDTETPEGLRDR----AL 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  579 YIVAYRAGLRLSEIQKLRLKDIERSpECWLYIRdtrldDGKSDSAtRKIPLGvlltPEERTRLDAYLSGLWPRKaknaNA 658
Cdd:COG4974   139 LLLLYATGLRVSELLGLKWSDIDLD-RGTIRVR-----RGKGGKE-RTVPLS----PEALEALREYLEERRPRD----SD 203

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 759449498  659 LAFPSQSGWliPMSDEEIRGPLTSILRQVG-GKYYTFHHLRHTALSRL 705
Cdd:COG4974   204 YLFPTRRGR--PLSRRAIRKILKRLAKRAGiPKRVTPHSLRHTFATHL 249
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
503-705 2.03e-08

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 56.89  E-value: 2.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  503 QKNAVSYMAARLTSLHS---YAVASYHLAPLPEELVPRERqRPHVRATYLSEPLFRQLLRGMErmthtSSSYRECLSALY 579
Cdd:COG4973    64 RGLSPRTLNRRLSALRSffnWAVREGLLEANPAAGVKAPK-APRKLPRALTVDELAQLLDALA-----DDPLAVRDRAIV 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  580 IVAYRAGLRLSEIQKLRLKDIERSpECWLYIRdtrlddGKSDSaTRKIPLGvlltPEERTRLDAYLSgLWPRKAKNANAL 659
Cdd:COG4973   138 ELLYSTGLRLGELVGLDWEDVDLD-AGEVRVR------GKTGK-SRTVPLG----PKALAALREWLA-VRPELAAPDEGA 204

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 759449498  660 AFPSQSGWliPMSDEEIRGPLTSILRQVG-GKYYTFHHLRHTALSRL 705
Cdd:COG4973   205 LFPSRRGT--RLSPRNVQKRLRRLAKKAGlPKHVHPHDLRHSFATHL 249
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 545-705 5.39e-08

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: 53.48  E-value: 5.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  545 RATYLSEPLFRQLLRGMERMThtsssyRECLSALYIVAYRAGLRLSEIQKLRLKDIerspecWLYIRDTRLDDGKSDSAt 624
Cdd:cd00796     1 RDRFLTEDEEARLLAALEEST------NPHLRLIVLLALYTGARRGEILSLRWDDI------DLEVGLIVLPETKNGKP- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  625 RKIPLgvllTPEERTRLDAylsglwpRKAKNANALAFPSQSGWLIPmsDEEIRGPLTSILRQVGGKYYTFHHLRHTALSR 704
Cdd:cd00796    68 RTVPL----SDEAIAILKE-------LKRKRGKDGFFVDGRFFGIP--IASLRRAFKKARKRAGLEDLRFHDLRHTFASR 134


                  .
gi 759449498  705 L 705
Cdd:cd00796   135 L 135
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 554-705 3.62e-07

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: 51.33  E-value: 3.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  554 FRQLLRGMERMTHTSSSYReclsALYIVAYRAGLRLSEIQKLRLKDIERsPECWLYIRDTRLDDGKsdsaTRKIPLGVLL 633
Cdd:cd00397     2 LEKLLDAIDEDKKIDLRDR----AILLLLLETGLRISELLALKVKDIDL-DNGTIRVRGKKTKGGK----ERTVPLPKEL 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 759449498  634 TPEERTRLDAYLSGLWPRKAKNANALAFPSQSGWliPMSDEEIRGpltsILRQVG---GKYYTFHHLRHTALSRL 705
Cdd:cd00397    73 AEELKEYLKERRDKRGPLLKSLYLNKLFGTKLGE--RLSRRTLRR----IFKKAGieaGRKITPHSLRHTFATNL 141
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 581-705 8.31e-07

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: 50.01  E-value: 8.31e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498   581 VAYRAGLRLSEIQKLRLKDIErspecwLYIRDTRLDDGKSdSATRKIPLGVlltpEERTRLDAYLSGLWPRKAKNaNALa 660
Cdd:pfam00589   29 LLYATGLRISELCSLRWSDID------FENGVIRVHRGKG-NKERTVPLSD----AALELLKEWLSKRLLEAPKS-DYL- 95

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 759449498   661 FPSQSGWliPMSDEEIRGPLTSILRQVGGKYY-TFHHLRHTALSRL 705
Cdd:pfam00589   96 FASKRGK--PLSRQTVRKIFKRAGKEAGLELPlHPHMLRHSFATHL 139
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 555-705 6.23e-03

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: 39.21  E-value: 6.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 759449498  555 RQLLRGMERMTHTSSSYRECLSALYIVAYRAGLRLSEIQKLRLKDIERSpECWLYIRDTRLddGKSdsatRKIPlgvlLT 634
Cdd:cd00797     7 RRLLAAADQLPPESPLRPLTYATLFGLLYATGLRVGEALRLRLEDVDLD-SGILTIRQTKF--GKS----RLVP----LH 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 759449498  635 PEERTRLDAYLSGLWPRKAKNANALAFPSQSGwlIPMSDEEIRGPLTSILRQVG------GKYYTFHHLRHT-ALSRL 705
Cdd:cd00797    76 PSTVGALRDYLARRDRLLPSPSSSYFFVSQQG--GRLTGGGVYRVFRRLLRRIGlrgagdGRGPRLHDLRHTfAVNRL 151
 
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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