NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2171443440|ref|WP_233126636|]
View 

MULTISPECIES: site-specific integrase [Polynucleobacter]

Protein Classification

tyrosine-type recombinase/integrase( domain architecture ID 11471964)

tyrosine-type recombinase/integrase cleaves 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.

Gene Ontology:  GO:0009009|GO:0006310
PubMed:  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
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
28-218 3.92e-38

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 133.58  E-value: 3.92e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  28 KTMAKQAKTLNQQELRRVLDYVATRKH-ALRNRALITISMYSGMRCGEISNLLYSDvIDAEgkvRNEIRLRaeDTKTKEA 106
Cdd:COG4974   104 KKPRKLPRVLTEEEIEALLEALDTETPeGLRDRALLLLLYATGLRVSELLGLKWSD-IDLD---RGTIRVR--RGKGGKE 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 107 RTVFVSEKLQKELQQYAKVYKPKDVNVKFIYSqkeNSEGFSPNTLCQLYFNIYKGAGLQ-NCSSHSGRRTFATEIANKGV 185
Cdd:COG4974   178 RTVPLSPEALEALREYLEERRPRDSDYLFPTR---RGRPLSRRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGV 254

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2171443440 186 SIRVLQKLLGHKNIQTTSIYVDANDDMLRKAVN 218
Cdd:COG4974   255 DLRTVQELLGHSSISTTQIYTHVSDEELREAVE 287
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
28-218 3.92e-38

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 133.58  E-value: 3.92e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  28 KTMAKQAKTLNQQELRRVLDYVATRKH-ALRNRALITISMYSGMRCGEISNLLYSDvIDAEgkvRNEIRLRaeDTKTKEA 106
Cdd:COG4974   104 KKPRKLPRVLTEEEIEALLEALDTETPeGLRDRALLLLLYATGLRVSELLGLKWSD-IDLD---RGTIRVR--RGKGGKE 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 107 RTVFVSEKLQKELQQYAKVYKPKDVNVKFIYSqkeNSEGFSPNTLCQLYFNIYKGAGLQ-NCSSHSGRRTFATEIANKGV 185
Cdd:COG4974   178 RTVPLSPEALEALREYLEERRPRDSDYLFPTR---RGRPLSRRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGV 254

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2171443440 186 SIRVLQKLLGHKNIQTTSIYVDANDDMLRKAVN 218
Cdd:COG4974   255 DLRTVQELLGHSSISTTQIYTHVSDEELREAVE 287
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 41-206 1.12e-30

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: 111.03  E-value: 1.12e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  41 ELRRVLDYVATRK-HALRNRALITISMYSGMRCGEISNLLYSDVIDAEgkvrNEIRLRAEDTKTKEARTVFVSEKLQKEL 119
Cdd:cd00397     1 ELEKLLDAIDEDKkIDLRDRAILLLLLETGLRISELLALKVKDIDLDN----GTIRVRGKKTKGGKERTVPLPKELAEEL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 120 QQYAKVYKPKDVNVKFI-YSQKENSEGFSPNTLCQLYFNIYKGAGLQ---NCSSHSGRRTFATEIANKGVSIRVLQKLLG 195
Cdd:cd00397    77 KEYLKERRDKRGPLLKSlYLNKLFGTKLGERLSRRTLRRIFKKAGIEagrKITPHSLRHTFATNLLENGVDIKVVQKLLG 156

                         170
                  ....*....|.
gi 2171443440 196 HKNIQTTSIYV 206
Cdd:cd00397   157 HSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 37-210 2.86e-25

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: 97.00  E-value: 2.86e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  37 LNQQELRRVLDYVATRKHALRNRALITISMYSGMRCGEISNLLYSDvIDAEGKvrneiRLRAEDTKTKEARTVFVSEKLQ 116
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSD-IDFENG-----VIRVHRGKGNKERTVPLSDAAL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 117 KELQQY-AKVYKPKDVNvKFIYSQKENSEgFSPNTLcQLYFN-IYKGAGLQN-CSSHSGRRTFATEIANKGVSIRVLQKL 193
Cdd:pfam00589  76 ELLKEWlSKRLLEAPKS-DYLFASKRGKP-LSRQTV-RKIFKrAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKL 152

                         170
                  ....*....|....*..
gi 2171443440 194 LGHKNIQTTSIYVDAND 210
Cdd:pfam00589 153 LGHSSISTTQIYTHVAD 169
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 35-220 3.66e-16

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 75.19  E-value: 3.66e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  35 KTLNQQELRRVLDYVA-TRKHALRNRALITIsMY-SGMRCGEISNLLYSDVIDAEGKVR-----NeirlraedtktKEaR 107
Cdd:PRK00236  114 KPLDVDQAKRLLDAIDeDDPLALRDRAILEL-LYgSGLRLSELVGLDIDDLDLASGTLRvlgkgN-----------KE-R 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 108 TVFVSEKLQKELQQYAKV--YKPKDVNVKFIysqkeNSEG--FSPNTLcQLYFNIY-KGAGL-QNCSSHSGRRTFATEIA 181
Cdd:PRK00236  181 TVPLGRAAREALEAYLALrpLFLPDDDALFL-----GARGgrLSPRVV-QRRVKKLgKKAGLpSHITPHKLRHSFATHLL 254

