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Conserved domains on  [gi|1802756715|ref|WP_161540294|]
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tyrosine-type recombinase/integrase [Rhodothermus marinus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 130-303 8.78e-89

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: 263.08  E-value: 8.78e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 130 LTRVEIEQLLAVLDQDTSQIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTLLGWYLRVQGKGHTAKDQQVPLDPPVVE 209
Cdd:cd01194     1 LTLEQARQLLASLPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQGKGKTSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 210 ALQAYLNTRVPLHPSEPLFVSHGHRSEGQRLNTRSVRSRIKQHLEAAGITRRGVTPHSLTHTAALIWLNQGMSIEEVQRR 289
Cdd:cd01194    81 ALQAYLKARGKLDFEEPLFTSLSNNSKGQRLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQL 160

                         170
                  ....*....|....
gi 1802756715 290 MRHGTLETTMIYYR 303
Cdd:cd01194   161 LRHSDPNTTMIYAH 174
Phage_int_SAM_5 super family cl44621
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 27-117 3.07e-08

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


The actual alignment was detected with superfamily member pfam13102:

Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 50.68  E-value: 3.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  27 RDFQQEYLKNKSPETVGTYRRALHEFERWfaTQRGQFRFRVAD---VQRYKQYLMREKKLHQVSVSTYLTALRRFCQYLV 103
Cdd:pfam13102   7 KEYIEELKKKGSKGTARNYKSTLKHLKKF--LKKKDITFEEITvdfLEKFEEYLKKKKGLSENTISKYFRTLRAVLNKAI 84

                          90
                  ....*....|....
gi 1802756715 104 DIGLLSENPARTVK 117
Cdd:pfam13102  85 KEGIIKKNPYPKYK 98
 
Name Accession Description Interval E-value
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 130-303 8.78e-89

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: 263.08  E-value: 8.78e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 130 LTRVEIEQLLAVLDQDTSQIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTLLGWYLRVQGKGHTAKDQQVPLDPPVVE 209
Cdd:cd01194     1 LTLEQARQLLASLPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQGKGKTSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 210 ALQAYLNTRVPLHPSEPLFVSHGHRSEGQRLNTRSVRSRIKQHLEAAGITRRGVTPHSLTHTAALIWLNQGMSIEEVQRR 289
Cdd:cd01194    81 ALQAYLKARGKLDFEEPLFTSLSNNSKGQRLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQL 160

                         170
                  ....*....|....
gi 1802756715 290 MRHGTLETTMIYYR 303
Cdd:cd01194   161 LRHSDPNTTMIYAH 174
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
22-303 1.49e-59

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 192.52  E-value: 1.49e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  22 LQRRLRDFQQEYL--KNKSPETVGTYRRALHEFERWFATQRGQF--RFRVADVQRYKQYLmREKKLHQVSVSTYLTALRR 97
Cdd:COG4974     3 LADLLEAFLEELKreKGLSPNTIKAYRRDLRRFLRFLEELGKIPlaEITPEDIRAYLNYL-RERGLSPSTINRYLAALRS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  98 FCQYLVDIGLLSENPARTVKGNRRPSSHSRsVLTRVEIEQLLAVLDQDTsQIGLRDRAIVHMMLFAGLSEVEIVRADVRD 177
Cdd:COG4974    82 FFRYAVREGLLEDNPAAKVKLPKKPRKLPR-VLTEEEIEALLEALDTET-PEGLRDRALLLLLYATGLRVSELLGLKWSD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 178 LDqtLLGWYLRV-QGKGhtAKDQQVPLDPPVVEALQAYLNTRVPlHPSEPLFVSHghrsEGQRLNTRSVRSRIKQHLEAA 256
Cdd:COG4974   160 ID--LDRGTIRVrRGKG--GKERTVPLSPEALEALREYLEERRP-RDSDYLFPTR----RGRPLSRRAIRKILKRLAKRA 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1802756715 257 GITRRgVTPHSLTHTAALIWLNQGMSIEEVQRRMRHGTLETTMIYYR 303
Cdd:COG4974   231 GIPKR-VTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTH 276
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 20-301 9.35e-44

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 151.85  E-value: 9.35e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  20 NELQRRLRDFQqEYL---KNKSPETVGTYRRALHEFERwFATQRGQFRFRVADVQRYKQYLMREKK--LHQVSVSTYLTA 94
Cdd:PRK00236    4 ADLPAALEAFL-EYLrveRGLSPHTLRAYRRDLRAFLA-FLEEHGISSLQDLDAADLRSFLARRRRqgLSARSLARRLSA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  95 LRRFCQYLVDIGLLSENPARTVKGNRRPSSHSRsVLTRVEIEQLLAVLDQDTsQIGLRDRAIVHMMLFAGLSEVEIVRAD 174
Cdd:PRK00236   82 LRSFYRWLVRRGLLKANPAAGLRAPKIPKRLPK-PLDVDQAKRLLDAIDEDD-PLALRDRAILELLYGSGLRLSELVGLD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 175 VRDLDqtLLGWYLRVQGKGhtAKDQQVPLDPPVVEALQAYLNTR-VPLHPSEPLFVShghrSEGQRLNTRSVRSRIKQHL 253
Cdd:PRK00236  160 IDDLD--LASGTLRVLGKG--NKERTVPLGRAAREALEAYLALRpLFLPDDDALFLG----ARGGRLSPRVVQRRVKKLG 231

