NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|545062084|ref|WP_021435029|]
View 

tyrosine-type recombinase/integrase [Clostridioides difficile]

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

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 ...
 4-172 2.36e-32

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: 114.31  E-value: 2.36e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   4 IQDYLRYKSYRNYVIFMLGITTGYRAGDLVKLKVRDVKealRRQEFTIMEgkkvnsknirEKNRKPRTVEVRPKIAQILK 83
Cdd:cd01192   15 IKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVT---NKDKLSIKE----------QKTGKQKTFPLNPTLVKALK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  84 KYIKD---KHDYEYMFPSRKKKYPHIGVEAVSKALKEAGEYFGLCD-ITAHSMRKTYAYKIYiDSGKDIVAVKELLGHSS 159
Cdd:cd01192   82 EYIDDldlKRNDYLFKSLKQGPEKPISRKQAYKILKKAADDLGLNYnIGTHSLRKTFGYHVY-KQGKDIELLMKLLNHSS 160

                        170
                 ....*....|...
gi 545062084 160 IEETKMYLGLDKE 172
Cdd:cd01192  161 PSITLRYLGIDQE 173
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 4-172 2.36e-32

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: 114.31  E-value: 2.36e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   4 IQDYLRYKSYRNYVIFMLGITTGYRAGDLVKLKVRDVKealRRQEFTIMEgkkvnsknirEKNRKPRTVEVRPKIAQILK 83
Cdd:cd01192   15 IKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVT---NKDKLSIKE----------QKTGKQKTFPLNPTLVKALK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  84 KYIKD---KHDYEYMFPSRKKKYPHIGVEAVSKALKEAGEYFGLCD-ITAHSMRKTYAYKIYiDSGKDIVAVKELLGHSS 159
Cdd:cd01192   82 EYIDDldlKRNDYLFKSLKQGPEKPISRKQAYKILKKAADDLGLNYnIGTHSLRKTFGYHVY-KQGKDIELLMKLLNHSS 160

                        170
                 ....*....|...
gi 545062084 160 IEETKMYLGLDKE 172
Cdd:cd01192  161 PSITLRYLGIDQE 173
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
1-172 3.83e-26

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 101.22  E-value: 3.83e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   1 MLDIQDYLRYKSYRNYVIFMLGITTGYRAGDLVKLKVRDVKeaLRRQEFTIMEGKkvnsknirekNRKPRTVEVRPKIAQ 80
Cdd:COG4974  121 LLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDID--LDRGTIRVRRGK----------GGKERTVPLSPEALE 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  81 ILKKYIKDKHDY--EYMFPSRKKKypHIGVEAVSKALKEAGEYFGL-CDITAHSMRKTYAyKIYIDSGKDIVAVKELLGH 157
Cdd:COG4974  189 ALREYLEERRPRdsDYLFPTRRGR--PLSRRAIRKILKRLAKRAGIpKRVTPHSLRHTFA-THLLEAGVDLRTVQELLGH 265

                        170
                 ....*....|....*
gi 545062084 158 SSIEETKMYLGLDKE 172
Cdd:COG4974  266 SSISTTQIYTHVSDE 280
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 12-171 4.29e-17

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


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 74.66  E-value: 4.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   12 SYRNYVIFMLGITTGYRAGDLVKLKVRDVKeaLRRQEFTIMEGKkvnsknirekNRKPRTVEVRPKIAQILKKYI----K 87
Cdd:pfam00589  20 SIRDKALLELLYATGLRISELCSLRWSDID--FENGVIRVHRGK----------GNKERTVPLSDAALELLKEWLskrlL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   88 DKHDYEYMFPSRKKKypHIGVEAVSKALKEAGEYFGL-CDITAHSMRKTYAYkIYIDSGKDIVAVKELLGHSSIEETKMY 166
Cdd:pfam00589  88 EAPKSDYLFASKRGK--PLSRQTVRKIFKRAGKEAGLeLPLHPHMLRHSFAT-HLLEAGVDLRVVQKLLGHSSISTTQIY 164


                  ....*
gi 545062084  167 LGLDK 171
Cdd:pfam00589 165 THVAD 169
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 12-172 7.73e-15

