NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1830360837|ref|WP_168175478|]
View 

site-specific integrase [Methylocaldum sp. 14B]

Protein Classification

site-specific integrase( domain architecture ID 10092426)

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 41-218 1.89e-62

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: 193.26  E-value: 1.89e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  41 SWEEIRTIW---NTDGFHLPYRLAIRLLLATGgQRSGEVTRAAWSEFDLDAGLWLLPAARVKNKRDHLIPLTRLALDILN 117
Cdd:cd00801     1 SPDELPELWralDTANLSPPTKLALRLLLLTG-QRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 118 DLRSIYPESKWLFPGRHNPLsvKPWNESTLPHAVQDFCTETGMvpWTPKDLRRTVKTRMGELGIDKLVRDRIQNHALNDI 197
Cdd:cd00801    80 ELKEFTGDSGYLFPSRRKKK--KPISENTINKALKRLGYKGKE--FTPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGV 155

                         170       180
                  ....*....|....*....|.
gi 1830360837 198 SAKHYDRYDYVAEKRAALEVW 218
Cdd:cd00801   156 VRAAYNRYDYLEERREALQAW 176
 
Name Accession Description Interval E-value
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 41-218 1.89e-62

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: 193.26  E-value: 1.89e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  41 SWEEIRTIW---NTDGFHLPYRLAIRLLLATGgQRSGEVTRAAWSEFDLDAGLWLLPAARVKNKRDHLIPLTRLALDILN 117
Cdd:cd00801     1 SPDELPELWralDTANLSPPTKLALRLLLLTG-QRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 118 DLRSIYPESKWLFPGRHNPLsvKPWNESTLPHAVQDFCTETGMvpWTPKDLRRTVKTRMGELGIDKLVRDRIQNHALNDI 197
Cdd:cd00801    80 ELKEFTGDSGYLFPSRRKKK--KPISENTINKALKRLGYKGKE--FTPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGV 155

                         170       180
                  ....*....|....*....|.
gi 1830360837 198 SAKHYDRYDYVAEKRAALEVW 218
Cdd:cd00801   156 VRAAYNRYDYLEERREALQAW 176
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 37-225 2.50e-51

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 170.99  E-value: 2.50e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  37 YDALSWEEIRTIWN---TDGFHLPYRLAIRLLLATGgQRSGEVTRAAWSEFDLDAGLWLLPAARVKNKRDHLIPLTRLAL 113
Cdd:COG0582   203 HPALTPEELPELLRaldAYRGSPVTRLALRLLLLTG-VRPGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQAL 281

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 114 DILNDLRSIYPESKWLFPGRHNPLsvKPWNESTLPHAVQdfctETGMVPWTPKDLRRTVKTRMGELGIDKLVRDRIQNHA 193
Cdd:COG0582   282 EILKELKPLTGDSEYVFPSRRGPK--KPMSENTLNKALR----RMGYGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHK 355

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1830360837 194 LNDISAKHYDRYDYVAEKRAALEVWCRQLEEL 225
Cdd:COG0582   356 DGNKVRAAYNRADYLEERREMMQWWADYLDAL 387
PRK09692 PRK09692
integrase; Provisional
 72-218 1.13e-16

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 78.14  E-value: 1.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  72 RSGEVTRAAWSEFDLDAGLWLLPAARVKNKRDHLIPLTRLALDILNDLRSIYPESKWLFPGRHNPLsvKPWNESTLPHAV 151
Cdd:PRK09692  248 RPAEAAEARWEEIDIEAQEWKIPAARMKMNRDHTVPLSDEALAILEMMKPLSGNREFIFPSRIKPN--QPMNSQTVNAAL 325

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1830360837 152 QDFCTETGMVpwtPKDLRRTVKTRMGELGIDKLVRDRIQNHALNDISAKHYDRYDYVAEKRAALEVW 218
Cdd:PRK09692  326 KRAGLGGVLV---SHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWW 389
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 43-202 3.84e-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: 73.12  E-value: 3.84e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  43 EEIRTIWNTDGFHLPYRLAIRLLLATGgQRSGEVTRAAWSEFDLDAGLWLLPaaRVKNKRDHLIPLTRLAL----DILND 118
Cdd:pfam00589   8 ERLLDAAETGPLSIRDKALLELLYATG-LRISELCSLRWSDIDFENGVIRVH--RGKGNKERTVPLSDAALellkEWLSK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 119 LRSIYPESKWLFPGRHNplsvKPWNESTLPHAVQDFCTETGMV-PWTPKDLRRTVKTRMGELGIDKLVRDRIQNHAlNDI 197
Cdd:pfam00589  85 RLLEAPKSDYLFASKRG----KPLSRQTVRKIFKRAGKEAGLElPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS-SIS 159


