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Conserved domains on  [gi|1174865724|ref|WP_081543171|]
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tyrosine-type recombinase/integrase [Streptococcus pneumoniae]

Protein Classification

Phage_int_SAM_1 and INT_C_like_4 domain-containing protein( domain architecture ID 10315029)

Phage_int_SAM_1 and INT_C_like_4 domain-containing protein

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 ...
 124-296 7.62e-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: 7.62e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 124 LTSRQTKEVLTSIET-STEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTVGENTVLFIQGKGREEKTEYIKISAPVEK 202
Cdd:cd01194     1 LTLEQARQLLASLPIdDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQGKGKTSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 203 ALRTYLKARGFTTEEQPLFTSTSNNSKGKRITTRTVSAVVKNALKNAGYDSNRLTAHSLRHTAITLALLAGRDITEVQQF 282
Cdd:cd01194    81 ALQAYLKARGKLDFEEPLFTSLSNNSKGQRLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQL 160

                         170
                  ....*....|....
gi 1174865724 283 ARHANLNTTMIYNH 296
Cdd:cd01194   161 LRHSDPNTTMIYAH 174
Phage_int_SAM_1 super family cl12235
Phage integrase, N-terminal SAM-like domain;
25-100 3.77e-08

Phage integrase, N-terminal SAM-like domain;


The actual alignment was detected with superfamily member pfam02899:

Pssm-ID: 472283 [Multi-domain]  Cd Length: 83  Bit Score: 49.95  E-value: 3.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  25 FDRFIDYLDA----SPKTVETYKKALRQFFNYLA--LHGIRQPQREDVLAFRDDLKTSGLKPTTVQNYITATRIFFKWTE 98
Cdd:pfam02899   1 IDQFLEYLSLerglSPHTLRAYRRDLLAFLKFLSegGSSLEQITTSDVRAFLAELRAQGLSASSLARRLSALRSFYQFLI 80


                  ..
gi 1174865724  99 QE 100
Cdd:pfam02899  81 RE 82
 
Name Accession Description Interval E-value
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 124-296 7.62e-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: 7.62e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 124 LTSRQTKEVLTSIET-STEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTVGENTVLFIQGKGREEKTEYIKISAPVEK 202
Cdd:cd01194     1 LTLEQARQLLASLPIdDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQGKGKTSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 203 ALRTYLKARGFTTEEQPLFTSTSNNSKGKRITTRTVSAVVKNALKNAGYDSNRLTAHSLRHTAITLALLAGRDITEVQQF 282
Cdd:cd01194    81 ALQAYLKARGKLDFEEPLFTSLSNNSKGQRLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQL 160

                         170
                  ....*....|....
gi 1174865724 283 ARHANLNTTMIYNH 296
Cdd:cd01194   161 LRHSDPNTTMIYAH 174
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
25-302 1.19e-62

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 200.22  E-value: 1.19e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  25 FDRFIDYL----DASPKTVETYKKALRQFFNYLALHGIRQPQ---REDVLAFRDDLKTSGLKPTTVQNYITATRIFFKWT 97
Cdd:COG4974     7 LEAFLEELkrekGLSPNTIKAYRRDLRRFLRFLEELGKIPLAeitPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  98 EQERLYP-NIAEHVKGAKLDKnHKKDYLTSRQTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTvGE 176
Cdd:COG4974    87 VREGLLEdNPAAKVKLPKKPR-KLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDIDL-DR 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 177 NTVLFIQGKGReeKTEYIKISAPVEKALRTYLKARGfTTEEQPLFTstsnNSKGKRITTRTVSAVVKNALKNAGYDSnRL 256
Cdd:COG4974   165 GTIRVRRGKGG--KERTVPLSPEALEALREYLEERR-PRDSDYLFP----TRRGRPLSRRAIRKILKRLAKRAGIPK-RV 236

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1174865724 257 TAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNHALDKAK 302
Cdd:COG4974   237 TPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEEL 282
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 26-301 5.40e-50

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 167.64  E-value: 5.40e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  26 DRFIDYL----DASPKTVETYKKALRQFFNYLALHGIRQPQR---EDVLAFRDDLKTSGLKPTTVQNYITATRIFFKWTE 98
Cdd:PRK00236   11 EAFLEYLrverGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDldaADLRSFLARRRRQGLSARSLARRLSALRSFYRWLV 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  99 QERLYP-NIAEHVKGAKLDKNHKKdYLTSRQTKEVLTSIETSTEEGLRNYAILSLMVTGGLRtieVSRA---NVGDLRTv 174
Cdd:PRK00236   91 RRGLLKaNPAAGLRAPKIPKRLPK-PLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLR---LSELvglDIDDLDL- 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 175 gENTVLFIQGKGReeKTEYIKISAPVEKALRTYLKARG-FTTEEQPLFTStsnnSKGKRITTRTVSAVVKNALKNAGYDS 253
Cdd:PRK00236  166 -ASGTLRVLGKGN--KERTVPLGRAAREALEAYLALRPlFLPDDDALFLG----ARGGRLSPRVVQRRVKKLGKKAGLPS 238