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 70.57  E-value: 7.73e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  12 SYRNYVIFMLGITTGYRAGDLVKLKVRDVKeaLRRQEFTIMeGKkvnsknirekNRKPRTVEVRPKIAQILKKYIKD--- 88
Cdd:PRK00236 135 ALRDRAILELLYGSGLRLSELVGLDIDDLD--LASGTLRVL-GK----------GNKERTVPLGRAAREALEAYLALrpl 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  89 -KHDYEYMFPSRKKKypHIGVEAVSKALKEAGEYFGL-CDITAHSMRKTYAYKIYiDSGKDIVAVKELLGHSSIEETKMY 166
Cdd:PRK00236 202 fLPDDDALFLGARGG--RLSPRVVQRRVKKLGKKAGLpSHITPHKLRHSFATHLL-ESGGDLRAVQELLGHASLSTTQIY 278


                 ....*.
gi 545062084 167 LGLDKE 172
Cdd:PRK00236 279 THVDFQ 284
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 4-172 2.36e-32

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: 114.31  E-value: 2.36e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   4 IQDYLRYKSYRNYVIFMLGITTGYRAGDLVKLKVRDVKealRRQEFTIMEgkkvnsknirEKNRKPRTVEVRPKIAQILK 83
Cdd:cd01192   15 IKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVT---NKDKLSIKE----------QKTGKQKTFPLNPTLVKALK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  84 KYIKD---KHDYEYMFPSRKKKYPHIGVEAVSKALKEAGEYFGLCD-ITAHSMRKTYAYKIYiDSGKDIVAVKELLGHSS 159
Cdd:cd01192   82 EYIDDldlKRNDYLFKSLKQGPEKPISRKQAYKILKKAADDLGLNYnIGTHSLRKTFGYHVY-KQGKDIELLMKLLNHSS 160

                        170
                 ....*....|...
gi 545062084 160 IEETKMYLGLDKE 172
Cdd:cd01192  161 PSITLRYLGIDQE 173
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
1-172 3.83e-26

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 101.22  E-value: 3.83e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   1 MLDIQDYLRYKSYRNYVIFMLGITTGYRAGDLVKLKVRDVKeaLRRQEFTIMEGKkvnsknirekNRKPRTVEVRPKIAQ 80
Cdd:COG4974  121 LLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDID--LDRGTIRVRRGK----------GGKERTVPLSPEALE 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  81 ILKKYIKDKHDY--EYMFPSRKKKypHIGVEAVSKALKEAGEYFGL-CDITAHSMRKTYAyKIYIDSGKDIVAVKELLGH 157
Cdd:COG4974  189 ALREYLEERRPRdsDYLFPTRRGR--PLSRRAIRKILKRLAKRAGIpKRVTPHSLRHTFA-THLLEAGVDLRTVQELLGH 265

                        170
                 ....*....|....*
gi 545062084 158 SSIEETKMYLGLDKE 172
Cdd:COG4974  266 SSISTTQIYTHVSDE 280
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 1-167 1.01e-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: 94.47  E-value: 1.01e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   1 MLDIQDYLRYKSYRNYVIFMLGITTGYRAGDLVKLKVRDVKEALRRqeFTIMEGKkvnsknirEKNRKPRTVEVRPKIAQ 80
Cdd:cd00397    5 LLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGT--IRVRGKK--------TKGGKERTVPLPKELAE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  81 ILKKYIKDKHDYEYM--------FPSRKKKYPHIGVEAVSKALKEAGEYFGLcDITAHSMRKTYAYkIYIDSGKDIVAVK 152
Cdd:cd00397   75 ELKEYLKERRDKRGPllkslylnKLFGTKLGERLSRRTLRRIFKKAGIEAGR-KITPHSLRHTFAT-NLLENGVDIKVVQ 152

                        170
                 ....*....|....*
gi 545062084 153 ELLGHSSIEETKMYL 167
Cdd:cd00397  153 KLLGHSSISTTQRYL 167
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 14-170 2.13e-22