                  ....*
gi 1830360837 198 SAKHY 202
Cdd:pfam00589 160 TTQIY 164
 
Name Accession Description Interval E-value
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 41-218 1.89e-62

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: 193.26  E-value: 1.89e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  41 SWEEIRTIW---NTDGFHLPYRLAIRLLLATGgQRSGEVTRAAWSEFDLDAGLWLLPAARVKNKRDHLIPLTRLALDILN 117
Cdd:cd00801     1 SPDELPELWralDTANLSPPTKLALRLLLLTG-QRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 118 DLRSIYPESKWLFPGRHNPLsvKPWNESTLPHAVQDFCTETGMvpWTPKDLRRTVKTRMGELGIDKLVRDRIQNHALNDI 197
Cdd:cd00801    80 ELKEFTGDSGYLFPSRRKKK--KPISENTINKALKRLGYKGKE--FTPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGV 155

                         170       180
                  ....*....|....*....|.
gi 1830360837 198 SAKHYDRYDYVAEKRAALEVW 218
Cdd:cd00801   156 VRAAYNRYDYLEERREALQAW 176
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 37-225 2.50e-51

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 170.99  E-value: 2.50e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  37 YDALSWEEIRTIWN---TDGFHLPYRLAIRLLLATGgQRSGEVTRAAWSEFDLDAGLWLLPAARVKNKRDHLIPLTRLAL 113
Cdd:COG0582   203 HPALTPEELPELLRaldAYRGSPVTRLALRLLLLTG-VRPGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQAL 281

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 114 DILNDLRSIYPESKWLFPGRHNPLsvKPWNESTLPHAVQdfctETGMVPWTPKDLRRTVKTRMGELGIDKLVRDRIQNHA 193
Cdd:COG0582   282 EILKELKPLTGDSEYVFPSRRGPK--KPMSENTLNKALR----RMGYGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHK 355

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1830360837 194 LNDISAKHYDRYDYVAEKRAALEVWCRQLEEL 225
Cdd:COG0582   356 DGNKVRAAYNRADYLEERREMMQWWADYLDAL 387
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
38-216 1.14e-18

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 82.73  E-value: 1.14e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  38 DALSWEEIRTIWNTDGFHLP----YRLAIRLLLATGgQRSGEVTRAAWSEFDLDAGLWLLPaaRVKNKRDHLIPLTRLAL 113
Cdd:COG4974   111 RVLTEEEIEALLEALDTETPeglrDRALLLLLYATG-LRVSELLGLKWSDIDLDRGTIRVR--RGKGGKERTVPLSPEAL 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 114 DILNDLRSIY--PESKWLFPGRHNplsvKPWNESTLPHAVQDFCTETGM-VPWTPKDLRRTVKTRMGELGIDKLVRDRIQ 190
Cdd:COG4974   188 EALREYLEERrpRDSDYLFPTRRG----RPLSRRAIRKILKRLAKRAGIpKRVTPHSLRHTFATHLLEAGVDLRTVQELL 263

                         170       180
                  ....*....|....*....|....*..
gi 1830360837 191 NHAlnDIS-AKHYDRYDyVAEKRAALE 216
Cdd:COG4974   264 GHS--SIStTQIYTHVS-DEELREAVE 287
PRK09692 PRK09692
integrase; Provisional
 72-218 1.13e-16

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 78.14  E-value: 1.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  72 RSGEVTRAAWSEFDLDAGLWLLPAARVKNKRDHLIPLTRLALDILNDLRSIYPESKWLFPGRHNPLsvKPWNESTLPHAV 151
Cdd:PRK09692  248 RPAEAAEARWEEIDIEAQEWKIPAARMKMNRDHTVPLSDEALAILEMMKPLSGNREFIFPSRIKPN--QPMNSQTVNAAL 325