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1802756715 254 EAAGITRRgVTPHSLTHTAALIWLNQGMSIEEVQRRMRHGTLETTMIY 301
Cdd:PRK00236  232 KKAGLPSH-ITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIY 278
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 129-305 1.06e-21

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: 89.69  E-value: 1.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 129 VLTRVEIEQLLAVLDqdTSQIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDqtLLGWYLRV-QGKGhtAKDQQVPLDPPV 207
Cdd:pfam00589   1 RLTEDEVERLLDAAE--TGPLSIRDKALLELLYATGLRISELCSLRWSDID--FENGVIRVhRGKG--NKERTVPLSDAA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 208 VEALQAYLNTRVPLHP-SEPLFVSHghrsEGQRLNTRSVRSRIKQHLEAAGITRRgVTPHSLTHTAALIWLNQGMSIEEV 286
Cdd:pfam00589  75 LELLKEWLSKRLLEAPkSDYLFASK----RGKPLSRQTVRKIFKRAGKEAGLELP-LHPHMLRHSFATHLLEAGVDLRVV 149

                         170
                  ....*....|....*....
gi 1802756715 287 QRRMRHGTLETTMIYYRKQ 305
Cdd:pfam00589 150 QKLLGHSSISTTQIYTHVA 168
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 27-117 3.07e-08

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 50.68  E-value: 3.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  27 RDFQQEYLKNKSPETVGTYRRALHEFERWfaTQRGQFRFRVAD---VQRYKQYLMREKKLHQVSVSTYLTALRRFCQYLV 103
Cdd:pfam13102   7 KEYIEELKKKGSKGTARNYKSTLKHLKKF--LKKKDITFEEITvdfLEKFEEYLKKKKGLSENTISKYFRTLRAVLNKAI 84

                          90
                  ....*....|....
gi 1802756715 104 DIGLLSENPARTVK 117
Cdd:pfam13102  85 KEGIIKKNPYPKYK 98
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 68-301 1.76e-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: 52.01  E-value: 1.76e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  68 ADVQRYKQYLMREKKLHQVSVSTYLTALRRFCQYLVDIGL-LSENPARTVKGNRRPSshsrsVLTRVEIEQLLAVLDQDT 146
Cdd:TIGR02249  44 TEVEAFLSDLAVDGKVAASTQNQALNALLFLYKEILKTPLsLMERFVRAKRPRKLPV-----VLTREEVRRLLEHLEGKY 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 147 sqiglrdRAIVHMMLFAGLSEVEIVRADVRDLDQTLLGWYLRvQGKGhtAKDQQVPLDPPVVEALQAYLNTRVPLH---- 222
Cdd:TIGR02249 119 -------RLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIR-QGKG--GKDRTVTLPKELIPPLREQIELARAYHeadl 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 223 -----------------PSEP-------LFVSHGH----RSEGQR---LNTRSVRSRIKQHLEAAGITRRgVTPHSLTHT 271
Cdd:TIGR02249 189 aegyggvylphalarkyPNAPkewgwqyLFPSHRLsrdpESGVIRrhhINETTIQRAVRRAVERAGIEKP-VTCHTLRHS 267

                         250       260       270
                  ....*....|....*....|....*....|
gi 1802756715 272 AALIWLNQGMSIEEVQRRMRHGTLETTMIY 301
Cdd:TIGR02249 268 FATHLLESGADIRTVQELLGHSDVKTTQIY 297
 
Name Accession Description Interval E-value
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 130-303 8.78e-89

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: 263.08  E-value: 8.78e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 130 LTRVEIEQLLAVLDQDTSQIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTLLGWYLRVQGKGHTAKDQQVPLDPPVVE 209
Cdd:cd01194     1 LTLEQARQLLASLPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQGKGKTSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 210 ALQAYLNTRVPLHPSEPLFVSHGHRSEGQRLNTRSVRSRIKQHLEAAGITRRGVTPHSLTHTAALIWLNQGMSIEEVQRR 289
Cdd:cd01194    81 ALQAYLKARGKLDFEEPLFTSLSNNSKGQRLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQL 160

                         170
                  ....*....|....
gi 1802756715 290 MRHGTLETTMIYYR 303
Cdd:cd01194   161 LRHSDPNTTMIYAH 174
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
22-303 1.49e-59