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1174865724 254 NrLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNHaLDKA 301
Cdd:PRK00236  239 H-ITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTH-VDFQ 284
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 123-299 1.47e-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: 89.30  E-value: 1.47e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 123 YLTSRQTKEVLTSIETSTEeGLRNYAILSLMVTGGLRTIEVSRANVGDLRTvgENTVLFI-QGKGREEKTeyIKISAPVE 201
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPL-SIRDKALLELLYATGLRISELCSLRWSDIDF--ENGVIRVhRGKGNKERT--VPLSDAAL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 202 KALRTYLKARGFTTEEQP-LFTSTsnnsKGKRITTRTVSAVVKNALKNAGyDSNRLTAHSLRHTAITLALLAGRDITEVQ 280
Cdd:pfam00589  76 ELLKEWLSKRLLEAPKSDyLFASK----RGKPLSRQTVRKIFKRAGKEAG-LELPLHPHMLRHSFATHLLEAGVDLRVVQ 150

                         170
                  ....*....|....*....
gi 1174865724 281 QFARHANLNTTMIYNHALD 299
Cdd:pfam00589 151 KLLGHSSISTTQIYTHVAD 169
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 23-304 5.10e-11

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: 62.41  E-value: 5.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  23 NTFDRFIDYLDASPKTVETYKKALRQFfnyLALHGIRQPQR---EDVLAFRDDLKTSGLKPTTVQNYITATRIFfkwteq 99
Cdd:TIGR02249   3 DQVREHMRTRHYAKRTEEAYLHWIKRF---IRFHNKRHPSTmgdTEVEAFLSDLAVDGKVAASTQNQALNALLF------ 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 100 erLYPNI-------AEHVKGAKLDKNHKKdYLTSRQTKEVLTSIETsteeglRNYAILSLMVTGGLRTIEVSRANVGDLr 172
Cdd:TIGR02249  74 --LYKEIlktplslMERFVRAKRPRKLPV-VLTREEVRRLLEHLEG------KYRLIAKLLYGSGMRLMECLRLRIQDI- 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 173 TVGENTVLFIQGKGREEKTE------YIKISAPVEKALRTYLK--ARGFTTEEQP------------------LFTStSN 226
Cdd:TIGR02249 144 DFDYGEIRIRQGKGGKDRTVtlpkelIPPLREQIELARAYHEAdlAEGYGGVYLPhalarkypnapkewgwqyLFPS-HR 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 227 NSKGKR--------ITTRTVSAVVKNALKNAGYDSNrLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNHAL 298
Cdd:TIGR02249 223 LSRDPEsgvirrhhINETTIQRAVRRAVERAGIEKP-VTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVL 301


                  ....*.
gi 1174865724 299 DKAKNG 304
Cdd:TIGR02249 302 NRGASG 307
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
25-100 3.77e-08

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 49.95  E-value: 3.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  25 FDRFIDYLDA----SPKTVETYKKALRQFFNYLA--LHGIRQPQREDVLAFRDDLKTSGLKPTTVQNYITATRIFFKWTE 98
Cdd:pfam02899   1 IDQFLEYLSLerglSPHTLRAYRRDLLAFLKFLSegGSSLEQITTSDVRAFLAELRAQGLSASSLARRLSALRSFYQFLI 80


                  ..
gi 1174865724  99 QE 100
Cdd:pfam02899  81 RE 82
 
Name Accession Description Interval E-value
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 124-296 7.62e-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: 7.62e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 124 LTSRQTKEVLTSIET-STEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTVGENTVLFIQGKGREEKTEYIKISAPVEK 202
Cdd:cd01194     1 LTLEQARQLLASLPIdDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQGKGKTSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 203 ALRTYLKARGFTTEEQPLFTSTSNNSKGKRITTRTVSAVVKNALKNAGYDSNRLTAHSLRHTAITLALLAGRDITEVQQF 282
Cdd:cd01194    81 ALQAYLKARGKLDFEEPLFTSLSNNSKGQRLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQL 160

                         170
                  ....*....|....
gi 1174865724 283 ARHANLNTTMIYNH 296
Cdd:cd01194   161 LRHSDPNTTMIYAH 174
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
25-302 1.19e-62