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2171443440 182 NKGVSIRVLQKLLGHKNIQTTSIYVDANDDMLRKAVNLA 220
Cdd:PRK00236  255 ESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 35-218 1.81e-14

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 70.30  E-value: 1.81e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  35 KTLNQQELRRVLDYVATRKHA-LRNRALITIsMY-SGMRCGEISNLLYSDVIDAEGKVRneirlrAEDTKTKEaRTVFVS 112
Cdd:TIGR02225 103 KVLTVEEVEALLAAPDVDTPLgLRDRAMLEL-LYaTGLRVSELVGLRLEDVNLDEGFVR------VRGKGNKE-RLVPLG 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 113 EKLQKELQQYAKVYKPkdvnVKFIYSQKENSEGFsPNTLC-----QLYFNIYKG----AGLQ-NCSSHSGRRTFATEIAN 182
Cdd:TIGR02225 175 EEAIEALERYLKEARP----LLLKKKVKESDALF-LNRRGgplsrQGVWKILKEyakrAGIEkPISPHTLRHSFATHLLE 249

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2171443440 183 KGVSIRVLQKLLGHKNIQTTSIYVDANDDMLRKAVN 218
Cdd:TIGR02225 250 NGADLRVVQELLGHADISTTQIYTHVARERLKEVHK 285
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
28-218 3.92e-38

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 133.58  E-value: 3.92e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  28 KTMAKQAKTLNQQELRRVLDYVATRKH-ALRNRALITISMYSGMRCGEISNLLYSDvIDAEgkvRNEIRLRaeDTKTKEA 106
Cdd:COG4974   104 KKPRKLPRVLTEEEIEALLEALDTETPeGLRDRALLLLLYATGLRVSELLGLKWSD-IDLD---RGTIRVR--RGKGGKE 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 107 RTVFVSEKLQKELQQYAKVYKPKDVNVKFIYSqkeNSEGFSPNTLCQLYFNIYKGAGLQ-NCSSHSGRRTFATEIANKGV 185
Cdd:COG4974   178 RTVPLSPEALEALREYLEERRPRDSDYLFPTR---RGRPLSRRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGV 254

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2171443440 186 SIRVLQKLLGHKNIQTTSIYVDANDDMLRKAVN 218
Cdd:COG4974   255 DLRTVQELLGHSSISTTQIYTHVSDEELREAVE 287
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 41-206 1.12e-30

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: 111.03  E-value: 1.12e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  41 ELRRVLDYVATRK-HALRNRALITISMYSGMRCGEISNLLYSDVIDAEgkvrNEIRLRAEDTKTKEARTVFVSEKLQKEL 119
Cdd:cd00397     1 ELEKLLDAIDEDKkIDLRDRAILLLLLETGLRISELLALKVKDIDLDN----GTIRVRGKKTKGGKERTVPLPKELAEEL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 120 QQYAKVYKPKDVNVKFI-YSQKENSEGFSPNTLCQLYFNIYKGAGLQ---NCSSHSGRRTFATEIANKGVSIRVLQKLLG 195
Cdd:cd00397    77 KEYLKERRDKRGPLLKSlYLNKLFGTKLGERLSRRTLRRIFKKAGIEagrKITPHSLRHTFATNLLENGVDIKVVQKLLG 156

                         170
                  ....*....|.
gi 2171443440 196 HKNIQTTSIYV 206
Cdd:cd00397   157 HSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
28-216 3.10e-27

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 105.04  E-value: 3.10e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  28 KTMAKQAKTLNQQELRRVLDYVATRKHALRNRALITISMYSGMRCGEISNLLYSDVIDAEGkvrnEIRLRaedTKTKEAR 107
Cdd:COG4973   103 KAPRKLPRALTVDELAQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAG----EVRVR---GKTGKSR 175

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 108 TVFVSEKLQKELQQYAKV---YKPKDVNVKFIySQKENSegFSPNTLcQLYFNIY-KGAGL-QNCSSHSGRRTFATEIAN 182
Cdd:COG4973   176 TVPLGPKALAALREWLAVrpeLAAPDEGALFP-SRRGTR--LSPRNV-QKRLRRLaKKAGLpKHVHPHDLRHSFATHLLE 251

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2171443440 183 KGVSIRVLQKLLGHKNIQTTSIYVDANDDMLRKA 216
Cdd:COG4973   252 SGGDLRAVQELLGHASISTTQIYTHLDFQHLAEV 285
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 37-210 2.86e-25