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1830360837 152 QDFCTETGMVpwtPKDLRRTVKTRMGELGIDKLVRDRIQNHALNDISAKHYDRYDYVAEKRAALEVW 218
Cdd:PRK09692  326 KRAGLGGVLV---SHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWW 389
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 43-202 3.84e-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: 73.12  E-value: 3.84e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  43 EEIRTIWNTDGFHLPYRLAIRLLLATGgQRSGEVTRAAWSEFDLDAGLWLLPaaRVKNKRDHLIPLTRLAL----DILND 118
Cdd:pfam00589   8 ERLLDAAETGPLSIRDKALLELLYATG-LRISELCSLRWSDIDFENGVIRVH--RGKGNKERTVPLSDAALellkEWLSK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 119 LRSIYPESKWLFPGRHNplsvKPWNESTLPHAVQDFCTETGMV-PWTPKDLRRTVKTRMGELGIDKLVRDRIQNHAlNDI 197
Cdd:pfam00589  85 RLLEAPKSDYLFASKRG----KPLSRQTVRKIFKRAGKEAGLElPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS-SIS 159


                  ....*
gi 1830360837 198 SAKHY 202
Cdd:pfam00589 160 TTQIY 164
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
39-207 2.45e-13

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 67.68  E-value: 2.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  39 ALSWEEIRTIWN---TDGFHLPYRLAIRLLLATGgQRSGEVTRAAWSEFDLDAG-LWLLPaarvKNKRDHLIPLTRLALD 114
Cdd:COG4973   111 ALTVDELAQLLDalaDDPLAVRDRAIVELLYSTG-LRLGELVGLDWEDVDLDAGeVRVRG----KTGKSRTVPLGPKALA 185

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 115 ILNDLRSI-----YPESKWLFPGRH-NPLSvkpwnestlPHAVQD----FCTETGM-VPWTPKDLRRTVKTRMGELGIDK 183
Cdd:COG4973   186 ALREWLAVrpelaAPDEGALFPSRRgTRLS---------PRNVQKrlrrLAKKAGLpKHVHPHDLRHSFATHLLESGGDL 256

                         170       180
                  ....*....|....*....|....*
gi 1830360837 184 LVRDRIQNHAlnDIS-AKHYDRYDY 207
Cdd:COG4973   257 RAVQELLGHA--SIStTQIYTHLDF 279
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 40-205 2.87e-10

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: 57.34  E-value: 2.87e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  40 LSWEEIRTIWNT-DGFHLPY-RLAIRLLLATGgQRSGEVTRAAWSEFDLDagLWLLPAARVKNKRDHLIPLTRLALDILN 117
Cdd:cd00796     5 LTEDEEARLLAAlEESTNPHlRLIVLLALYTG-ARRGEILSLRWDDIDLE--VGLIVLPETKNGKPRTVPLSDEAIAILK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 118 DLRSIYPESKWLFPGRHNPLSVkpwneSTLPHAVQDFCTETGMVPWTPKDLRRTVKTRMGELGIDKLVRDRIQNHAlndi 197
Cdd:cd00796    82 ELKRKRGKDGFFVDGRFFGIPI-----ASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHS---- 152


                  ....*...
gi 1830360837 198 SAKHYDRY 205
Cdd:cd00796   153 SIKMTMRY 160
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 44-203 4.02e-08

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: 4.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  44 EIRTIWN---TDGFHLPYRLAIRLLLATGGQRSGEVTRAAWSEFDLDAGLWLLPAARVKNKRDHLIPLT----RLALDIL 116
Cdd:cd00397     1 ELEKLLDaidEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPkelaEELKEYL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837 117 NDLRSIYPESKWLFpgRHNPLSVKPWNESTLPHAVQDFCTETGM---VPWTPKDLRRTVKTRMGELGIDKLVRDRIQNHA 193
Cdd:cd00397    81 KERRDKRGPLLKSL--YLNKLFGTKLGERLSRRTLRRIFKKAGIeagRKITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158

                         170
                  ....*....|
gi 1830360837 194 lNDISAKHYD 203
Cdd:cd00397   159 -SISTTQRYL 167
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 41-176 1.04e-07