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 200.22  E-value: 1.19e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  25 FDRFIDYL----DASPKTVETYKKALRQFFNYLALHGIRQPQ---REDVLAFRDDLKTSGLKPTTVQNYITATRIFFKWT 97
Cdd:COG4974     7 LEAFLEELkrekGLSPNTIKAYRRDLRRFLRFLEELGKIPLAeitPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  98 EQERLYP-NIAEHVKGAKLDKnHKKDYLTSRQTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTvGE 176
Cdd:COG4974    87 VREGLLEdNPAAKVKLPKKPR-KLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDIDL-DR 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 177 NTVLFIQGKGReeKTEYIKISAPVEKALRTYLKARGfTTEEQPLFTstsnNSKGKRITTRTVSAVVKNALKNAGYDSnRL 256
Cdd:COG4974   165 GTIRVRRGKGG--KERTVPLSPEALEALREYLEERR-PRDSDYLFP----TRRGRPLSRRAIRKILKRLAKRAGIPK-RV 236

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1174865724 257 TAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNHALDKAK 302
Cdd:COG4974   237 TPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEEL 282
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
25-297 1.46e-52

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 173.99  E-value: 1.46e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  25 FDRFIDYL---DASPKTVETYKKALRQFFNYLALHG--IRQPQREDVLAFRDDLKTSGLKPTTVQNYITATRIFFKW-TE 98
Cdd:COG4973     8 LEAYLEHLrerRLSPKTLEAYRRDLRRLIPLLGDADlpLEELTPADVRRFLARLHRRGLSPRTLNRRLSALRSFFNWaVR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  99 QERLYPNIAEHVKGAKLDKNHKKdYLTSRQTKEVLtSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTvgENT 178
Cdd:COG4973    88 EGLLEANPAAGVKAPKAPRKLPR-ALTVDELAQLL-DALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDL--DAG 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 179 VLFIQGKGReeKTEYIKISAPVEKALRTYLKARGFTT--EEQPLFTSTsnnsKGKRITTRTVSAVVKNALKNAGYDSnRL 256
Cdd:COG4973   164 EVRVRGKTG--KSRTVPLGPKALAALREWLAVRPELAapDEGALFPSR----RGTRLSPRNVQKRLRRLAKKAGLPK-HV 236

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1174865724 257 TAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNHA 297
Cdd:COG4973   237 HPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHL 277
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 26-301 5.40e-50

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 167.64  E-value: 5.40e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  26 DRFIDYL----DASPKTVETYKKALRQFFNYLALHGIRQPQR---EDVLAFRDDLKTSGLKPTTVQNYITATRIFFKWTE 98
Cdd:PRK00236   11 EAFLEYLrverGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDldaADLRSFLARRRRQGLSARSLARRLSALRSFYRWLV 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  99 QERLYP-NIAEHVKGAKLDKNHKKdYLTSRQTKEVLTSIETSTEEGLRNYAILSLMVTGGLRtieVSRA---NVGDLRTv 174
Cdd:PRK00236   91 RRGLLKaNPAAGLRAPKIPKRLPK-PLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLR---LSELvglDIDDLDL- 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 175 gENTVLFIQGKGReeKTEYIKISAPVEKALRTYLKARG-FTTEEQPLFTStsnnSKGKRITTRTVSAVVKNALKNAGYDS 253
Cdd:PRK00236  166 -ASGTLRVLGKGN--KERTVPLGRAAREALEAYLALRPlFLPDDDALFLG----ARGGRLSPRVVQRRVKKLGKKAGLPS 238

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1174865724 254 NrLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNHaLDKA 301
Cdd:PRK00236  239 H-ITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTH-VDFQ 284
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 128-297 2.27e-35

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: 126.05  E-value: 2.27e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 128 QTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTvgENTVLFIQGKGREEKtEYIKISAPVEKALRTY 207
Cdd:cd01195     4 EARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEK--EHRRLRILGKGKKQR-EVVTLPPTTREALAAW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 208 LKARGftTEEQPLFTSTSNNSKGKRITTRTVSAVVKNALKNAGYDsNRLTAHSLRHTAITLALLAGRD-ITEVQQFARHA 286
Cdd:cd01195    81 LAARG--EAEGPLFVSLDRASRGRRLSPQAVYRIVRRLAERIGLG-KRLSPHGLRHSAITLALDAGAGlIRKVQDFSRHA 157

                         170
                  ....*....|.
gi 1174865724 287 NLNTTMIYNHA 297
Cdd:cd01195   158 DLRTLQVYDDQ 168
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 128-294 1.21e-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: 113.34  E-value: 1.21e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 128 QTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTvGENTVLFIQGKGREEKTEYIKISAPVEKALRTY 207
Cdd:cd00397     1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDL-DNGTIRVRGKKTKGGKERTVPLPKELAEELKEY 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 208 LKARGFTTEEQpLFTSTSNNSKGKRITTRTVSAVVKNALKNAGYDSN-RLTAHSLRHTAITLALLAGRDITEVQQFARHA 286
Cdd:cd00397    80 LKERRDKRGPL-LKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGrKITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158