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: 97.00  E-value: 2.86e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  37 LNQQELRRVLDYVATRKHALRNRALITISMYSGMRCGEISNLLYSDvIDAEGKvrneiRLRAEDTKTKEARTVFVSEKLQ 116
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSD-IDFENG-----VIRVHRGKGNKERTVPLSDAAL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 117 KELQQY-AKVYKPKDVNvKFIYSQKENSEgFSPNTLcQLYFN-IYKGAGLQN-CSSHSGRRTFATEIANKGVSIRVLQKL 193
Cdd:pfam00589  76 ELLKEWlSKRLLEAPKS-DYLFASKRGKP-LSRQTV-RKIFKrAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKL 152

                         170
                  ....*....|....*..
gi 2171443440 194 LGHKNIQTTSIYVDAND 210
Cdd:pfam00589 153 LGHSSISTTQIYTHVAD 169
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 33-206 4.22e-25

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: 96.24  E-value: 4.22e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  33 QAKTLNQQELRRVLDYVATRKHAlRNRALITISMYSGMRCGEISNLLYSDvIDAEGkvrneIRLRAEDTKTKEARTVFVS 112
Cdd:cd00796     1 RDRFLTEDEEARLLAALEESTNP-HLRLIVLLALYTGARRGEILSLRWDD-IDLEV-----GLIVLPETKNGKPRTVPLS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 113 EKLQKELQQYAKVYKPKDVNVKFIysqkenSEGFSPNTLCQLYFNIYKGAGLQNCSSHSGRRTFATEIANKGVSIRVLQK 192
Cdd:cd00796    74 DEAIAILKELKRKRGKDGFFVDGR------FFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAK 147

                         170
                  ....*....|....
gi 2171443440 193 LLGHKNIQTTSIYV 206
Cdd:cd00796   148 ILGHSSIKMTMRYA 161
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 37-205 1.12e-19

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: 82.32  E-value: 1.12e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  37 LNQQELRRVLDYVATRKHalrnRALITISMYSGMRCGEISNLLYSDvIDAEgkvRNEIRLRaeDTKTKEARTVFVSEKLQ 116
Cdd:cd01193     6 LSPDEVRRILGALTELRH----RLILSLLYGAGLRISELLRLRVKD-IDFE---RGVIRVR--QGKGGKDRVVPLPEKLL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 117 KELQQYAKVYKPK--------DVNVKFIYSQKENSEGFSPNTLCQLYFNIYKGAGLQN-CSSHSGRRTFATEIANKGVSI 187
Cdd:cd01193    76 EPLRRYLKSARPKeeldpaegRAGVLDPRTGVERRHHISETTVQRALKKAVEQAGITKrVTPHTLRHSFATHLLEAGTDI 155

                         170
                  ....*....|....*...
gi 2171443440 188 RVLQKLLGHKNIQTTSIY 205
Cdd:cd01193   156 RTIQELLGHSDLSTTMIY 173
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 41-213 3.10e-19

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: 80.77  E-value: 3.10e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  41 ELRRV--LDYVATRKHALRNRALItISMYSGMRCGEISNLLYSDVIDAEGkvRNEIRLRAedTKTKEARTVFVSEKLQKE 118
Cdd:cd01185     2 ELKRLmaLELSDTSRLELVRDMFL-FSCYTGLRFSDLKNLTWKNIVEASG--RTWIRYRR--KKTGKPVTVPLLPVAREI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 119 LQQYAKVYKPKDVNvKFIYSQKENsegfspNTLCQlyfnIYKGAGL-QNCSSHSGRRTFATEIANKGVSIRVLQKLLGHK 197
Cdd:cd01185    77 LEKYKDDRSEGKLF-PVLSNQKIN------RYLKE----IAKIAGIdKHLTFHVARHTFATLLLLKGVDIETISKLLGHS 145

                         170
                  ....*....|....*.
gi 2171443440 198 NIQTTSIYVDANDDML 213
Cdd:cd01185   146 SIKTTQIYAKIVDSKK 161
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 41-215 1.91e-18

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: 79.21  E-value: 1.91e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  41 ELRRVLDYVATRKHA-LRNRALITISMYSGMRCGEISNLLYSDvIDAEgkvRNEIRLRAedTKTKEARTVFVSEKLQKEL 119
Cdd:cd01188     4 EVRRLLAAIDRLTPVgLRDYAILLLLARLGLRAGDVAGLRLDD-IDWR---SGTITVRQ--KKTGRPVELPLTEPVGEAL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 120 QQYAKVYKPKdVNVKFIY-SQKENSEGFS-PNTLCQLYFNIYKGAGLQNC--SSHSGRRTFATEIANKGVSIRVLQKLLG 195
Cdd:cd01188    78 ADYLRDGRPR-TDSREVFlRARAPYRPLSsTSQISSIVRRYLRKAGIEPShrGTHSLRHSLATRMLRAGTSLKVIADLLG 156

                         170       180
                  ....*....|....*....|
gi 2171443440 196 HKNIQTTSIYVDANDDMLRK 215
Cdd:cd01188   157 HRSIETTAIYAKIDVDDLRE 176
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 39-206 1.77e-17