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 192.52  E-value: 1.49e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  22 LQRRLRDFQQEYL--KNKSPETVGTYRRALHEFERWFATQRGQF--RFRVADVQRYKQYLmREKKLHQVSVSTYLTALRR 97
Cdd:COG4974     3 LADLLEAFLEELKreKGLSPNTIKAYRRDLRRFLRFLEELGKIPlaEITPEDIRAYLNYL-RERGLSPSTINRYLAALRS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  98 FCQYLVDIGLLSENPARTVKGNRRPSSHSRsVLTRVEIEQLLAVLDQDTsQIGLRDRAIVHMMLFAGLSEVEIVRADVRD 177
Cdd:COG4974    82 FFRYAVREGLLEDNPAAKVKLPKKPRKLPR-VLTEEEIEALLEALDTET-PEGLRDRALLLLLYATGLRVSELLGLKWSD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 178 LDqtLLGWYLRV-QGKGhtAKDQQVPLDPPVVEALQAYLNTRVPlHPSEPLFVSHghrsEGQRLNTRSVRSRIKQHLEAA 256
Cdd:COG4974   160 ID--LDRGTIRVrRGKG--GKERTVPLSPEALEALREYLEERRP-RDSDYLFPTR----RGRPLSRRAIRKILKRLAKRA 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1802756715 257 GITRRgVTPHSLTHTAALIWLNQGMSIEEVQRRMRHGTLETTMIYYR 303
Cdd:COG4974   231 GIPKR-VTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTH 276
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
23-301 7.99e-57

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 185.17  E-value: 7.99e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  23 QRRLRDFQQEYL-----KNKSPETVGTYRRALHEFERWFATQRGQFR-FRVADVQRYKQYLmREKKLHQVSVSTYLTALR 96
Cdd:COG4973     1 KLTLAEALEAYLehlreRRLSPKTLEAYRRDLRRLIPLLGDADLPLEeLTPADVRRFLARL-HRRGLSPRTLNRRLSALR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  97 RFCQYLVDIGLLSENPARTVKGNRRPSSHSRsVLTRVEIEQLLAVLDQDTsqIGLRDRAIVHMMLFAGLSEVEIVRADVR 176
Cdd:COG4973    80 SFFNWAVREGLLEANPAAGVKAPKAPRKLPR-ALTVDELAQLLDALADDP--LAVRDRAIVELLYSTGLRLGELVGLDWE 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 177 DLDqtLLGWYLRVQGKGHtaKDQQVPLDPPVVEALQAYLNTR--VPLHPSEPLFVShghrSEGQRLNTRSVRSRIKQHLE 254
Cdd:COG4973   157 DVD--LDAGEVRVRGKTG--KSRTVPLGPKALAALREWLAVRpeLAAPDEGALFPS----RRGTRLSPRNVQKRLRRLAK 228

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1802756715 255 AAGITRRgVTPHSLTHTAALIWLNQGMSIEEVQRRMRHGTLETTMIY 301
Cdd:COG4973   229 KAGLPKH-VHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIY 274
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 20-301 9.35e-44

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 151.85  E-value: 9.35e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  20 NELQRRLRDFQqEYL---KNKSPETVGTYRRALHEFERwFATQRGQFRFRVADVQRYKQYLMREKK--LHQVSVSTYLTA 94
Cdd:PRK00236    4 ADLPAALEAFL-EYLrveRGLSPHTLRAYRRDLRAFLA-FLEEHGISSLQDLDAADLRSFLARRRRqgLSARSLARRLSA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  95 LRRFCQYLVDIGLLSENPARTVKGNRRPSSHSRsVLTRVEIEQLLAVLDQDTsQIGLRDRAIVHMMLFAGLSEVEIVRAD 174
Cdd:PRK00236   82 LRSFYRWLVRRGLLKANPAAGLRAPKIPKRLPK-PLDVDQAKRLLDAIDEDD-PLALRDRAILELLYGSGLRLSELVGLD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 175 VRDLDqtLLGWYLRVQGKGhtAKDQQVPLDPPVVEALQAYLNTR-VPLHPSEPLFVShghrSEGQRLNTRSVRSRIKQHL 253
Cdd:PRK00236  160 IDDLD--LASGTLRVLGKG--NKERTVPLGRAAREALEAYLALRpLFLPDDDALFLG----ARGGRLSPRVVQRRVKKLG 231

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1802756715 254 EAAGITRRgVTPHSLTHTAALIWLNQGMSIEEVQRRMRHGTLETTMIY 301
Cdd:PRK00236  232 KKAGLPSH-ITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIY 278
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 134-301 2.00e-31

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: 115.69  E-value: 2.00e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 134 EIEQLLAVLDQDTsQIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDqtLLGWYLRVQGKGhtAKDQQVPLDPPVVEALQA 213
Cdd:cd00798     3 EVERLLDAPDTDT-PLGLRDRAILELLYASGLRVSELVGLDLSDVD--LDEGLVRVTGKG--NKERLVPFGSYAVEALEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 214 YLNTRVPL----HPSEPLFVSHGhrseGQRLNTRSVRSRIKQHLEAAGITRRgVTPHSLTHTAALIWLNQGMSIEEVQRR 289
Cdd:cd00798    78 YLEERRPLllkkKPPDALFLNKR----GKRLSRRGVWRILKKYAERAGLPKH-VSPHTLRHSFATHLLEGGADLRVVQEL 152

                         170
                  ....*....|..
gi 1802756715 290 MRHGTLETTMIY 301
Cdd:cd00798   153 LGHASLSTTQIY 164
xerD PRK00283
tyrosine recombinase;
38-301 1.07e-29