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: 88.45  E-value: 2.13e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  14 RNYVIFMLGITTGYRAGDLVKLKVRDVkeALRRQEFTImegkkvnsknIREKNRKPRTVEVRPKIAQILKKYIKD---KH 90
Cdd:cd01188   21 RDYAILLLLARLGLRAGDVAGLRLDDI--DWRSGTITV----------RQKKTGRPVELPLTEPVGEALADYLRDgrpRT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  91 DYEYMFPSRKKKYPHIGVEA-----VSKALKEAG---EYFGlcditAHSMRKTYAYKIYiDSGKDIVAVKELLGHSSIEE 162
Cdd:cd01188   89 DSREVFLRARAPYRPLSSTSqissiVRRYLRKAGiepSHRG-----THSLRHSLATRML-RAGTSLKVIADLLGHRSIET 162


                 ....*...
gi 545062084 163 TKMYLGLD 170
Cdd:cd01188  163 TAIYAKID 170
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
12-172 2.06e-21

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 88.48  E-value: 2.06e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  12 SYRNYVIFMLGITTGYRAGDLVKLKVRDVkeALRRQEFTImegkkvnskniREKNRKPRTVEVRPKIAQILKKYIK---- 87
Cdd:COG4973  130 AVRDRAIVELLYSTGLRLGELVGLDWEDV--DLDAGEVRV-----------RGKTGKSRTVPLGPKALAALREWLAvrpe 196

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  88 -DKHDYEYMFPSRKKKypHIGVEAVSKALKEAGEYFGL-CDITAHSMRKTYAyKIYIDSGKDIVAVKELLGHSSIEETKM 165
Cdd:COG4973  197 lAAPDEGALFPSRRGT--RLSPRNVQKRLRRLAKKAGLpKHVHPHDLRHSFA-THLLESGGDLRAVQELLGHASISTTQI 273


                 ....*..
gi 545062084 166 YLGLDKE 172
Cdd:COG4973  274 YTHLDFQ 280
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 12-171 4.29e-17

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


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 74.66  E-value: 4.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   12 SYRNYVIFMLGITTGYRAGDLVKLKVRDVKeaLRRQEFTIMEGKkvnsknirekNRKPRTVEVRPKIAQILKKYI----K 87
Cdd:pfam00589  20 SIRDKALLELLYATGLRISELCSLRWSDID--FENGVIRVHRGK----------GNKERTVPLSDAALELLKEWLskrlL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   88 DKHDYEYMFPSRKKKypHIGVEAVSKALKEAGEYFGL-CDITAHSMRKTYAYkIYIDSGKDIVAVKELLGHSSIEETKMY 166
Cdd:pfam00589  88 EAPKSDYLFASKRGK--PLSRQTVRKIFKRAGKEAGLeLPLHPHMLRHSFAT-HLLEAGVDLRVVQKLLGHSSISTTQIY 164


                  ....*
gi 545062084  167 LGLDK 171
Cdd:pfam00589 165 THVAD 169
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 7-172 4.52e-17

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: 74.22  E-value: 4.52e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   7 YLRYKSYRNYV--IFMLGITTGYRAGDLVKLKVRDVKEALRRQEFtimegkkvnsKNIREKNRKPRTVEVRPKIAQILKK 84
Cdd:cd01185   10 ELSDTSRLELVrdMFLFSCYTGLRFSDLKNLTWKNIVEASGRTWI----------RYRRKKTGKPVTVPLLPVAREILEK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  85 YIKDKHDyEYMFPSRKKKYphigveaVSKALKEAGEYFGL-CDITAHSMRKTYAYKIYIdSGKDIVAVKELLGHSSIEET 163
Cdd:cd01185   80 YKDDRSE-GKLFPVLSNQK-------INRYLKEIAKIAGIdKHLTFHVARHTFATLLLL-KGVDIETISKLLGHSSIKTT 150


                 ....*....
gi 545062084 164 KMYLGLDKE 172
Cdd:cd01185  151 QIYAKIVDS 159
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 9-166 4.41e-16

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: 71.59  E-value: 4.41e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   9 RYKSYRNYVIFMLGITTGYRAGDLVKLKVRDVKEALRRQEFTimegkkvnskniREKNRKPRTVEVRPKIAQILKKYIKD 88
Cdd:cd00796   19 ESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLP------------ETKNGKPRTVPLSDEAIAILKELKRK 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 545062084  89 KHDYEYMFPSRKKKYPHIGVE-AVSKALKEAGeyfgLCDITAHSMRKTYAyKIYIDSGKDIVAVKELLGHSSIEETKMY 166
Cdd:cd00796   87 RGKDGFFVDGRFFGIPIASLRrAFKKARKRAG----LEDLRFHDLRHTFA-SRLVQAGVPIKTVAKILGHSSIKMTMRY 160
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 14-167 1.08e-15