                  ....*...
gi 1174865724 287 NLNTTMIY 294
Cdd:cd00397   159 SISTTQRY 166
xerD PRK00283
tyrosine recombinase;
26-296 6.45e-30

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 114.90  E-value: 6.45e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  26 DRFIDYL----DASPKTVETYKKALRQFFNYLALHGIR--QPQREDVLAFRDDLKTSGLKPTTVQNYITATRIFFKWTEQ 99
Cdd:PRK00283   10 EQFLDALwverGLAENTLSSYRRDLELFAEWLAARGLSlaEATRDDLQAFLAELAEGGYKATSSARRLSALRRFFQFLLR 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 100 ERLYP-NIAEHVKGAKLDKNHKKDyLTSRQTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTVGEnt 178
Cdd:PRK00283   90 EGLREdDPSALLDSPKLPRRLPKT-LSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQG-- 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 179 VLFIQGKGReeKTEYIKISAPVEKALRTYL-KARGFTTEEQP---LFTstsnNSKGKRITTRTVSAVVKNALKNAGYDSN 254
Cdd:PRK00283  167 VVRVTGKGN--KERLVPLGEEAVYAIERYLeRGRPALLNGRSsdaLFP----SARGGQLTRQTFWHRIKHYAKRAGIDPK 240

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1174865724 255 RLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNH 296
Cdd:PRK00283  241 KLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTH 282
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 128-294 6.55e-27

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: 103.86  E-value: 6.55e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 128 QTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTvGENTVLFIQGKGREEKTeyIKISAPVEKALRTY 207
Cdd:cd01188     4 EVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDW-RSGTITVRQKKTGRPVE--LPLTEPVGEALADY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 208 LKARGFTTEEQPLFTSTSNnSKGKRITTRTVSAVVKNALKNAGYDSNRLTAHSLRHTAITLALLAGRDITEVQQFARHAN 287
Cdd:cd01188    81 LRDGRPRTDSREVFLRARA-PYRPLSSTSQISSIVRRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRS 159


                  ....*..
gi 1174865724 288 LNTTMIY 294
Cdd:cd01188   160 IETTAIY 166
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 128-296 7.36e-27

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: 103.36  E-value: 7.36e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 128 QTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTvgENTVLFIQGKGReeKTEYIKISAPVEKALRTY 207
Cdd:cd00798     3 EVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDL--DEGLVRVTGKGN--KERLVPFGSYAVEALEEY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 208 LKARG----FTTEEQPLFTstsnNSKGKRITTRTVSAVVKNALKNAGyDSNRLTAHSLRHTAITLALLAGRDITEVQQFA 283
Cdd:cd00798    79 LEERRplllKKKPPDALFL----NKRGKRLSRRGVWRILKKYAERAG-LPKHVSPHTLRHSFATHLLEGGADLRVVQELL 153

                         170
                  ....*....|...
gi 1174865724 284 RHANLNTTMIYNH 296
Cdd:cd00798   154 GHASLSTTQIYTH 166
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 130-303 2.36e-23

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: 94.67  E-value: 2.36e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 130 KEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTVGEN-TVLFI-------QGKGREEKTEYIKISAPVe 201
Cdd:cd00799     2 KAMLATLDDTTLRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVDGgLLIRLrrsktdqDGEGEIKALPYGPETCPV- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 202 KALRTYLKARGFTteEQPLFTSTSNNSK--GKRITTRTVSAVVKNALKNAGYDSNRLTAHSLRHTAITLALLAGRDITEV 279
Cdd:cd00799    81 RALRAWLEAAGIP--SGPLFRRIRRGGSvgTTRLSDRSVARIVKRRAALAGLDPGDFSGHSLRRGFATEAARAGASLPEI 158

                         170       180
                  ....*....|....*....|....
gi 1174865724 280 QQFARHANLNTTMIYNHALDKAKN 303
Cdd:cd00799   159 MAQGGHKSVATVMRYIREADRFKD 182
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 27-296 9.48e-23

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 96.74  E-value: 9.48e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  27 RFIDYLDA---SPKTVETYKKALRQFFNYLALHGIRQP-----------QREdVLAFRddlKTSG--LKPTTVQNYITAT 90
Cdd:PRK01287   27 RFLAWLQErnwSERTLKVYTEHLYPFILWCEERGLYYAadvtlpvleryQRY-LYGYR---KANGepLSTRTQRTQLSPL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  91 RIFFKWTEQER--LYpNIAEHVKGAKLDKNHKKDYLTSRQTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANV 168
Cdd:PRK01287  103 RVWFRWLLKRHhiLY-NPAEDLELPKEEKRLPRQILSEAETEQVLASPDLTTLQGLRDRALLELLWSTGIRRGELARLDL 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 169 GDLrTVGENTVLFIQGKGREEKTeyikisAPV-EKAL---RTYLKA---RGFTTEEQP-LFTSTsnnsKGKRITTRTVSA 240
Cdd:PRK01287  182 YDV-DASRGVVTVRQGKGNKDRV------VPVgERALawlQRYLQDvrpQLAVRPDSGaLFVAM----DGDGLARNTLTN 250