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 114.52  E-value: 1.07e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  38 SPETVGTYRRALHEFERWFATQRGQFRF-RVADVQRYKQYLmREKKLHQVSVSTYLTALRRFCQYLVDIGLLSENPARTV 116
Cdd:PRK00283   23 AENTLSSYRRDLELFAEWLAARGLSLAEaTRDDLQAFLAEL-AEGGYKATSSARRLSALRRFFQFLLREGLREDDPSALL 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 117 ----KGNRRPsshsrSVLTRVEIEQLLAVLDQDTSqIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTllGWYLRVQGK 192
Cdd:PRK00283  102 dspkLPRRLP-----KTLSEAQVEALLDAPDIDTP-LGLRDRAMLELLYATGLRVSELVGLTLDDVSLR--QGVVRVTGK 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 193 GhtAKDQQVPLDPPVVEALQAYLNTRVPL----HPSEPLFVSHghrsEGQRLNTRSVRSRIKQHLEAAGITRRGVTPHSL 268
Cdd:PRK00283  174 G--NKERLVPLGEEAVYAIERYLERGRPAllngRSSDALFPSA----RGGQLTRQTFWHRIKHYAKRAGIDPKKLSPHVL 247

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1802756715 269 THTAALIWLNQGMSIEEVQRRMRHGTLETTMIY 301
Cdd:PRK00283  248 RHAFATHLLNHGADLRVVQELLGHSDISTTQIY 280
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 134-301 1.77e-27

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: 105.25  E-value: 1.77e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 134 EIEQLLAVLDQDTsQIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDqtLLGWYLRVQGKGHTA-KDQQVPLDPPVVEALQ 212
Cdd:cd00397     1 ELEKLLDAIDEDK-KIDLRDRAILLLLLETGLRISELLALKVKDID--LDNGTIRVRGKKTKGgKERTVPLPKELAEELK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 213 AYLNTRVPLHPSEpLFVSHGHRSEGQRLNTRSVRSRIKQHLEAAGITR-RGVTPHSLTHTAALIWLNQGMSIEEVQRRMR 291
Cdd:cd00397    78 EYLKERRDKRGPL-LKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAgRKITPHSLRHTFATNLLENGVDIKVVQKLLG 156

                         170
                  ....*....|
gi 1802756715 292 HGTLETTMIY 301
Cdd:cd00397   157 HSSISTTQRY 166
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 134-301 9.69e-26

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: 100.78  E-value: 9.69e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 134 EIEQLLAVLDQDTSqIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDqtllgW---YLRVQGKGhTAKDQQVPLDPPVVEA 210
Cdd:cd01188     4 EVRRLLAAIDRLTP-VGLRDYAILLLLARLGLRAGDVAGLRLDDID-----WrsgTITVRQKK-TGRPVELPLTEPVGEA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 211 LQAYLNTRVPLHPSEPLFVSHGHRSEGQRlNTRSVRSRIKQHLEAAGITRRGVTPHSLTHTAALIWLNQGMSIEEVQRRM 290
Cdd:cd01188    77 LADYLRDGRPRTDSREVFLRARAPYRPLS-STSQISSIVRRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLL 155

                         170
                  ....*....|.
gi 1802756715 291 RHGTLETTMIY 301
Cdd:cd01188   156 GHRSIETTAIY 166
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 131-306 3.99e-22

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: 90.99  E-value: 3.99e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 131 TRVEIEQLLAVLDQDTSQiGLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTLLgwYLRVQGKGHTAKdQQVPLDPPVVEA 210
Cdd:cd01195     1 SREEARQRLDAADRHTAK-GKRDEALVRLLLDNALRRSEAVALDVEDLEKEHR--RLRILGKGKKQR-EVVTLPPTTREA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 211 LQAYLNTRVPlhPSEPLFVSHGHRSEGQRLNTRSVRSRIKQHLEAAGITRRgVTPHSLTHTAALIWLNQGMS-IEEVQRR 289
Cdd:cd01195    77 LAAWLAARGE--AEGPLFVSLDRASRGRRLSPQAVYRIVRRLAERIGLGKR-LSPHGLRHSAITLALDAGAGlIRKVQDF 153

                         170
                  ....*....|....*..
gi 1802756715 290 MRHGTLETTMIYYRKQG 306
Cdd:cd01195   154 SRHADLRTLQVYDDQRD 170
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 1-303 9.40e-22

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 94.04  E-value: 9.40e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715   1 MAEREAKDGRAevglkLTLNELQRRLRDFQQEYLK-----NKSPETVGTYRRALHEFERWfATQRGQFRfrVADV----- 70
Cdd:PRK01287    1 MANRKPRKGSL-----LTVAHDPKTLRQLLERFLAwlqerNWSERTLKVYTEHLYPFILW-CEERGLYY--AADVtlpvl 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  71 QRYKQYLMREKK-----LHQVSVSTYLTALRRFCQYLVDIGLLSENPARTVKGNRRPSSHSRSVLTRVEIEQLLAVLDQD 145
Cdd:PRK01287   73 ERYQRYLYGYRKangepLSTRTQRTQLSPLRVWFRWLLKRHHILYNPAEDLELPKEEKRLPRQILSEAETEQVLASPDLT 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 146 TSQiGLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTlLGWYLRVQGKGhtAKDQQVPLDPPVVEALQAYLNTRVP----L 221
Cdd:PRK01287  153 TLQ-GLRDRALLELLWSTGIRRGELARLDLYDVDAS-RGVVTVRQGKG--NKDRVVPVGERALAWLQRYLQDVRPqlavR 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 222 HPSEPLFVSHghrsEGQRLNTRSVRSRIKQHLEAAGITRRGVTpHSLTHTAALIWLNQGMSIEEVQRRMRHGTLETTMIY 301
Cdd:PRK01287  229 PDSGALFVAM----DGDGLARNTLTNMVGRYIRAAGIEKAGAC-HLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303