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: 75.67  E-value: 1.77e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  39 QQELRRVLDYVATRKHalRNRALITISMYSGMRCGEISNLLYSDVIDAEGKVR--------NEIRLRAEDTKTKEA-RTV 109
Cdd:cd01189     1 PEELKKLLEALKKRGD--RYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRinrtlvrkKKGGYVIKPPKTKSSiRTI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 110 FVSEKLQKELQQYaKVYKPkdvnvkfiysqkensegfspntlcqlyfnIYKGAGLQNCSSHSGRRTFATEIANKGVSIRV 189
Cdd:cd01189    79 PLPDELIELLKEL-KAFKK-----------------------------LLKKAGLPRITPHDLRHTFASLLLEAGVPLKV 128

                         170
                  ....*....|....*...
gi 2171443440 190 LQKLLGHKNIQTT-SIYV 206
Cdd:cd01189   129 IAERLGHSDISTTlDVYA 146
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 35-220 3.66e-16

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 75.19  E-value: 3.66e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  35 KTLNQQELRRVLDYVA-TRKHALRNRALITIsMY-SGMRCGEISNLLYSDVIDAEGKVR-----NeirlraedtktKEaR 107
Cdd:PRK00236  114 KPLDVDQAKRLLDAIDeDDPLALRDRAILEL-LYgSGLRLSELVGLDIDDLDLASGTLRvlgkgN-----------KE-R 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 108 TVFVSEKLQKELQQYAKV--YKPKDVNVKFIysqkeNSEG--FSPNTLcQLYFNIY-KGAGL-QNCSSHSGRRTFATEIA 181
Cdd:PRK00236  181 TVPLGRAAREALEAYLALrpLFLPDDDALFL-----GARGgrLSPRVV-QRRVKKLgKKAGLpSHITPHKLRHSFATHLL 254

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2171443440 182 NKGVSIRVLQKLLGHKNIQTTSIYVDANDDMLRKAVNLA 220
Cdd:PRK00236  255 ESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 34-205 2.73e-15

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 73.24  E-value: 2.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  34 AKTLNQQELRRVLDYV-ATRKHALRNRALITISMYSGMRCGEISNLLYSDViDAEGKVRNeIRlraeDTKTKEARTVFVS 112
Cdd:PRK01287  134 RQILSEAETEQVLASPdLTTLQGLRDRALLELLWSTGIRRGELARLDLYDV-DASRGVVT-VR----QGKGNKDRVVPVG 207

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 113 EKLQKELQQYAKVYKPK-----DVNVKFIysqKENSEGFSPNTLCQLYFNIYKGAGLQNCSS-HSGRRTFATEIANKGVS 186
Cdd:PRK01287  208 ERALAWLQRYLQDVRPQlavrpDSGALFV---AMDGDGLARNTLTNMVGRYIRAAGIEKAGAcHLFRHAMATQMLENGAD 284

                         170
                  ....*....|....*....
gi 2171443440 187 IRVLQKLLGHKNIQTTSIY 205
Cdd:PRK01287  285 TRHIQAILGHAKLETTQIY 303
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 35-218 1.81e-14

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 70.30  E-value: 1.81e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  35 KTLNQQELRRVLDYVATRKHA-LRNRALITIsMY-SGMRCGEISNLLYSDVIDAEGKVRneirlrAEDTKTKEaRTVFVS 112
Cdd:TIGR02225 103 KVLTVEEVEALLAAPDVDTPLgLRDRAMLEL-LYaTGLRVSELVGLRLEDVNLDEGFVR------VRGKGNKE-RLVPLG 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 113 EKLQKELQQYAKVYKPkdvnVKFIYSQKENSEGFsPNTLC-----QLYFNIYKG----AGLQ-NCSSHSGRRTFATEIAN 182
Cdd:TIGR02225 175 EEAIEALERYLKEARP----LLLKKKVKESDALF-LNRRGgplsrQGVWKILKEyakrAGIEkPISPHTLRHSFATHLLE 249

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2171443440 183 KGVSIRVLQKLLGHKNIQTTSIYVDANDDMLRKAVN 218
Cdd:TIGR02225 250 NGADLRVVQELLGHADISTTQIYTHVARERLKEVHK 285
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 39-205 8.72e-14

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: 66.77  E-value: 8.72e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  39 QQELRRVLDYVATRK-HALRNRALITIsMY-SGMRCGEISNLLYSDvIDAEgkvRNEIRLRAedtKTKEARTVFVSEKLQ 116
Cdd:cd00798     1 VDEVERLLDAPDTDTpLGLRDRAILEL-LYaSGLRVSELVGLDLSD-VDLD---EGLVRVTG---KGNKERLVPFGSYAV 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 117 KELQQYAKVYKPKDVNVK-----FIysqkeNSEG--FSPntlcQLYFNIYKG----AGLQN-CSSHSGRRTFATEIANKG 184
Cdd:cd00798    73 EALEEYLEERRPLLLKKKppdalFL-----NKRGkrLSR----RGVWRILKKyaerAGLPKhVSPHTLRHSFATHLLEGG 143

