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Conserved domains on  [gi|1358808310|ref|WP_105612169|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Enterobacteriaceae]

Protein Classification

site-specific integrase( domain architecture ID 332)

tyrosine based site-specific recombinase (integrase) is involved in cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct

CATH:  1.10.443.10
Gene Ontology:  GO:0015074|GO:0003677|GO:0006310
PubMed:  10577069|10047575|9278480
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 220-386 7.94e-41

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


The actual alignment was detected with superfamily member cd01184:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 180  Bit Score: 142.83  E-value: 7.94e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 220 FEPQQLQALTKEAG--------SELRDVIIIGLYSGMRLDEIASIKRDEIVTVEGVRCFYVS------KSKTKAGIRYVP 285
Cdd:cd01184     1 FTPEELAKIFSSPLytgckkkdPALYWLPLIGLYTGARLNEICQLRVDDIKEEDGIWCIDINddaegrRLKTKASRRLVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 286 IHSLLFGI-VDKYLEQNKGEYLLPQSNKIKRADGKRGPWYSQAFTRLRRRVLPAATDRQCFHSLRGHFITCLDRAGVPEQ 364
Cdd:cd01184    81 IHPRLIELgFLDYVEALRADGKLFLFPEKRDKDGKYSKAASKWFNRLLRKLGIKDDERKSFHSFRHTFITALKRAGVPEE 160

                         170       180
                  ....*....|....*....|..
gi 1358808310 365 RIGAITGHTEkkaKTEAFKTYS 386
Cdd:cd01184   161 LIAQIVGHSR---GGVTHDTYG 179
 
Name Accession Description Interval E-value
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 220-386 7.94e-41

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


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 142.83  E-value: 7.94e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 220 FEPQQLQALTKEAG--------SELRDVIIIGLYSGMRLDEIASIKRDEIVTVEGVRCFYVS------KSKTKAGIRYVP 285
Cdd:cd01184     1 FTPEELAKIFSSPLytgckkkdPALYWLPLIGLYTGARLNEICQLRVDDIKEEDGIWCIDINddaegrRLKTKASRRLVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 286 IHSLLFGI-VDKYLEQNKGEYLLPQSNKIKRADGKRGPWYSQAFTRLRRRVLPAATDRQCFHSLRGHFITCLDRAGVPEQ 364
Cdd:cd01184    81 IHPRLIELgFLDYVEALRADGKLFLFPEKRDKDGKYSKAASKWFNRLLRKLGIKDDERKSFHSFRHTFITALKRAGVPEE 160

                         170       180
                  ....*....|....*....|..
gi 1358808310 365 RIGAITGHTEkkaKTEAFKTYS 386
Cdd:cd01184   161 LIAQIVGHSR---GGVTHDTYG 179
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
116-373 6.17e-22

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 95.06  E-value: 6.17e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 116 KEYIEQYKDRRSYS--TLSKSVRAVSAFTKSIKRP-TITINGIGRRLVSDFL-EVNQDKFSRQTLQNWLTCLGTLYDFAR 191
Cdd:COG4974     8 EAFLEELKREKGLSpnTIKAYRRDLRRFLRFLEELgKIPLAEITPEDIRAYLnYLRERGLSPSTINRYLAALRSFFRYAV 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 192 RkyDNITPDNPFHGHNLeARQSNESYQPFEPQQLQALTKEAGSE----LRD--VIIIGLYSGMRLDEIASIKRDEIVTVE 265
Cdd:COG4974    88 R--EGLLEDNPAAKVKL-PKKPRKLPRVLTEEEIEALLEALDTEtpegLRDraLLLLLYATGLRVSELLGLKWSDIDLDR 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 266 GVrcFYVSKSKTKaGIRYVPIHSLLFGIVDKYLEQ---NKGEYLLPQSnkikradgKRGPWYSQAFTRLRRRVLPAA--T 340
Cdd:COG4974   165 GT--IRVRRGKGG-KERTVPLSPEALEALREYLEErrpRDSDYLFPTR--------RGRPLSRRAIRKILKRLAKRAgiP 233