                  ..
gi 1802756715 302 YR 303
Cdd:PRK01287  304 TR 305
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 129-305 1.06e-21

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: 89.69  E-value: 1.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 129 VLTRVEIEQLLAVLDqdTSQIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDqtLLGWYLRV-QGKGhtAKDQQVPLDPPV 207
Cdd:pfam00589   1 RLTEDEVERLLDAAE--TGPLSIRDKALLELLYATGLRISELCSLRWSDID--FENGVIRVhRGKG--NKERTVPLSDAA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 208 VEALQAYLNTRVPLHP-SEPLFVSHghrsEGQRLNTRSVRSRIKQHLEAAGITRRgVTPHSLTHTAALIWLNQGMSIEEV 286
Cdd:pfam00589  75 LELLKEWLSKRLLEAPkSDYLFASK----RGKPLSRQTVRKIFKRAGKEAGLELP-LHPHMLRHSFATHLLEAGVDLRVV 149

                         170
                  ....*....|....*....
gi 1802756715 287 QRRMRHGTLETTMIYYRKQ 305
Cdd:pfam00589 150 QKLLGHSSISTTQIYTHVA 168
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 130-301 7.59e-19

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: 82.71  E-value: 7.59e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 130 LTRVEIEQLLAVLDQDTSQiGLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTLlGWYLRVQGKGHtaKDQQVPLDPPVVE 209
Cdd:cd01182     1 LTREEMKALLAAPDRNTSL-GRRDHALLLLLYDTGARVQELADLTIRDLRLDD-PATVRLHGKGR--KERTVPLWKETVA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 210 ALQAYL---NTRVPLHPSEPLFVSHGhrseGQRLNTRSVRSRIKQHLEAAGIT----RRGVTPHSLTHTAALIWLNQGMS 282
Cdd:cd01182    77 ALKAYLqefHLTPDPKQLFPLFPNRR----GQPLTRDGVAYILNKYVALASNRcpslPKRITPHTLRHTKAMHLLQAGVD 152

                         170
                  ....*....|....*....
gi 1802756715 283 IEEVQRRMRHGTLETTMIY 301
Cdd:cd01182   153 LTVIRDWLGHESVETTQIY 171
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 129-301 3.68e-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: 72.31  E-value: 3.68e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 129 VLTRVEIEQLL-AVLDqdtsqigLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTLlGWyLRV-QGKGHtaKDQQVPLDPP 206
Cdd:cd01193     5 VLSPDEVRRILgALTE-------LRHRLILSLLYGAGLRISELLRLRVKDIDFER-GV-IRVrQGKGG--KDRVVPLPEK 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 207 VVEALQAYLNTRVPLHPSEPLFVSHGHR--SEGQR----LNTRSVRSRIKQHLEAAGITRRgVTPHSLTHTAALIWLNQG 280
Cdd:cd01193    74 LLEPLRRYLKSARPKEELDPAEGRAGVLdpRTGVErrhhISETTVQRALKKAVEQAGITKR-VTPHTLRHSFATHLLEAG 152

                         170       180
                  ....*....|....*....|.
gi 1802756715 281 MSIEEVQRRMRHGTLETTMIY 301
Cdd:cd01193   153 TDIRTIQELLGHSDLSTTMIY 173
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 135-303 5.08e-14

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: 69.25  E-value: 5.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 135 IEQLLAVLDqDTSQIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTLLGWYL--------RVQGKGHTAKDQQVPLDPP 206
Cdd:cd00799     1 LKAMLATLD-DTTLRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVDGGLLirlrrsktDQDGEGEIKALPYGPETCP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 207 VVeALQAYLNTRvpLHPSEPLFVS---HGHRSeGQRLNTRSVRSRIKQHLEAAGITRRGVTPHSLTHTAALIWLNQGMSI 283
Cdd:cd00799    80 VR-ALRAWLEAA--GIPSGPLFRRirrGGSVG-TTRLSDRSVARIVKRRAALAGLDPGDFSGHSLRRGFATEAARAGASL 155

                         170       180
                  ....*....|....*....|
gi 1802756715 284 EEVQRRMRHGTLETTMIYYR 303
Cdd:cd00799   156 PEIMAQGGHKSVATVMRYIR 175
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 130-303 9.50e-12