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: 71.15  E-value: 1.08e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  14 RNYVIFMLGITTGYRAGDLVKLKVRDVKeaLRRQEFTIMEGKkvnsknirekNRKPRTVEVRPKIAQILKKYIKDKHDYE 93
Cdd:cd01193   22 RHRLILSLLYGAGLRISELLRLRVKDID--FERGVIRVRQGK----------GGKDRVVPLPEKLLEPLRRYLKSARPKE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  94 YMFPSRKKKYP-----------HIGVEAVSKALKEAGEYFGLC-DITAHSMRKTYAYKIyIDSGKDIVAVKELLGHSSIE 161
Cdd:cd01193   90 ELDPAEGRAGVldprtgverrhHISETTVQRALKKAVEQAGITkRVTPHTLRHSFATHL-LEAGTDIRTIQELLGHSDLS 168


                 ....*.
gi 545062084 162 ETKMYL 167
Cdd:cd01193  169 TTMIYT 174
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 12-172 7.73e-15

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 70.57  E-value: 7.73e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  12 SYRNYVIFMLGITTGYRAGDLVKLKVRDVKeaLRRQEFTIMeGKkvnsknirekNRKPRTVEVRPKIAQILKKYIKD--- 88
Cdd:PRK00236 135 ALRDRAILELLYGSGLRLSELVGLDIDDLD--LASGTLRVL-GK----------GNKERTVPLGRAAREALEAYLALrpl 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  89 -KHDYEYMFPSRKKKypHIGVEAVSKALKEAGEYFGL-CDITAHSMRKTYAYKIYiDSGKDIVAVKELLGHSSIEETKMY 166
Cdd:PRK00236 202 fLPDDDALFLGARGG--RLSPRVVQRRVKKLGKKAGLpSHITPHKLRHSFATHLL-ESGGDLRAVQELLGHASLSTTQIY 278


                 ....*.
gi 545062084 167 LGLDKE 172
Cdd:PRK00236 279 THVDFQ 284
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 4-167 6.13e-13

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: 63.55  E-value: 6.13e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   4 IQDYLRYKSYRNYVIFMLGITTGYRAGDLVKLKVRDVKEalrRQEFTIM--EGKKVNSKNireknrkpRTVEVRPKIAQI 81
Cdd:cd01194   13 LPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQ---EGEGTILyvQGKGKTSKD--------DFVYLRPDVLKA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  82 LKKYIKDK---HDYEYMFPSRKKKY-----PHIGVEA-VSKALKEAGeyFGLCDITAHSMRKTyAYKIYIDSGKDIVAVK 152
Cdd:cd01194   82 LQAYLKARgklDFEEPLFTSLSNNSkgqrlTTRSIRRiIKKYLRKAG--LDDDRLTAHSLRHT-AGTLALKAGKSLREVQ 158

                        170
                 ....*....|....*
gi 545062084 153 ELLGHSSIEETKMYL 167
Cdd:cd01194  159 QLLRHSDPNTTMIYA 173
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 13-173 7.44e-12

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: 60.75  E-value: 7.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  13 YRNYVIFMLGITTGYRAGDLVKLKVRDVKealrrqeFTimegkKVNSKNIREKNRKPRTVEVRPKIAQILKKYIK----- 87
Cdd:cd01182   21 RRDHALLLLLYDTGARVQELADLTIRDLR-------LD-----DPATVRLHGKGRKERTVPLWKETVAALKAYLQefhlt 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  88 -DKHDYEYMFPS-RKKKYPHIGVE-AVSKALKEAGEYF-GLCD-ITAHSMRKTYAYKIYiDSGKDIVAVKELLGHSSIEE 162
Cdd:cd01182   89 pDPKQLFPLFPNrRGQPLTRDGVAyILNKYVALASNRCpSLPKrITPHTLRHTKAMHLL-QAGVDLTVIRDWLGHESVET 167