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1358808310 341 DRQCFHSLRGHFITCLDRAGVPEQRIGAITGHT 373
Cdd:COG4974   234 KRVTPHSLRHTFATHLLEAGVDLRTVQELLGHS 266
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 219-373 2.05e-06

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: 47.70  E-value: 2.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 219 PFEPQQLQALTKEAGSELRDVIIIGL--YSGMRLDEIASIKRDEIVTVEGVrcFYVSKSKTKaGIRYVPI-----HSLLF 291
Cdd:pfam00589   4 EDEVERLLDAAETGPLSIRDKALLELlyATGLRISELCSLRWSDIDFENGV--IRVHRGKGN-KERTVPLsdaalELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 292 GIVDKYLEQNKGEYLLPqSNKIKRADgkrgpwYSQAFTRLRRRVLPAA-TDRQCFHSLRGHFITCLDRAGVPEQRIGAIT 370
Cdd:pfam00589  81 WLSKRLLEAPKSDYLFA-SKRGKPLS------RQTVRKIFKRAGKEAGlELPLHPHMLRHSFATHLLEAGVDLRVVQKLL 153


                  ...
gi 1358808310 371 GHT 373
Cdd:pfam00589 154 GHS 156
int PHA02601
integrase; Provisional
 157-354 6.34e-04

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 41.64  E-value: 6.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 157 RRLvSDFLEVNQDKFSRQTLQNW-LTCLGTLYDfARRKYDNITPDNPFHGHNLEARQSNES---YQPFEPQQLQALTKEA 232
Cdd:PHA02601  112 RRL-SGEFKVNKGRPIKPATVNReLAYLSAVFN-ELIKLGKWSGPNPLDGIRPFKEAEPELaflTKEEIERLLDACDGSR 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 233 GSELRDVIIIGLYSGMRLDEIASIKRDEIVTvegvrcFYVSKSKTKAG-IRYVPIHSLLFgivdKYLEQNKGEYLlpqsn 311
Cdd:PHA02601  190 SPDLGLIAKICLATGARWSEAETLKRSQISP------YKITFVKTKGKkNRTVPISEELY----KMLPKRRGRLF----- 254

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1358808310 312 kikradgkrGPWYsQAFTRLRRRVLPAATDRQCFHSLRGHFIT 354
Cdd:PHA02601  255 ---------KDAY-ESFERAVKRAGIDLPEGQATHVLRHTFAS 287
 
Name Accession Description Interval E-value
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 220-386 7.94e-41

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


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 142.83  E-value: 7.94e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 220 FEPQQLQALTKEAG--------SELRDVIIIGLYSGMRLDEIASIKRDEIVTVEGVRCFYVS------KSKTKAGIRYVP 285
Cdd:cd01184     1 FTPEELAKIFSSPLytgckkkdPALYWLPLIGLYTGARLNEICQLRVDDIKEEDGIWCIDINddaegrRLKTKASRRLVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 286 IHSLLFGI-VDKYLEQNKGEYLLPQSNKIKRADGKRGPWYSQAFTRLRRRVLPAATDRQCFHSLRGHFITCLDRAGVPEQ 364
Cdd:cd01184    81 IHPRLIELgFLDYVEALRADGKLFLFPEKRDKDGKYSKAASKWFNRLLRKLGIKDDERKSFHSFRHTFITALKRAGVPEE 160

                         170       180
                  ....*....|....*....|..
gi 1358808310 365 RIGAITGHTEkkaKTEAFKTYS 386
Cdd:cd01184   161 LIAQIVGHSR---GGVTHDTYG 179
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
116-373 6.17e-22