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: 50.32  E-value: 1.04e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  41 SWEEIRTIWNTDGFHLPYR---LAIRLLLATGGQRSGEVTRAAWSEFDLDAGlwllpAARV---KNKRDHLIPLTRLALD 114
Cdd:cd01188     1 SPDEVRRLLAAIDRLTPVGlrdYAILLLLARLGLRAGDVAGLRLDDIDWRSG-----TITVrqkKTGRPVELPLTEPVGE 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1830360837 115 ILND-LRSIYP--ESKWLFPGRHNPLsVKPWNESTLPHAVQDFCTETGMVPWT--PKDLRRTVKTRM 176
Cdd:cd01188    76 ALADyLRDGRPrtDSREVFLRARAPY-RPLSSTSQISSIVRRYLRKAGIEPSHrgTHSLRHSLATRM 141
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 55-139 3.65e-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: 40.37  E-value: 3.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  55 HLPYRLAIRLLLATGgQRSGEVTRAAWSEFDLDAGlwLLPAARVKNKRDHLIPL---TRLALDILNDLR---SIYPESKW 128
Cdd:cd00797    24 PLTYATLFGLLYATG-LRVGEALRLRLEDVDLDSG--ILTIRQTKFGKSRLVPLhpsTVGALRDYLARRdrlLPSPSSSY 100

                          90
                  ....*....|..
gi 1830360837 129 LFPG-RHNPLSV 139
Cdd:cd00797   101 FFVSqQGGRLTG 112
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 59-204 4.54e-04

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase 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: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 39.63  E-value: 4.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  59 RLAIRLLLATGgQRSGEVTRAAWSEFDlDAGLWLLPA---ARVknkrdhLIPLT---RLALDILNDLRSiyPESKWLFPG 132
Cdd:cd00800    15 RLAMELALLTG-QRQGDLLRLKWSDIT-DGGLLVEQSktgKKL------LIPWTpslRALVDRIRALPR--KRSEYLINS 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1830360837 133 RhnplSVKPWNESTLP----HAVQDFCTETGMVPWTPKDLRRTVKTRMGELGIDKLVRdRIQNHAlNDISAKHYDR 204
Cdd:cd00800    85 R----KGGPLSYDTLKsawrRARKAAGLKGETEGFTFHDLRAKAATDYAEQGGSTDAQ-ALLGHK-SDAMTERYTR 154
COG4342 COG4342
Phage integrase/recombinase [Mobilome: prophages, transposons];
149-202 1.08e-03

Phage integrase/recombinase [Mobilome: prophages, transposons];


Pssm-ID: 443483 [Multi-domain]  Cd Length: 278  Bit Score: 39.31  E-value: 1.08e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1830360837 149 HAVQDFCTETGMVPwtPKDLRRTVKTRMGELGIDKLVRDRIQNHALNDISAKHY 202
Cdd:COG4342   201 RTVKDRLRRKGLVS--AKYIRKWVANKMIELGIPEEVIDFIQGRAPLSVGEKHY 252
int PHA00730
integrase
 150-202 3.44e-03

integrase


Pssm-ID: 222813 [Multi-domain]  Cd Length: 337  Bit Score: 37.86  E-value: 3.44e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1830360837 150 AVQDFCTETGMVPwtPKDLRRTVKTRMGELGIDKLVRDRIQNHALNDISAKHY 202
Cdd:PHA00730  265 YIDKFVRRLDLIP--PKYIRKFVATKMLELGIPSEVVDFIQGRTPSRILTKHY 315
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 43-136 9.53e-03

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: 35.70  E-value: 9.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830360837  43 EEIRTIWNTDGFHLPYRLAIR---LLLATGGQRSGEVTRAAWSEFDLDAGLWLLPAARVKNKRDHLIPLTRLALDILNDL 119
Cdd:cd01185     1 EELKRLMALELSDTSRLELVRdmfLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPVTVPLLPVAREILEKY 80

                          90
                  ....*....|....*..
gi 1830360837 120 RSIYPEsKWLFPGRHNP 136
Cdd:cd01185    81 KDDRSE-GKLFPVLSNQ 96
 
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