                        170
                 ....*....|.
gi 545062084 163 TKMYLGLDKEL 173
Cdd:cd01182  168 TQIYAEADLEM 178
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 25-172 9.90e-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: 9.90e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  25 TGYRAGDLVKLKVRDVkeALRRQEFTIMeGKKvnsknireknRKPRTVEVRPKIAQILKKYIK-------DKHDYEYMFP 97
Cdd:cd00798   31 SGLRVSELVGLDLSDV--DLDEGLVRVT-GKG----------NKERLVPFGSYAVEALEEYLEerrplllKKKPPDALFL 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 545062084  98 SRKKKYphIGVEAVSKALKEAGEYFGLC-DITAHSMRKTYAYKIyIDSGKDIVAVKELLGHSSIEETKMYLGLDKE 172
Cdd:cd00798   98 NKRGKR--LSRRGVWRILKKYAERAGLPkHVSPHTLRHSFATHL-LEGGADLRVVQELLGHASLSTTQIYTHVSFE 170
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 6-166 1.04e-10

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: 57.18  E-value: 1.04e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   6 DYLRYKSYRNYVIFMLGITTGYRAGDLVKLKVRDVKeaLRRQEFTIMEG-KKVNSKNIREKNRKP----RTVEVRPKIAQ 80
Cdd:cd01189    9 EALKKRGDRYYLLFLLALLTGLRRGELLALTWSDID--FENGTIRINRTlVRKKKGGYVIKPPKTkssiRTIPLPDELIE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  81 ILKKYIkdkhdyeymfpsrkkkyphigveAVSKALKEAGeyfgLCDITAHSMRKTYAyKIYIDSGKDIVAVKELLGHSSI 160
Cdd:cd01189   87 LLKELK-----------------------AFKKLLKKAG----LPRITPHDLRHTFA-SLLLEAGVPLKVIAERLGHSDI 138


                 ....*.
gi 545062084 161 EETKMY 166
Cdd:cd01189  139 STTLDV 144
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 1-177 1.11e-09

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 56.59  E-value: 1.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   1 MLDIQDYLRYKSYRNYVIFMLGitTGYRAGDLVKLKVRDVKeaLRRQEFTI-MEgkkvnskniREKNRKPRTVEVRPKIA 79
Cdd:COG0582  215 LRALDAYRGSPVTRLALRLLLL--TGVRPGELRGARWSEID--LEAALWTIpAE---------RMKTRRPHIVPLSRQAL 281

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  80 QILKKYIKDKHDYEYMFPSRKKKYPHIGVEAVSKALKEAGeyFGlcDITAHSMRKTYAyKIYIDSGKDIVAVKELLGHSS 159
Cdd:COG0582  282 EILKELKPLTGDSEYVFPSRRGPKKPMSENTLNKALRRMG--YG--RFTPHGFRHTAS-TLLNEAGFPPDVIERQLAHKD 356

                        170
                 ....*....|....*...
gi 545062084 160 IEETKMYlgldkelYHHY 177
Cdd:COG0582  357 GNKVRAA-------YNRA 367
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 1-158 3.15e-09

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: 53.81  E-value: 3.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084   1 MLDIQDYLRYKSYRNYVIFMLgiTTGYRAGDLVKLKVRDVKeaLRRQEFTIMEGkkvnskniREKNRKPRTVEVRPKIAQ 80
Cdd:cd00801    9 WRALDTANLSPPTKLALRLLL--LTGQRIGELARARWSEID--LEEKTWTIPAE--------RTKNKRPHRVPLSDQALE 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 545062084  81 ILKKYIKDKHDYEYMFPSRKKKYPHIGVEAVSKALKEAGEYFGLcdITAHSMRKTYAyKIYIDSGKDIVAVKELLGHS 158
Cdd:cd00801   77 ILEELKEFTGDSGYLFPSRRKKKKPISENTINKALKRLGYKGKE--FTPHDLRRTFS-TLLNELGIDPEVIERLLNHV 151
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 16-181 6.76e-09

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: 53.08  E-value: 6.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  16 YVIFMLGITTGYRAGDLVKLKVRDVKeaLRRQEFTIMEGKkvnsknirekNRKPRTVEVRPKIAQILKKYIKDKH----- 90
Cdd:cd00797   28 ATLFGLLYATGLRVGEALRLRLEDVD--LDSGILTIRQTK----------FGKSRLVPLHPSTVGALRDYLARRDrllps 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  91 -DYEYMFPS-RKKKYPHIGVE----AVSKA--LKEAGEYFGLcdiTAHSMRKTYA-------YKiyidSGKDIVA----V 151
Cdd:cd00797   96 pSSSYFFVSqQGGRLTGGGVYrvfrRLLRRigLRGAGDGRGP---RLHDLRHTFAvnrltrwYR----EGADVERklpvL 168