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 95.06  E-value: 6.17e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 116 KEYIEQYKDRRSYS--TLSKSVRAVSAFTKSIKRP-TITINGIGRRLVSDFL-EVNQDKFSRQTLQNWLTCLGTLYDFAR 191
Cdd:COG4974     8 EAFLEELKREKGLSpnTIKAYRRDLRRFLRFLEELgKIPLAEITPEDIRAYLnYLRERGLSPSTINRYLAALRSFFRYAV 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 192 RkyDNITPDNPFHGHNLeARQSNESYQPFEPQQLQALTKEAGSE----LRD--VIIIGLYSGMRLDEIASIKRDEIVTVE 265
Cdd:COG4974    88 R--EGLLEDNPAAKVKL-PKKPRKLPRVLTEEEIEALLEALDTEtpegLRDraLLLLLYATGLRVSELLGLKWSDIDLDR 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 266 GVrcFYVSKSKTKaGIRYVPIHSLLFGIVDKYLEQ---NKGEYLLPQSnkikradgKRGPWYSQAFTRLRRRVLPAA--T 340
Cdd:COG4974   165 GT--IRVRRGKGG-KERTVPLSPEALEALREYLEErrpRDSDYLFPTR--------RGRPLSRRAIRKILKRLAKRAgiP 233

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1358808310 341 DRQCFHSLRGHFITCLDRAGVPEQRIGAITGHT 373
Cdd:COG4974   234 KRVTPHSLRHTFATHLLEAGVDLRTVQELLGHS 266
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
116-373 5.74e-14

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 71.92  E-value: 5.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 116 KEYIEQYKD-----RRSYSTLSKSVRAVSAFTKSIKRPTITINGIGRRLVSDFL-EVNQDKFSRQTLQNWLTCLGTLYDF 189
Cdd:COG4973     5 AEALEAYLEhlrerRLSPKTLEAYRRDLRRLIPLLGDADLPLEELTPADVRRFLaRLHRRGLSPRTLNRRLSALRSFFNW 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 190 ARRkyDNITPDNPFHGhnLEA-RQSNESYQPFEPQQLQAL-----TKEAGSELRDVIIIGLYSGMRLDEIASIKRDEI-- 261
Cdd:COG4973    85 AVR--EGLLEANPAAG--VKApKAPRKLPRALTVDELAQLldalaDDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVdl 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 262 ----VTVEGvrcfyvsksKTKAGiRYVPIHSLLFGIVDKYLEQnKGEYLLPQSNKIKRadGKRGPWYS-----QAFTRLR 332
Cdd:COG4973   161 dageVRVRG---------KTGKS-RTVPLGPKALAALREWLAV-RPELAAPDEGALFP--SRRGTRLSprnvqKRLRRLA 227

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1358808310 333 RRV-LPAATDrqcFHSLRGHFITCLDRAGVPEQRIGAITGHT 373
Cdd:COG4973   228 KKAgLPKHVH---PHDLRHSFATHLLESGGDLRAVQELLGHA 266
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 225-385 1.44e-13

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: 68.12  E-value: 1.44e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 225 LQALTKEAGSELRDVIIIGLYSGMRLDEIASIKRDEIVTVEGVRCFYVSKSKTKagiRYVPIHSLLFGIVDKYLEQNKGE 304
Cdd:cd00796    14 LAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKP---RTVPLSDEAIAILKELKRKRGKD 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 305 YLLPqsnkIKRADGKRGPWYSQAFTRLRRRV-LPAATdrqcFHSLRGHFITCLDRAGVPEQRIGAITGHTEkkakTEAFK 383
Cdd:cd00796    91 GFFV----DGRFFGIPIASLRRAFKKARKRAgLEDLR----FHDLRHTFASRLVQAGVPIKTVAKILGHSS----IKMTM 158


                  ..
gi 1358808310 384 TY 385
Cdd:cd00796   159 RY 160
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 225-373 2.51e-12

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: 64.81  E-value: 2.51e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 225 LQALTKEAGSELRD--VIIIGLYSGMRLDEIASIKRDEIVTVEGvrCFYVSKSKTKAGI-RYVPIHSLLFGIVDKYLEQ- 300
Cdd:cd00397     6 LDAIDEDKKIDLRDraILLLLLETGLRISELLALKVKDIDLDNG--TIRVRGKKTKGGKeRTVPLPKELAEELKEYLKEr 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1358808310 301 --NKGEYLLPQSNKIKRADGKRGPWYSQAFTRLRRRVLPAATDRQCFHSLRGHFITCLDRAGVPEQRIGAITGHT 373
Cdd:cd00397    84 rdKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 113-393 2.58e-08