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: 62.34  E-value: 9.50e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 130 LTRVEIEQLLAVLDQDTSQiglRDRAIVHMMLFAGLSEVEIVRADVRDLDqtlLGWYLRVQGKGHTAKDQQVPLDPPVVE 209
Cdd:cd00796     5 LTEDEEARLLAALEESTNP---HLRLIVLLALYTGARRGEILSLRWDDID---LEVGLIVLPETKNGKPRTVPLSDEAIA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 210 ALQAYLntrvPLHPSEPLFVSHGhrseGQRLNTRSVRSRIKQHLEAAGITrrGVTPHSLTHTAALIWLNQGMSIEEVQRR 289
Cdd:cd00796    79 ILKELK----RKRGKDGFFVDGR----FFGIPIASLRRAFKKARKRAGLE--DLRFHDLRHTFASRLVQAGVPIKTVAKI 148

                         170
                  ....*....|....
gi 1802756715 290 MRHGTLETTMIYYR 303
Cdd:cd00796   149 LGHSSIKMTMRYAH 162
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 134-301 2.19e-11

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: 61.13  E-value: 2.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 134 EIEQLLAVLDQDTSQIGLRDRAIVhMMLFAGLSEVEIVRADVRDLDQTLLGWYLRV-QGKghTAKDQQVPLDPPVVEALQ 212
Cdd:cd01185     2 ELKRLMALELSDTSRLELVRDMFL-FSCYTGLRFSDLKNLTWKNIVEASGRTWIRYrRKK--TGKPVTVPLLPVAREILE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 213 AYLNTRvplhPSEPLFvshghrsegQRLNTRSVRSRIKQHLEAAGITRRgVTPHSLTHTAALIWLNQGMSIEEVQRRMRH 292
Cdd:cd01185    79 KYKDDR----SEGKLF---------PVLSNQKINRYLKEIAKIAGIDKH-LTFHVARHTFATLLLLKGVDIETISKLLGH 144


                  ....*....
gi 1802756715 293 GTLETTMIY 301
Cdd:cd01185   145 SSIKTTQIY 153
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 19-301 1.08e-10

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 61.86  E-value: 1.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  19 LNELQRRLRDFQQEYLKNK-----SPETVGTYrraLHEFERWF----------ATQRGQF------RFRVADVQRYKQYL 77
Cdd:PRK05084   10 IDKLKAKMPWYVQEYYQSKlatpySPTTLYEY---LTEYRRFFnwliseglsdASKIKDIplstleNLTKKDVEAFILYL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  78 MREKKLH---------QVSVSTYLTALRRFCQYLVDIG-------LLSENPARTVKGNR-RPSSHSRS------VLTRVE 134
Cdd:PRK05084   87 RERPLLNghstkkgnsQTTINRTLSALKSLFKYLTEEAenedgepYFYRNVMKKIELKKkKETLAARAhnlkqkLFLGDE 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 135 IEQLLAVLDQDTSQI------------GLRDRAIVHMMLFAGLSEVEIVRADVRDLDqtLLGWYLRVQGKGhtAKDQQVP 202
Cdd:PRK05084  167 DYEFLDFIDNEYEQKlsnralssfkknKERDLAIIALILGSGLRVSELVNLDLSDLN--LKQMTIDVTRKG--GKRDSVN 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 203 LDPPVVEALQAYLNTRV----PLHPSEPLFVSHGHrSEGQRLNTRSVRSRIKQHLEAAGITrrgVTPHSLTHTAALIWLN 278
Cdd:PRK05084  243 IAPFALPYLEEYLKIRAsrykAEKQEKALFLTKYR-GKPNRISARAIEKMVAKYSEAFGVR---LTPHKLRHTLATRLYD 318

                         330       340
                  ....*....|....*....|...
gi 1802756715 279 QGMSIEEVQRRMRHGTLETTMIY 301
Cdd:PRK05084  319 ATKDQVLVADQLGHTSTETTDLY 341
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 134-311 3.51e-10

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: 58.26  E-value: 3.51e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 134 EIEQLLAVLDqDTSQIGLRDRAIVHMML--FAGLSEVEIVR-ADVRDLDQTLlgwYLRVQGKGhtAKDQQVPLDPPVVEA 210
Cdd:cd01196     4 EARRLLESID-STHPVGLRDRALIALMVysFARIGAVLAMRvEDVYDQGRRL---WVRLAEKG--GKQHEMPCHHDLEEY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 211 LQAYLN-TRVPLHPSEPLFVSHGHRSE---GQRLNTRSVRSRIKQHLEAAGITRRgVTPHSLTHTAALIWLNQGMSIEEV 286
Cdd:cd01196    78 LRAYLEaAEIEEDPKGPLFRTTRGGTRkltHNPLTQANAYRMVRRRAIAADIPTA-IGNHSFRATGITAYLKNGGTLEDA 156

                         170       180
                  ....*....|....*....|....*
gi 1802756715 287 QRRMRHGTLETTMIYYRKQGLLNRD 311
Cdd:cd01196   157 QNMANHASTRTTQLYDRRSDKITLD 181
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 134-302 4.67e-09