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1174865724 241 VVKNALKNAGYDSNRlTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNH 296
Cdd:PRK01287  251 MVGRYIRAAGIEKAG-ACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTR 305
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 123-299 1.47e-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: 89.30  E-value: 1.47e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 123 YLTSRQTKEVLTSIETSTEeGLRNYAILSLMVTGGLRTIEVSRANVGDLRTvgENTVLFI-QGKGREEKTeyIKISAPVE 201
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPL-SIRDKALLELLYATGLRISELCSLRWSDIDF--ENGVIRVhRGKGNKERT--VPLSDAAL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 202 KALRTYLKARGFTTEEQP-LFTSTsnnsKGKRITTRTVSAVVKNALKNAGyDSNRLTAHSLRHTAITLALLAGRDITEVQ 280
Cdd:pfam00589  76 ELLKEWLSKRLLEAPKSDyLFASK----RGKPLSRQTVRKIFKRAGKEAG-LELPLHPHMLRHSFATHLLEAGVDLRVVQ 150

                         170
                  ....*....|....*....
gi 1174865724 281 QFARHANLNTTMIYNHALD 299
Cdd:pfam00589 151 KLLGHSSISTTQIYTHVAD 169
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 131-296 1.04e-18

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: 81.94  E-value: 1.04e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 131 EVLTSIETSTEegLRNYAILSLMVTGGLRTIEVSRANVGDLRtvGENTVLFI-QGKGReeKTEYIKISAPVEKALRTYLK 209
Cdd:cd01193    10 EVRRILGALTE--LRHRLILSLLYGAGLRISELLRLRVKDID--FERGVIRVrQGKGG--KDRVVPLPEKLLEPLRRYLK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 210 ARG------FTTEEQPLFTSTSNNSKGKRITTRTVSAVVKNALKNAGYDSnRLTAHSLRHTAITLALLAGRDITEVQQFA 283
Cdd:cd01193    84 SARpkeeldPAEGRAGVLDPRTGVERRHHISETTVQRALKKAVEQAGITK-RVTPHTLRHSFATHLLEAGTDIRTIQELL 162

                         170
                  ....*....|...
gi 1174865724 284 RHANLNTTMIYNH 296
Cdd:cd01193   163 GHSDLSTTMIYTH 175
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 124-294 2.24e-17

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: 78.47  E-value: 2.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 124 LTSRQTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRtVGENTVLFIQGKGREEKTeyIKISAPVEKA 203
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLR-LDDPATVRLHGKGRKERT--VPLWKETVAA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 204 LRTYLKARGFTTEEQPLFTSTSNNSKGK-------RITTRTVSAVVKnalKNAGYdSNRLTAHSLRHTAITLALLAGRDI 276
Cdd:cd01182    78 LKAYLQEFHLTPDPKQLFPLFPNRRGQPltrdgvaYILNKYVALASN---RCPSL-PKRITPHTLRHTKAMHLLQAGVDL 153

                         170
                  ....*....|....*...
gi 1174865724 277 TEVQQFARHANLNTTMIY 294
Cdd:cd01182   154 TVIRDWLGHESVETTQIY 171
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 125-302 1.06e-14

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: 70.97  E-value: 1.06e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 125 TSRQTKEVLTSIETSTEEGLRNYAILSLMVTGGLRTIEVSRANVGDLRTVGENTVLFIQGKGreEKTEYIKISAPVEKAL 204
Cdd:cd01196     1 TAPEARRLLESIDSTHPVGLRDRALIALMVYSFARIGAVLAMRVEDVYDQGRRLWVRLAEKG--GKQHEMPCHHDLEEYL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 205 RTYLKARGFTTEEQ-PLFTSTSNNSkgKRITTRTVSA-----VVKNALKNAGYDSnRLTAHSLRHTAITLALLAGRDITE 278
Cdd:cd01196    79 RAYLEAAEIEEDPKgPLFRTTRGGT--RKLTHNPLTQanayrMVRRRAIAADIPT-AIGNHSFRATGITAYLKNGGTLED 155

                         170       180
                  ....*....|....*....|....
gi 1174865724 279 VQQFARHANLNTTMIYNHALDKAK 302
Cdd:cd01196   156 AQNMANHASTRTTQLYDRRSDKIT 179
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 33-302 6.40e-14