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 55.43  E-value: 2.58e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 113 DVSKEYIEQYKDRRSYSTLSksvRAVSAFTKSI-----KRPtitINGIGRRLVSDFLEVNQDKFSRQTLQNWLTCLGTLY 187
Cdd:COG0582   101 EVAEEWLEEKKPEWKEKTAA---QVRRTLEKHIfpvlgDRP---IAEITPPDLLAVLRPIEARGAPETARRVRQRLRQVF 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 188 DFARRKYdnITPDNPFHG-HNLEARQSNESYQPFEPQQ----LQALTKEAGSEL-RDVIIIGLYSGMRLDEIASIKRDEI 261
Cdd:COG0582   175 RYAVARG--LIERNPAADlKGALPKPKVKHHPALTPEElpelLRALDAYRGSPVtRLALRLLLLTGVRPGELRGARWSEI 252

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 262 VTVEGVrcFYVSKSKTKAG-IRYVPIHSLLFGIVDKYLE-QNKGEYLLPqsnkikRADGKRGPWYSQAFTRLRRRvlpAA 339
Cdd:COG0582   253 DLEAAL--WTIPAERMKTRrPHIVPLSRQALEILKELKPlTGDSEYVFP------SRRGPKKPMSENTLNKALRR---MG 321

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1358808310 340 TDRQCFHSLRGHFITCLDRAGVPEQRIGAITGHTEKKaKTEAfkTYSQGAEMKE 393
Cdd:COG0582   322 YGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGN-KVRA--AYNRADYLEE 372
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 235-376 3.35e-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: 52.65  E-value: 3.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 235 ELRDVIIIGLYSGMRLDEIASIKRDEIVTVEGVRCFYVSKSKTKAGIrYVPIHSLLFGIVDKYLEQNKGEYLLPQSNkik 314
Cdd:cd01185    19 LVRDMFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPV-TVPLLPVAREILEKYKDDRSEGKLFPVLS--- 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1358808310 315 radgkrgpwYSQAFTRLRRRVLPAATDRQ-CFHSLRGHFITCLDRAGVPEQRIGAITGHTEKK 376
Cdd:cd01185    95 ---------NQKINRYLKEIAKIAGIDKHlTFHVARHTFATLLLLKGVDIETISKLLGHSSIK 148
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 219-373 2.05e-06

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: 47.70  E-value: 2.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 219 PFEPQQLQALTKEAGSELRDVIIIGL--YSGMRLDEIASIKRDEIVTVEGVrcFYVSKSKTKaGIRYVPI-----HSLLF 291
Cdd:pfam00589   4 EDEVERLLDAAETGPLSIRDKALLELlyATGLRISELCSLRWSDIDFENGV--IRVHRGKGN-KERTVPLsdaalELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 292 GIVDKYLEQNKGEYLLPqSNKIKRADgkrgpwYSQAFTRLRRRVLPAA-TDRQCFHSLRGHFITCLDRAGVPEQRIGAIT 370
Cdd:pfam00589  81 WLSKRLLEAPKSDYLFA-SKRGKPLS------RQTVRKIFKRAGKEAGlELPLHPHMLRHSFATHLLEAGVDLRVVQKLL 153


                  ...
gi 1358808310 371 GHT 373
Cdd:pfam00589 154 GHS 156
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 224-394 1.92e-05

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 44.64  E-value: 1.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 224 QLQALTKEAGSELRDVIIIGLYSGMRLDEIASIKRDEIvTVEGVrcfYVSKSKTKAGIRyVPIHSLLFGIVD--KYLEQN 301
Cdd:cd00800     2 EYAAIYAEAPPLLRLAMELALLTGQRQGDLLRLKWSDI-TDGGL---LVEQSKTGKKLL-IPWTPSLRALVDriRALPRK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 302 KGEYLLpqsnkikraDGKRGPWYS-----QAFTRLRRRV-LPAATDRQCFHSLRGHFITCLDRAGVPEQrIGAITGHTeK 375
Cdd:cd00800    77 RSEYLI---------NSRKGGPLSydtlkSAWRRARKAAgLKGETEGFTFHDLRAKAATDYAEQGGSTD-AQALLGHK-S 145