                         170       180
                  ....*....|....*....|.
gi 2171443440 185 VSIRVLQKLLGHKNIQTTSIY 205
Cdd:cd00798   144 ADLRVVQELLGHASLSTTQIY 164
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 35-202 3.04e-12

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 64.67  E-value: 3.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  35 KTLNQQELRRVLDYVATRKHALRNRALITISMYSGMRCGEISNLLYSDvIDAEGKVrneIRLRAEDTKTKEARTVFVSEK 114
Cdd:COG0582   204 PALTPEELPELLRALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSE-IDLEAAL---WTIPAERMKTRRPHIVPLSRQ 279

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 115 LQKELQQYakvyKPKDVNVKFIY-SQKENSEGFSPNTLCQLYfniyKGAGLQNCSSHSGRRTFATEIANKGVSIRVLQKL 193
Cdd:COG0582   280 ALEILKEL----KPLTGDSEYVFpSRRGPKKPMSENTLNKAL----RRMGYGRFTPHGFRHTASTLLNEAGFPPDVIERQ 351


                  ....*....
gi 2171443440 194 LGHKNIQTT 202
Cdd:COG0582   352 LAHKDGNKV 360
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 36-216 1.56e-11

Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase A from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 60.89  E-value: 1.56e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  36 TLNQQELRRVLDYVATrkhaLRNRALITISMYSGMRCGEISNLLYSDVIDAEgkvrNEIRLRAEDTKTKEA-------RT 108
Cdd:cd01186     1 VLTPREVQELINACNN----LRDKFLLALLYETGLRIGEALGLRIEDIDMAD----NQIELVPREDNTNEAraksmreRR 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 109 VFVSEKLQKELQQY--AKVYKPKDVNVKFIYSQKENSEGFSPNtlcqlYFNIYKGAGLQ------NCSSHSGRRTFATEI 180
Cdd:cd01186    73 IPVSQDLIDLYADYltYIYCEEAEFSITVFVNVKGGNQGKAMN-----YSDVYDLVRRLkkrtgiDFTPHMFRHTHATAL 147

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2171443440 181 ANKGVSIRVLQKLLGHKNIQTT-SIYVDANDDMLRKA 216
Cdd:cd01186   148 IRAGWSIEVVARRLGHAHVQTTlNTYGHLSEEDIRRE 184
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 32-209 1.92e-11

FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar to E.coli FimE and FimB and Proteus mirabilis MrpI. FimB and FimE are the regulatory proteins during expression of type 1 fimbriae in Escherichia coli. The fimB and fimE proteins direct the phase switch into the 'on' and 'off' position. MrpI is the regulatory protein of proteus mirabilis fimbriae expression. This family belongs to the integrase/recombinase superfamily.


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 60.60  E-value: 1.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  32 KQAKTLNQQELRRVLDYVATRKHALRNRALITISMYSGMRCGEISNLLYSDViDAEGKVRNEIRLRAEDTKTKEARTVfV 111
Cdd:cd01197     2 KQRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDV-DLESRRLHIRRLKNGFSTTHPLRFD-E 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 112 SEKLQKELQQYAKvYKPKDVNVKFIySQKENseGFSPNTLCQLYFNIYKGAGLQNCS-SHSGRRTFATEIANKGVSIRVL 190
Cdd:cd01197    80 REALEAWLKERAN-WKGADTDWIFL-SRRGG--PLSRQQAYRIIRDLGKEAGTVTQThPHMLRHACGYALADRGADTRLI 155

                         170
                  ....*....|....*....
gi 2171443440 191 QKLLGHKNIQTTSIYVDAN 209
Cdd:cd01197   156 QDYLGHRNIRHTVIYTASN 174
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 57-220 2.52e-10

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: 57.29  E-value: 2.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  57 RNRALITISMYSGMRCGEISNLLYSDVIDaeGKVRNeIRLRAEDTKTkeaRTVFVSEKLQKELQQYAKVY----KPKDVN 132
Cdd:cd01182    22 RDHALLLLLYDTGARVQELADLTIRDLRL--DDPAT-VRLHGKGRKE---RTVPLWKETVAALKAYLQEFhltpDPKQLF 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 133 VKFIysqKENSEGFSPNTLCQLyFNIYKGAGLQNCSS-------HSGRRTFATEIANKGVSIRVLQKLLGHKNIQTTSIY 205
Cdd:cd01182    96 PLFP---NRRGQPLTRDGVAYI-LNKYVALASNRCPSlpkritpHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIY 171

                         170
                  ....*....|....*
gi 2171443440 206 VDANDDMLRKAVNLA 220
Cdd:cd01182   172 AEADLEMKREALEKA 186
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 41-197 3.00e-10