                        170       180       190
                 ....*....|....*....|....*....|
gi 545062084 152 KELLGHSSIEETKMYLGLDKELYHHYSESL 181
Cdd:cd00797  169 STYLGHVNVTDTYWYLTATPELMELASLRL 198
int PHA02601
integrase; Provisional
 18-166 1.39e-05

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 44.33  E-value: 1.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  18 IFMLGITTGYRAGdlvklkvrdvkEALRRQEFTIMEGKKVNSKNireKNRKPRTVEVRPKIAQILkkyikdkhdyeymfP 97
Cdd:PHA02601 196 IAKICLATGARWS-----------EAETLKRSQISPYKITFVKT---KGKKNRTVPISEELYKML--------------P 247

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 545062084  98 SRKKKYPHIGVEAVSKALKEAGeyfglCDITA----HSMRKTYAYKIYIDSGkDIVAVKELLGHSSIEETKMY 166
Cdd:PHA02601 248 KRRGRLFKDAYESFERAVKRAG-----IDLPEgqatHVLRHTFASHFMMNGG-NILVLQRILGHATIEMTMAY 314
xerD PRK00283
tyrosine recombinase;
25-176 1.08e-04

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 41.72  E-value: 1.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  25 TGYRAGDLVKLKVRDVKealRRQEFTIMEGKkvnsknirekNRKPRTVEVRPKIAQILKKYIKDKHD-------YEYMFP 97
Cdd:PRK00283 146 TGLRVSELVGLTLDDVS---LRQGVVRVTGK----------GNKERLVPLGEEAVYAIERYLERGRPallngrsSDALFP 212

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  98 SRKKKYphIGVEAVSKALKEAGEYFGLC--DITAHSMRKTYAYKIyIDSGKDIVAVKELLGHSSIEETKMY-------Lg 168
Cdd:PRK00283 213 SARGGQ--LTRQTFWHRIKHYAKRAGIDpkKLSPHVLRHAFATHL-LNHGADLRVVQELLGHSDISTTQIYthvaterL- 288

                        170
                 ....*....|
gi 545062084 169 ldKELY--HH 176
Cdd:PRK00283 289 --KELHaqHH 296
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 17-167 2.21e-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: 40.02  E-value: 2.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  17 VIFMLGITTGYRAGDLVKLKVRDVKEA--LRRQEFTimeGKKVnsknireknRKPRTVEVRPKIAQILKKYIKDKHdyeY 94
Cdd:cd00800   16 LAMELALLTGQRQGDLLRLKWSDITDGglLVEQSKT---GKKL---------LIPWTPSLRALVDRIRALPRKRSE---Y 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 545062084  95 MFPSRK-KKYPHIGVE-AVSKALKEAGEYFGLCDITAHSMRKTyAYKIYIDSGKDIVAVKeLLGHSSIEETKMYL 167
Cdd:cd00800   81 LINSRKgGPLSYDTLKsAWRRARKAAGLKGETEGFTFHDLRAK-AATDYAEQGGSTDAQA-LLGHKSDAMTERYT 153
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 16-167 5.71e-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: 271191  Cd Length: 176  Bit Score: 38.94  E-value: 5.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062084  16 YVIFMLGiTTGYRAGDLVKLKVRDVKEALRrqeftimegkkvnskNIREKNRKPRTVEVRPKIAQILKKYIKDKH-DYEY 94
Cdd:cd01191   24 FVVRFLA-ATGARVSELIKIKVEHVELGYF---------------DIYSKGGKLRRLYIPKKLRNEALEWLKSTNrKSGY 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 545062084  95 MFPSRKKKypHIGVEAVSKALKEAGEYFGLCD--ITAHSMRKTYAyKIYIDSGKDIVAVKELLGHSSIEETKMYL 167
Cdd:cd01191   88 IFLNRFGE--RITTRGIAQQLKNYARKYGLNPkvVYPHSFRHRFA-KNFLEKYNDIALLADLMGHESIETTRIYL 159
 
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