                         170
                  ....*....|....*....
gi 1358808310 376 KAKTEafkTYSQGAEMKEL 394
Cdd:cd00800   146 DAMTE---RYTRKRGQKWV 161
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 222-373 2.46e-05

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: 44.09  E-value: 2.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 222 PQQLQALTKEA---GSELRDVIIIGLYSGMRLDEIASIKRDEI------------VTVEGVRCFYVSKSKTKAGIRYVPI 286
Cdd:cd01189     1 PEELKKLLEALkkrGDRYYLLFLLALLTGLRRGELLALTWSDIdfengtirinrtLVRKKKGGYVIKPPKTKSSIRTIPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 287 HSLLFGIVDKYLEQNKgeyllpqsnkikradgkrgpwysqaftRLRRRVLPAATdrqcFHSLRgH-FITCLDRAGVPEQR 365
Cdd:cd01189    81 PDELIELLKELKAFKK---------------------------LLKKAGLPRIT----PHDLR-HtFASLLLEAGVPLKV 128


                  ....*...
gi 1358808310 366 IGAITGHT 373
Cdd:cd01189   129 IAERLGHS 136
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 223-373 7.50e-05

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: 43.44  E-value: 7.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 223 QQLQALTKEAGSELRD--VIIIGLYSGMRLDEIASIKRDEIVTV--EGVRCFyVSKSKT---KAGIRyVPIHSLLFGIVD 295
Cdd:cd00799     3 AMLATLDDTTLRGLRDraLLLLGFAGALRRSELVALRVEDLTRFvdGGLLIR-LRRSKTdqdGEGEI-KALPYGPETCPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 296 KYLEQnkgeYLLP---QSNKIKRADGKRG-----PWYSQAFTRL-RRRVLPAATDRQCF--HSLRGHFITCLDRAGVPEQ 364
Cdd:cd00799    81 RALRA----WLEAagiPSGPLFRRIRRGGsvgttRLSDRSVARIvKRRAALAGLDPGDFsgHSLRRGFATEAARAGASLP 156


                  ....*....
gi 1358808310 365 RIGAITGHT 373
Cdd:cd00799   157 EIMAQGGHK 165
int PHA02601
integrase; Provisional
 157-354 6.34e-04

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 41.64  E-value: 6.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 157 RRLvSDFLEVNQDKFSRQTLQNW-LTCLGTLYDfARRKYDNITPDNPFHGHNLEARQSNES---YQPFEPQQLQALTKEA 232
Cdd:PHA02601  112 RRL-SGEFKVNKGRPIKPATVNReLAYLSAVFN-ELIKLGKWSGPNPLDGIRPFKEAEPELaflTKEEIERLLDACDGSR 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 233 GSELRDVIIIGLYSGMRLDEIASIKRDEIVTvegvrcFYVSKSKTKAG-IRYVPIHSLLFgivdKYLEQNKGEYLlpqsn 311
Cdd:PHA02601  190 SPDLGLIAKICLATGARWSEAETLKRSQISP------YKITFVKTKGKkNRTVPISEELY----KMLPKRRGRLF----- 254

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1358808310 312 kikradgkrGPWYsQAFTRLRRRVLPAATDRQCFHSLRGHFIT 354
Cdd:PHA02601  255 ---------KDAY-ESFERAVKRAGIDLPEGQATHVLRHTFAS 287
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 220-354 1.34e-03

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: 39.60  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1358808310 220 FEPQQLQALTKEA-----GSELRDVI---IIGLY--SGMRLDEIASIKRDEIVTVEGVrcFYVSKSKTKAGiRYVPIHSL 289
Cdd:cd00797     1 YTDAEIRRLLAAAdqlppESPLRPLTyatLFGLLyaTGLRVGEALRLRLEDVDLDSGI--LTIRQTKFGKS-RLVPLHPS 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1358808310 290 LFGIVDKYLEQNKGEYLLPQSNKI-KRADGKR--GPWYSQAFTRLRRRV-LPAATDRQC--FHSLRGHFIT 354
Cdd:cd00797    78 TVGALRDYLARRDRLLPSPSSSYFfVSQQGGRltGGGVYRVFRRLLRRIgLRGAGDGRGprLHDLRHTFAV 148
 
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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