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: 54.10  E-value: 4.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 134 EIEQLLAVLDQDtsqiGLRDRAIVHMMLFAGL--SE---------------VEIVRAdvrdLDQTLLGWYLRVQGKGHTA 196
Cdd:cd01189     3 ELKKLLEALKKR----GDRYYLLFLLALLTGLrrGEllaltwsdidfengtIRINRT----LVRKKKGGYVIKPPKTKSS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 197 KDQqVPLDPPVVEALQAYLntrvplhpseplfvshghrsegqrlntrsvrsRIKQHLEAAGItrRGVTPHSLTHTAALIW 276
Cdd:cd01189    75 IRT-IPLPDELIELLKELK--------------------------------AFKKLLKKAGL--PRITPHDLRHTFASLL 119

                         170       180
                  ....*....|....*....|....*.
gi 1802756715 277 LNQGMSIEEVQRRMRHGTLETTMIYY 302
Cdd:cd01189   120 LEAGVPLKVIAERLGHSDISTTLDVY 145
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 80-292 4.73e-09

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 56.97  E-value: 4.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  80 EKKLHQVSVSTYLTALRRFCQYLVDIGLLSENPARTVKGN-RRPSSHSRSVLTRVEIEQLLAVLDQdtSQIGLRDRAIVH 158
Cdd:COG0582   155 EARGAPETARRVRQRLRQVFRYAVARGLIERNPAADLKGAlPKPKVKHHPALTPEELPELLRALDA--YRGSPVTRLALR 232

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 159 MMLFAGLSEVEIVRA---DVrDLDQTLlgWYLRVQG-KghTAKDQQVPLDPPVVEALQAYLntrvPLHPSEPlFVSHGHR 234
Cdd:COG0582   233 LLLLTGVRPGELRGArwsEI-DLEAAL--WTIPAERmK--TRRPHIVPLSRQALEILKELK----PLTGDSE-YVFPSRR 302

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1802756715 235 SEGQRLNTRSVRsrikQHLEAAGITRrgVTPHSLTHTAALIWLNQGMSIEEVQRRMRH 292
Cdd:COG0582   303 GPKKPMSENTLN----KALRRMGYGR--FTPHGFRHTASTLLNEAGFPPDVIERQLAH 354
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 130-273 2.25e-08

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: 53.46  E-value: 2.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 130 LTRVEIEQLLAVLDQDTSQIGLRdrAIVHMMLF-----AGLSEVEIVRADVRDLDqtLLGWYLRV-QGKGHtaKDQQVPL 203
Cdd:cd00797     1 YTDAEIRRLLAAADQLPPESPLR--PLTYATLFgllyaTGLRVGEALRLRLEDVD--LDSGILTIrQTKFG--KSRLVPL 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1802756715 204 DPPVVEALQAYLNTR---VPLHPSEPLFVSHGhrseGQRLNTRSVRSRIKQHLEAAGIT----RRGVTPHSLTHTAA 273
Cdd:cd00797    75 HPSTVGALRDYLARRdrlLPSPSSSYFFVSQQ----GGRLTGGGVYRVFRRLLRRIGLRgagdGRGPRLHDLRHTFA 147
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 27-117 3.07e-08

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 50.68  E-value: 3.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  27 RDFQQEYLKNKSPETVGTYRRALHEFERWfaTQRGQFRFRVAD---VQRYKQYLMREKKLHQVSVSTYLTALRRFCQYLV 103
Cdd:pfam13102   7 KEYIEELKKKGSKGTARNYKSTLKHLKKF--LKKKDITFEEITvdfLEKFEEYLKKKKGLSENTISKYFRTLRAVLNKAI 84

                          90
                  ....*....|....
gi 1802756715 104 DIGLLSENPARTVK 117
Cdd:pfam13102  85 KEGIIKKNPYPKYK 98
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 68-301 1.76e-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: 52.01  E-value: 1.76e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  68 ADVQRYKQYLMREKKLHQVSVSTYLTALRRFCQYLVDIGL-LSENPARTVKGNRRPSshsrsVLTRVEIEQLLAVLDQDT 146
Cdd:TIGR02249  44 TEVEAFLSDLAVDGKVAASTQNQALNALLFLYKEILKTPLsLMERFVRAKRPRKLPV-----VLTREEVRRLLEHLEGKY 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 147 sqiglrdRAIVHMMLFAGLSEVEIVRADVRDLDQTLLGWYLRvQGKGhtAKDQQVPLDPPVVEALQAYLNTRVPLH---- 222
Cdd:TIGR02249 119 -------RLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIR-QGKG--GKDRTVTLPKELIPPLREQIELARAYHeadl 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 223 -----------------PSEP-------LFVSHGH----RSEGQR---LNTRSVRSRIKQHLEAAGITRRgVTPHSLTHT 271
Cdd:TIGR02249 189 aegyggvylphalarkyPNAPkewgwqyLFPSHRLsrdpESGVIRrhhINETTIQRAVRRAVERAGIEKP-VTCHTLRHS 267

                         250       260       270
                  ....*....|....*....|....*....|
gi 1802756715 272 AALIWLNQGMSIEEVQRRMRHGTLETTMIY 301
Cdd:TIGR02249 268 FATHLLESGADIRTVQELLGHSDVKTTQIY 297
PRK09870 PRK09870
tyrosine recombinase; Provisional
 127-301 6.91e-06