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 71.49  E-value: 6.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  33 DASPKTVETYKKALRQFFNYLALHGIRQPQ--------------REDVLAFRDDLKTS----------GLKPTTVQNYIT 88
Cdd:PRK05084   32 PYSPTTLYEYLTEYRRFFNWLISEGLSDASkikdiplstlenltKKDVEAFILYLRERpllnghstkkGNSQTTINRTLS 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  89 ATRIFFKW----TEQERLYPNIAEHVKgAKLDKNHKKDYLTSR------------QTKEVLTSIETSTEEGL-------- 144
Cdd:PRK05084  112 ALKSLFKYlteeAENEDGEPYFYRNVM-KKIELKKKKETLAARahnlkqklflgdEDYEFLDFIDNEYEQKLsnralssf 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 145 -----RNYAILSLMVTGGLRTIEVSRANVGDLRTvgENTVLFIQGKGREEKTeyIKISAPVEKALRTYLKAR----GFTT 215
Cdd:PRK05084  191 kknkeRDLAIIALILGSGLRVSELVNLDLSDLNL--KQMTIDVTRKGGKRDS--VNIAPFALPYLEEYLKIRasryKAEK 266

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 216 EEQPLFTSTSNNsKGKRITTRTVSAVVKNALKNAGYdsnRLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYN 295
Cdd:PRK05084  267 QEKALFLTKYRG-KPNRISARAIEKMVAKYSEAFGV---RLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYT 342


                  ....*..
gi 1174865724 296 HALDKAK 302
Cdd:PRK05084  343 HIVNDEQ 349
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 23-297 4.07e-13

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 69.30  E-value: 4.07e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  23 NTFDRFID-YLD--ASPKTVETYKKALRQFFNYLALHG----IRQPQREDVLAFRDDLKTSGlKPTTVQNYITATRIFFK 95
Cdd:COG0582    97 NTFEEVAEeWLEekKPEWKEKTAAQVRRTLEKHIFPVLgdrpIAEITPPDLLAVLRPIEARG-APETARRVRQRLRQVFR 175

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  96 W-TEQERLYPNIAEHVKGA-KLDKNHKKDYLTSRQTKEVLTSIETSTEEGLRNYAILSLMVTGgLRTIEVSRANVG--DL 171
Cdd:COG0582   176 YaVARGLIERNPAADLKGAlPKPKVKHHPALTPEELPELLRALDAYRGSPVTRLALRLLLLTG-VRPGELRGARWSeiDL 254

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 172 rtvgENTVLFIQG---KGReeKTEYIKISAPVEKALRtylKARGFTTEEQPLFTSTsnNSKGKRITTRTVSAvvknALKN 248
Cdd:COG0582   255 ----EAALWTIPAermKTR--RPHIVPLSRQALEILK---ELKPLTGDSEYVFPSR--RGPKKPMSENTLNK----ALRR 319

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1174865724 249 AGYDsnRLTAHSLRHTAITLALLAG--RDITEvQQFArHANLNTTM-IYNHA 297
Cdd:COG0582   320 MGYG--RFTPHGFRHTASTLLNEAGfpPDVIE-RQLA-HKDGNKVRaAYNRA 367
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 23-304 5.10e-11

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: 62.41  E-value: 5.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  23 NTFDRFIDYLDASPKTVETYKKALRQFfnyLALHGIRQPQR---EDVLAFRDDLKTSGLKPTTVQNYITATRIFfkwteq 99
Cdd:TIGR02249   3 DQVREHMRTRHYAKRTEEAYLHWIKRF---IRFHNKRHPSTmgdTEVEAFLSDLAVDGKVAASTQNQALNALLF------ 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 100 erLYPNI-------AEHVKGAKLDKNHKKdYLTSRQTKEVLTSIETsteeglRNYAILSLMVTGGLRTIEVSRANVGDLr 172
Cdd:TIGR02249  74 --LYKEIlktplslMERFVRAKRPRKLPV-VLTREEVRRLLEHLEG------KYRLIAKLLYGSGMRLMECLRLRIQDI- 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 173 TVGENTVLFIQGKGREEKTE------YIKISAPVEKALRTYLK--ARGFTTEEQP------------------LFTStSN 226
Cdd:TIGR02249 144 DFDYGEIRIRQGKGGKDRTVtlpkelIPPLREQIELARAYHEAdlAEGYGGVYLPhalarkypnapkewgwqyLFPS-HR 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 227 NSKGKR--------ITTRTVSAVVKNALKNAGYDSNrLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNHAL 298
Cdd:TIGR02249 223 LSRDPEsgvirrhhINETTIQRAVRRAVERAGIEKP-VTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVL 301


                  ....*.
gi 1174865724 299 DKAKNG 304
Cdd:TIGR02249 302 NRGASG 307
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 123-296 1.51e-10