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 57.28  E-value: 3.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  41 ELRRVLDYVATRKHALRNRALITISMYSGMRCGEISNLLYSDvIDAEGKVrneIRLRAEDTKTKEARTVFVSEKLQKELQ 120
Cdd:cd00801     4 ELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSE-IDLEEKT---WTIPAERTKNKRPHRVPLSDQALEILE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2171443440 121 QYAKVYKPKDvnvkFIY-SQKENSEGFSPNTLCQLYFNIYKGAGLQncSSHSGRRTFATEIANKGVSIRVLQKLLGHK 197
Cdd:cd00801    80 ELKEFTGDSG----YLFpSRRKKKKPISENTINKALKRLGYKGKEF--TPHDLRRTFSTLLNELGIDPEVIERLLNHV 151
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 56-205 1.28e-09

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: 55.46  E-value: 1.28e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  56 LRNRALITISMYSGMRCGEISNLLYSDVIDAEGKVRNEIRLRAEDTKTkeaRTVFVSEKLQKELQQYAKVYKPKDVNVKF 135
Cdd:cd01194    22 LRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQGKGKTSKD---DFVYLRPDVLKALQAYLKARGKLDFEEPL 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2171443440 136 IYSQKENSEG--FSPNTLCQLYFNIYKGAGLQN--CSSHSGRRTFATEIANKGVSIRVLQKLLGHKNIQTTSIY 205
Cdd:cd01194    99 FTSLSNNSKGqrLTTRSIRRIIKKYLRKAGLDDdrLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIY 172
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 42-218 1.53e-09

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


Pssm-ID: 271180  Cd Length: 188  Bit Score: 55.38  E-value: 1.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  42 LRRVLDYV-ATRKHALRNRALITISMYSGMRCGEISNLlysDVIDAEGKVRNEIRLRAEDTKT---KEARTVFVSEKLQ- 116
Cdd:cd00799     1 LKAMLATLdDTTLRGLRDRALLLLGFAGALRRSELVAL---RVEDLTRFVDGGLLIRLRRSKTdqdGEGEIKALPYGPEt 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 117 ---KELQQYAKVYKPKDVnvkFIYSQ-----KENSEGFSPNTLCQLYFNIYKGAGLQ--NCSSHSGRRTFATEIANKGVS 186
Cdd:cd00799    78 cpvRALRAWLEAAGIPSG---PLFRRirrggSVGTTRLSDRSVARIVKRRAALAGLDpgDFSGHSLRRGFATEAARAGAS 154

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2171443440 187 IRVLQKLLGHKNIQTTSIYVDANDDMLRKAVN 218
Cdd:cd00799   155 LPEIMAQGGHKSVATVMRYIREADRFKDNAAA 186
int PHA02601
integrase; Provisional
 37-219 1.60e-09

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 56.66  E-value: 1.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  37 LNQQELRRVLDYVA-TRKHALRNRALITISmySGMRCGEISNLLYSDVIdaegkvrnEIRLRAEDTKTKEARTVFVSEKL 115
Cdd:PHA02601  173 LTKEEIERLLDACDgSRSPDLGLIAKICLA--TGARWSEAETLKRSQIS--------PYKITFVKTKGKKNRTVPISEEL 242

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 116 QKELqqyakvykpkdvnvkfiysqkENSEGFSPNTLCQLYFNIYKGAGL---QNCSSHSGRRTFATEIANKGVSIRVLQK 192
Cdd:PHA02601  243 YKML---------------------PKRRGRLFKDAYESFERAVKRAGIdlpEGQATHVLRHTFASHFMMNGGNILVLQR 301

                         170       180
                  ....*....|....*....|....*..
gi 2171443440 193 LLGHKNIQTTSIYVDANDDMLRKAVNL 219
Cdd:PHA02601  302 ILGHATIEMTMAYAHFAPDHLEDAVSL 328
PRK09870 PRK09870
tyrosine recombinase; Provisional
 32-209 4.38e-09

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 54.17  E-value: 4.38e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  32 KQAKTLNQQELRRVLDYVATRKHALRNRALITISMYSGMRCGEISNLLYSDvIDAEGKVRNEIRLRAEDTKTKEArtvfv 111
Cdd:PRK09870    8 KKRNFLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISD-IDLKAKCIYIHRLKKGFSTTHPL----- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 112 sekLQKELQQYAKVykpkdVNVKFIYSQKENSEGF-----SPNTLCQLYFNIY---KGAGLQNC-SSHSGRRTFATEIAN 182
Cdd:PRK09870   82 ---LNKEIQALKNW-----LSIRTSYPHAESEWVFlsrkgNPLSRQQFYHIIStsgGNAGLSLEiHPHMLRHSCGFALAN 153

                         170       180
                  ....*....|....*....|....*..
gi 2171443440 183 KGVSIRVLQKLLGHKNIQTTSIYVDAN 209
Cdd:PRK09870  154 MGIDTRLIQDYLGHRNIRHTVWYTASN 180
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 52-216 6.74e-09