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 46.08  E-value: 6.91e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 127 RSVLTRVEIEQLLAVLDqdTSQIGLRDRAIVHMMLFAGLSEVEIVRADVRDLDQTLLGWYLRVQGKGHTAKDqqvPLDPP 206
Cdd:PRK09870   10 RNFLTHSEIESLLKAAN--TGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTH---PLLNK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 207 VVEALQAYLNTRV--PLHPSEPLFVSHghrsEGQRLNTRSVRSRIKQHLEAAGITRRgVTPHSLTHTAALIWLNQGMSIE 284
Cdd:PRK09870   85 EIQALKNWLSIRTsyPHAESEWVFLSR----KGNPLSRQQFYHIISTSGGNAGLSLE-IHPHMLRHSCGFALANMGIDTR 159

                         170
                  ....*....|....*..
gi 1802756715 285 EVQRRMRHGTLETTMIY 301
Cdd:PRK09870  160 LIQDYLGHRNIRHTVWY 176
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 224-302 1.61e-05

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: 44.71  E-value: 1.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 224 SEPLFVSHGHRSEGQRLNTRSVRS---RIKQHleaagiTRRGVTPHSLTHTAALIWLNQGMSIEEVQRRMRHGTLETTMI 300
Cdd:cd01186    98 SITVFVNVKGGNQGKAMNYSDVYDlvrRLKKR------TGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTLN 171


                  ..
gi 1802756715 301 YY 302
Cdd:cd01186   172 TY 173
PRK15417 PRK15417
integron integrase;
68-303 6.88e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 43.88  E-value: 6.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715  68 ADVQRYKQYLMREKKlhqVSVSTYLTALRRFCQYLVDIgLLSENPARTVKGNRRPSSHSRSVLTRVEIEQLLAVLDQDts 147
Cdd:PRK15417   59 SEVEAFLSWLANERK---VSVSTHRQALAALLFFYGKV-LCTDLPWLQEIGRPRPSRRLPVVLTPDEVVRILGFLEGE-- 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 148 qiglrDRAIVHMMLFAGLSEVEIVRADVRDLDQTLlGWYLRVQGKGHTAKDQQVP--LDPPVVEAL----------QAYL 215
Cdd:PRK15417  133 -----HRLFAQLLYGTGMRISEGLQLRVKDLDFDH-GTIIVREGKGSKDRALMLPesLAPSLREQLsrarawwlkdQAEG 206

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 216 NTRVPL-------HP----SEP---LFVSHGHRSEGQ-------RLNTRSVRSRIKQHLEAAGITRRGvTPHSLTHTAAL 274
Cdd:PRK15417  207 RSGVALpdalerkYPraghSWPwfwVFAQHTHSTDPRsgvvrrhHMYDQTFQRAFKRAVEQAGITKPA-TPHTLRHSFAT 285

                         250       260
                  ....*....|....*....|....*....
gi 1802756715 275 IWLNQGMSIEEVQRRMRHGTLETTMIYYR 303
Cdd:PRK15417  286 ALLRSGYDIRTVQDLLGHSDVSTTMIYTH 314
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 150-301 8.13e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 42.66  E-value: 8.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802756715 150 GLRDRAIVHMMLFAGLSEVEIVRADVRDLdqtLLGWYLRVQGKgHTAKDQQVPLDPPVVEALQAYLNTRVPLHPSEPLFV 229
Cdd:cd01192    23 NPRNYLLFIVGINTGLRISDLLSLKVEDV---TNKDKLSIKEQ-KTGKQKTFPLNPTLVKALKEYIDDLDLKRNDYLFKS 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1802756715 230 SHGHRseGQRLNTRSVR---SRIKQHLEAAGitrrGVTPHSLTHTAALIWLNQGMSIEEVQRRMRHGTLETTMIY 301
Cdd:cd01192    99 LKQGP--EKPISRKQAYkilKKAADDLGLNY----NIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
32-103 6.21e-04

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 38.01  E-value: 6.21e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1802756715  32 EYL---KNKSPETVGTYRRALHEFERWFA-TQRGQFRFRVADVQRYKQYLmREKKLHQVSVSTYLTALRRFCQYLV 103
Cdd:pfam02899   6 EYLsleRGLSPHTLRAYRRDLLAFLKFLSeGGSSLEQITTSDVRAFLAEL-RAQGLSASSLARRLSALRSFYQFLI 80
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 237-304 6.48e-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: 40.10  E-value: 6.48e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1802756715 237 GQRLNTRSVRSRIKQHLEAAGITRRGVTPHSLTHTAALIWLNQGMSIEEVQRRMRHGTLETTMIYYRK 304
Cdd:cd01191    94 GERITTRGIAQQLKNYARKYGLNPKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRK 161
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
34-107 3.82e-03

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 35.67  E-value: 3.82e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802756715  34 LKNKSPETVGTYRRALHEFERWFaTQRGQFRFRVADVQRYKQYLMREKKLHQVSVSTYLTALRRFCQYLVDIGL 107
Cdd:pfam13495  11 LRGYAERTIKAYLRWIRRFLRFH-DKKHPEELTEEDIEAYLSHLANERNVSASTQNQALNALSFFYRWVLEREL 83
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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