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 58.88  E-value: 1.51e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 123 YLTSRQTKEVLTSIETSTEEGLRNYAILSLMvTGgLRTIEVSRANVGDLRtvGENTVLFIQG-KGREEKTeyIKISAPVE 201
Cdd:cd00796     4 FLTEDEEARLLAALEESTNPHLRLIVLLALY-TG-ARRGEILSLRWDDID--LEVGLIVLPEtKNGKPRT--VPLSDEAI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 202 KALRTYLKARGFTTEEQPLftstsnnsKGKRITTRTVSAVVKNALKNAGYDSnrLTAHSLRHTAITLALLAGRDITEVQQ 281
Cdd:cd00796    78 AILKELKRKRGKDGFFVDG--------RFFGIPIASLRRAFKKARKRAGLED--LRFHDLRHTFASRLVQAGVPIKTVAK 147

                         170
                  ....*....|....*
gi 1174865724 282 FARHANLNTTMIYNH 296
Cdd:cd00796   148 ILGHSSIKMTMRYAH 162
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 147-297 1.68e-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: 53.85  E-value: 1.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 147 YAIL-SLMVTGGLRTIEVSRANVGDLRTvgENTVLFIQGkGREEKTEYIKISAPVEKALRTYLKARG---FTTEEQPLFT 222
Cdd:cd00797    27 YATLfGLLYATGLRVGEALRLRLEDVDL--DSGILTIRQ-TKFGKSRLVPLHPSTVGALRDYLARRDrllPSPSSSYFFV 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 223 StsnnSKGKRITTRTVSAVVKNALKNAGY----DSNRLTAHSLRHTAITLALL----AGRDI----TEVQQFARHANLNT 290
Cdd:cd00797   104 S----QQGGRLTGGGVYRVFRRLLRRIGLrgagDGRGPRLHDLRHTFAVNRLTrwyrEGADVerklPVLSTYLGHVNVTD 179


                  ....*..
gi 1174865724 291 TMIYNHA 297
Cdd:cd00797   180 TYWYLTA 186
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 157-300 2.52e-08

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: 52.27  E-value: 2.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 157 GLRTIEVSRANVGDLRTVGENTVL-FIQGKGreEKTEYIKISAPVEKALRTYLKARGftteEQPLFtstsnnskgKRITT 235
Cdd:cd01185    31 GLRFSDLKNLTWKNIVEASGRTWIrYRRKKT--GKPVTVPLLPVAREILEKYKDDRS----EGKLF---------PVLSN 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174865724 236 RTVSAVVKNALKNAGYDSNrLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNHALDK 300
Cdd:cd01185    96 QKINRYLKEIAKIAGIDKH-LTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVDS 159
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
25-100 3.77e-08

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 49.95  E-value: 3.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  25 FDRFIDYLDA----SPKTVETYKKALRQFFNYLA--LHGIRQPQREDVLAFRDDLKTSGLKPTTVQNYITATRIFFKWTE 98
Cdd:pfam02899   1 IDQFLEYLSLerglSPHTLRAYRRDLLAFLKFLSegGSSLEQITTSDVRAFLAELRAQGLSASSLARRLSALRSFYQFLI 80


                  ..
gi 1174865724  99 QE 100
Cdd:pfam02899  81 RE 82
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 243-296 2.77e-07

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: 49.09  E-value: 2.77e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1174865724 243 KNALKNAGydSNRLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTM-IYNH 296
Cdd:cd01189    95 KKLLKKAG--LPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLdVYAH 147
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
25-102 3.66e-07

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 47.22  E-value: 3.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  25 FDRFIDYLDA---SPKTVETYKKALRQFFNYLALHGIRQPQREDVLAFRDDLKTS-GLKPTTVQNYITATRIFFKWTEQE 100
Cdd:pfam13495   2 LERFREALRLrgyAERTIKAYLRWIRRFLRFHDKKHPEELTEEDIEAYLSHLANErNVSASTQNQALNALSFFYRWVLER 81


                  ..
gi 1174865724 101 RL 102
Cdd:pfam13495  82 EL 83
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 130-297 2.52e-06

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: 46.88  E-value: 2.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 130 KEVLTSIETSTEEGLRNYAILSLMVTGgLRTIEVSRANVGDLRtvGENTVLFIQGKGREEKTEY-IKISAPVEKALRTyl 208
Cdd:cd00801     6 PELWRALDTANLSPPTKLALRLLLLTG-QRIGELARARWSEID--LEEKTWTIPAERTKNKRPHrVPLSDQALEILEE-- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 209 kARGFTTEEQPLFTSTSNNSKgkrittRTVSAVVKNALKNAGYDSNRLTAHSLRHTAITLALLAG--RDITEVQQfaRHA 286
Cdd:cd00801    81 -LKEFTGDSGYLFPSRRKKKK------PISENTINKALKRLGYKGKEFTPHDLRRTFSTLLNELGidPEVIERLL--NHV 151