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: 53.45  E-value: 6.74e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  52 RKHALRNRALITISMYSGMRCGEISNLLYSDVidaegkvRNEIRLRAEDTKTKEARTVFVSEKLQKELQQYAKVYKPKDV 131
Cdd:cd01192    20 KKANPRNYLLFIVGINTGLRISDLLSLKVEDV-------TNKDKLSIKEQKTGKQKTFPLNPTLVKALKEYIDDLDLKRN 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 132 NVKFiYSQKENSEGfsPNTLCQLYfNIYKGAGLQ-----NCSSHSGRRTFATEIANKGVSIRVLQKLLGHKNIQTTSIYV 206
Cdd:cd01192    93 DYLF-KSLKQGPEK--PISRKQAY-KILKKAADDlglnyNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYL 168

                         170
                  ....*....|
gi 2171443440 207 DANDDMLRKA 216
Cdd:cd01192   169 GIDQEDVDKA 178
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 37-197 7.21e-08

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


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 50.38  E-value: 7.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  37 LNQQELRRVLDYVATRKHALRNRA---LITISMYSGMRCGEISNLLYSDVIDAEGKVRNEIRLRAEDTKTKEA---RTVF 110
Cdd:cd01184     1 FTPEELAKIFSSPLYTGCKKKDPAlywLPLIGLYTGARLNEICQLRVDDIKEEDGIWCIDINDDAEGRRLKTKasrRLVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 111 VSEKLQ--------KELQQYAKVYKPKDVNVKFIYSQKENSEGFSpntlcqLYFNIYKGAGLQNCSSHSGRRTFATEIAN 182
Cdd:cd01184    81 IHPRLIelgfldyvEALRADGKLFLFPEKRDKDGKYSKAASKWFN------RLLRKLGIKDDERKSFHSFRHTFITALKR 154

                         170
                  ....*....|....*
gi 2171443440 183 KGVSIRVLQKLLGHK 197
Cdd:cd01184   155 AGVPEELIAQIVGHS 169
xerD PRK00283
tyrosine recombinase;
35-205 8.34e-08

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 51.35  E-value: 8.34e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  35 KTLNQQELRRVLDYVATRKH-ALRNRALITIsMY-SGMRCGEISNLLYSDVIDAEGKVRneirLRAEDTKTkeaRTVFVS 112
Cdd:PRK00283  112 KTLSEAQVEALLDAPDIDTPlGLRDRAMLEL-LYaTGLRVSELVGLTLDDVSLRQGVVR----VTGKGNKE---RLVPLG 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 113 EKLQKELQQYAKVYKPKDVNvkfiysqKENSEGFSPNTLC-----QLYFNIYKGAGLQ------NCSSHSGRRTFATEIA 181
Cdd:PRK00283  184 EEAVYAIERYLERGRPALLN-------GRSSDALFPSARGgqltrQTFWHRIKHYAKRagidpkKLSPHVLRHAFATHLL 256

                         170       180
                  ....*....|....*....|....
gi 2171443440 182 NKGVSIRVLQKLLGHKNIQTTSIY 205
Cdd:PRK00283  257 NHGADLRVVQELLGHSDISTTQIY 280
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 57-218 1.72e-07

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 50.69  E-value: 1.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  57 RNRALITISMYSGMRCGEISNLLYSDvIDAEGKVRNEIRlraedtKTKEARTVFVS----EKLQKELQQYAKVYK-PKDV 131
Cdd:PRK05084  196 RDLAIIALILGSGLRVSELVNLDLSD-LNLKQMTIDVTR------KGGKRDSVNIApfalPYLEEYLKIRASRYKaEKQE 268

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 132 NVKFIYSQKENSEGFSPNTLcQLYFNIYKGAGLQNCSSHSGRRTFATEIANKGVSIRVLQKLLGHKNIQTTSIYVDANDD 211
Cdd:PRK05084  269 KALFLTKYRGKPNRISARAI-EKMVAKYSEAFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVND 347


                  ....*..
gi 2171443440 212 MLRKAVN 218
Cdd:PRK05084  348 EQKEALD 354
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 37-205 2.76e-07

integron integrase; Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 50.08  E-value: 2.76e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  37 LNQQELRRVLDYVATrKHALRNRALitismY-SGMRCGEISNLLYSDvIDAegkVRNEIRLRaeDTKTKEARTVFVSEKL 115
Cdd:TIGR02249 102 LTREEVRRLLEHLEG-KYRLIAKLL-----YgSGMRLMECLRLRIQD-IDF---DYGEIRIR--QGKGGKDRTVTLPKEL 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 116 QKELQQ----------------YAKVYKP-----------KDVNVKFIYSQKENSEG----------FSPNTLCQLYFNI 158
Cdd:TIGR02249 170 IPPLREqielarayheadlaegYGGVYLPhalarkypnapKEWGWQYLFPSHRLSRDpesgvirrhhINETTIQRAVRRA 249

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2171443440 159 YKGAGL-QNCSSHSGRRTFATEIANKGVSIRVLQKLLGHKNIQTTSIY 205
Cdd:TIGR02249 250 VERAGIeKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 168-206 7.01e-07

Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase B from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 47.04  E-value: 7.01e-07
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2171443440 168 SSHSGRRTFATEIANKGVSIRVLQKLLGHKNIQTTSIYV 206
Cdd:cd01187   103 HTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYA 141
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 41-217 7.15e-07

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: 271196  Cd Length: 183  Bit Score: 47.86  E-value: 7.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  41 ELRRVLDYV-ATRKHALRNRALITISMYSGMRCGEISNLLYSDVIDaEGKvRNEIRLraeDTKTKEARTVFVSEKLQKEL 119
Cdd:cd01196     4 EARRLLESIdSTHPVGLRDRALIALMVYSFARIGAVLAMRVEDVYD-QGR-RLWVRL---AEKGGKQHEMPCHHDLEEYL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 120 QQYAKV----YKPKDVNVKFIYSQkenSEGFSPNTLCQLyfNIYK-------GAGLQN-CSSHSGRRTFATEIANKGVSI 187
Cdd:cd01196    79 RAYLEAaeieEDPKGPLFRTTRGG---TRKLTHNPLTQA--NAYRmvrrraiAADIPTaIGNHSFRATGITAYLKNGGTL 153

                         170       180       190
                  ....*....|....*....|....*....|
gi 2171443440 188 RVLQKLLGHKNIQTTSIYVDANDDMLRKAV 217
Cdd:cd01196   154 EDAQNMANHASTRTTQLYDRRSDKITLDEV 183
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 37-216 7.27e-07

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: 48.07  E-value: 7.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  37 LNQQELRRVLDYVA--TRKHALRN---RALITISMYSGMRCGEISNLLYSDVIDAEGkvrneiRLRAEDTKTKEARTVFV 111
Cdd:cd00797     1 YTDAEIRRLLAAADqlPPESPLRPltyATLFGLLYATGLRVGEALRLRLEDVDLDSG------ILTIRQTKFGKSRLVPL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 112 SEKLQKELQQYAKVYK---PKDVNVKFIYSQKENseGFSPNTLCQLYFNIYKGAGLQNCSS------HSGRRTFAT---- 178
Cdd:cd00797    75 HPSTVGALRDYLARRDrllPSPSSSYFFVSQQGG--RLTGGGVYRVFRRLLRRIGLRGAGDgrgprlHDLRHTFAVnrlt 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2171443440 179 ----EIANKGVSIRVLQKLLGHKNIQTTSIYVDANDDMLRKA 216
Cdd:cd00797   153 rwyrEGADVERKLPVLSTYLGHVNVTDTYWYLTATPELMELA 194
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 40-210 8.78e-05

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


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 41.69  E-value: 8.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  40 QELRRVLDyVATRKHAL--RNRALITISMYSGMRCGEISNLlysDVIDAEGKVRneiRLRAEDTKTKEARTVFVSEKLQK 117
Cdd:cd01195     3 EEARQRLD-AADRHTAKgkRDEALVRLLLDNALRRSEAVAL---DVEDLEKEHR---RLRILGKGKKQREVVTLPPTTRE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440 118 ELQQYAKVYKPKDVNVKFIYSQKENSEGFSPNTLCQLYFNIYKGAGL-QNCSSHSGRRTFATEIANKGVS-IRVLQKLLG 195
Cdd:cd01195    76 ALAAWLAARGEAEGPLFVSLDRASRGRRLSPQAVYRIVRRLAERIGLgKRLSPHGLRHSAITLALDAGAGlIRKVQDFSR 155

                         170
                  ....*....|....*
gi 2171443440 196 HKNIQTTSIYVDAND 210
Cdd:cd01195   156 HADLRTLQVYDDQRD 170
PRK15417 PRK15417
integron integrase;
168-205 2.99e-04

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 40.80  E-value: 2.99e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2171443440 168 SSHSGRRTFATEIANKGVSIRVLQKLLGHKNIQTTSIY 205
Cdd:PRK15417  275 TPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIY 312
PRK09871 PRK09871
tyrosine recombinase; Provisional
 57-209 3.03e-04

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 40.35  E-value: 3.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2171443440  57 RNRALITISMYSGMRCGEISNLLYSDVIDAEGKVrnEIRLRAEDTKTKEARTVFVSEKLQKELQQYAKVYKPKDVNVKFI 136
Cdd:PRK09871   27 RDYCLILLAYRHGMRISELLDLHYQDLDLNEGRI--NIRRLKNGFSTVHPLRFDEREAVERWTQERANWKGADRTDAIFI 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2171443440 137 ysqkenSEGFSPNTLCQLYfNIYKGAGLQNCSS-----HSGRRTFATEIANKGVSIRVLQKLLGHKNIQTTSIYVDAN 209
Cdd:PRK09871  105 ------SRRGSRLSRQQAY-RIIRDAGIEAGTVtqthpHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTASN 175
 
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