                         170
                  ....*....|..
gi 1174865724 287 NLNTTM-IYNHA 297
Cdd:cd00801   152 LGGVVRaAYNRY 163
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 124-300 8.91e-06

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: 45.48  E-value: 8.91e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 124 LTSRQTKEVLTSIETsteegLRNYAILSLMVTGGLRTIEV---------SRANVGDLRTVGENTVLFIQGKGREEKteyI 194
Cdd:cd01186     2 LTPREVQELINACNN-----LRDKFLLALLYETGLRIGEAlglriedidMADNQIELVPREDNTNEARAKSMRERR---I 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 195 KISAPVEKALRTYLKArgFTTEEQ----PLFTSTSNNSKGKRITTRTVSAVVKNALKNAGYDsnrLTAHSLRHTAITLAL 270
Cdd:cd01186    74 PVSQDLIDLYADYLTY--IYCEEAefsiTVFVNVKGGNQGKAMNYSDVYDLVRRLKKRTGID---FTPHMFRHTHATALI 148

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1174865724 271 LAGRDITEVQQFARHANLNTTM-IYNHALDK 300
Cdd:cd01186   149 RAGWSIEVVARRLGHAHVQTTLnTYGHLSEE 179
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 141-294 1.08e-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: 44.98  E-value: 1.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 141 EEGLRNYAILSLMVTGGLRTIEVSRANVGDlrtVGENTVLFIqgkgREEKT---EYIKISAPVEKALRTYLKARGFttEE 217
Cdd:cd01192    21 KANPRNYLLFIVGINTGLRISDLLSLKVED---VTNKDKLSI----KEQKTgkqKTFPLNPTLVKALKEYIDDLDL--KR 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1174865724 218 QPLFTSTSNNSKGKRITTRTVSAVVKNALKNAGYDSNrLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIY 294
Cdd:cd01192    92 NDYLFKSLKQGPEKPISRKQAYKILKKAADDLGLNYN-IGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
PRK15417 PRK15417
integron integrase;
236-298 3.42e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 45.04  E-value: 3.42e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1174865724 236 RTVSAVVKNALKNAGYdSNRLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNHAL 298
Cdd:PRK15417  255 QTFQRAFKRAVEQAGI-TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVL 316
int PHA02601
integrase; Provisional
 78-296 1.29e-03

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 40.10  E-value: 1.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724  78 LKPTTV---QNYITATriffkWTEQERLYPNIAEH-VKGAKLDKNHKKD--YLTSRQTKEVLTSIETSTEEGLRNYAILS 151
Cdd:PHA02601  126 IKPATVnreLAYLSAV-----FNELIKLGKWSGPNpLDGIRPFKEAEPElaFLTKEEIERLLDACDGSRSPDLGLIAKIC 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 152 LmVTGGlRTIEV---SRANVGdlrtvgENTVLFIQGKGREEKTeyIKISAPVEKALRtylKARGFtteeqpLFTSTSnns 228
Cdd:PHA02601  201 L-ATGA-RWSEAetlKRSQIS------PYKITFVKTKGKKNRT--VPISEELYKMLP---KRRGR------LFKDAY--- 258

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 229 kgkrittrtvsAVVKNALKNAGYD--SNRLTaHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIYNH 296
Cdd:PHA02601  259 -----------ESFERAVKRAGIDlpEGQAT-HVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAH 316
PRK09870 PRK09870
tyrosine recombinase; Provisional
 118-294 3.01e-03

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 38.00  E-value: 3.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 118 NHKKDYLTSRQTKEVLTSIETSTEeGLRNYAILSLMVTGGLRTIEVSRANVGDLRTVGENTVLFIQGKGREekTEYIKIS 197
Cdd:PRK09870    7 NKKRNFLTHSEIESLLKAANTGPH-AARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFS--TTHPLLN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174865724 198 APVeKALRTYLKARGFT--TEEQPLFTStsnnSKGKRITTRTVSAVVKNALKNAGYdSNRLTAHSLRHT-AITLALLaGR 274
Cdd:PRK09870   84 KEI-QALKNWLSIRTSYphAESEWVFLS----RKGNPLSRQQFYHIISTSGGNAGL-SLEIHPHMLRHScGFALANM-GI 156

                         170       180
                  ....*....|....*....|
gi 1174865724 275 DITEVQQFARHANLNTTMIY 294
Cdd:PRK09870  157 DTRLIQDYLGHRNIRHTVWY 176
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 227-294 9.15e-03

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: 36.63  E-value: 9.15e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1174865724 227 NSKGKRITTRTVSAVVKNALKNAGYDSNRLTAHSLRHTAITLALLAGRDITEVQQFARHANLNTTMIY 294
Cdd:cd01191    91 NRFGERITTRGIAQQLKNYARKYGLNPKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY 158
 
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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