NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1081141252|gb|OFS89345|]
View 

site-specific tyrosine recombinase XerD [Oligella sp. HMSC05A10]

Protein Classification

site-specific tyrosine recombinase XerD( domain architecture ID 11478438)

site-specific tyrosine recombinase XerD acts by catalyzing the cutting and rejoining of recombining DNA molecules

CATH:  1.10.443.10|1.10.150.130
Gene Ontology:  GO:0009037|GO:0003677|GO:0007049|GO:0051301|GO:0006313|GO:0009009|GO:0006310
PubMed:  10047575|9278480|10577069|9268326|10361305
SCOP:  4002347|4001040

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
xerD PRK00283
tyrosine recombinase;
6-297 2.08e-147

tyrosine recombinase;


:

Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 415.36  E-value: 2.08e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   6 LSAFLDSLWLEDGLAKNTLAAYRQDMHAFIEFLQRERpaVSVFTVKAEDIQAWLAQMHVET-KPSTANRRLATLRRFYAW 84
Cdd:PRK00283    9 IEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARG--LSLAEATRDDLQAFLAELAEGGyKATSSARRLSALRRFFQF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  85 AMQHHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREG 164
Cdd:PRK00283   87 LLREGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQG 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 165 FLRVVeAKGSKERIVPLGEEALYWLERYLLEARPELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQV-PLSPH 243
Cdd:PRK00283  167 VVRVT-GKGNKERLVPLGEEAVYAIERYLERGRPALLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPkKLSPH 245

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1081141252 244 VLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHPRA 297
Cdd:PRK00283  246 VLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 299
 
Name Accession Description Interval E-value
xerD PRK00283
tyrosine recombinase;
6-297 2.08e-147

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 415.36  E-value: 2.08e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   6 LSAFLDSLWLEDGLAKNTLAAYRQDMHAFIEFLQRERpaVSVFTVKAEDIQAWLAQMHVET-KPSTANRRLATLRRFYAW 84
Cdd:PRK00283    9 IEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARG--LSLAEATRDDLQAFLAELAEGGyKATSSARRLSALRRFFQF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  85 AMQHHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREG 164
Cdd:PRK00283   87 LLREGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQG 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 165 FLRVVeAKGSKERIVPLGEEALYWLERYLLEARPELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQV-PLSPH 243
Cdd:PRK00283  167 VVRVT-GKGNKERLVPLGEEAVYAIERYLERGRPALLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPkKLSPH 245

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1081141252 244 VLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHPRA 297
Cdd:PRK00283  246 VLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 299
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 9-297 1.81e-143

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


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 405.04  E-value: 1.81e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   9 FLDSLWLEDGLAKNTLAAYRQDMHAFIEFLqrERPAVSVFTVKAEDIQAWLAQMHVETK-PSTANRRLATLRRFYAWAMQ 87
Cdd:TIGR02225   3 FLDYLWVERGLSQNTLEAYRRDLEKFLEFL--EERGIDLEEVDRGDIVDFLAELKEAGLsARSIARALSALRSFYRFLLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  88 HHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLR 167
Cdd:TIGR02225  81 EGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 168 VvEAKGSKERIVPLGEEALYWLERYLLEARPELLKGRL--DDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVL 245
Cdd:TIGR02225 161 V-RGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVkeSDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1081141252 246 RHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHPRA 297
Cdd:TIGR02225 240 RHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
6-295 2.07e-106

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 311.16  E-value: 2.07e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   6 LSAFLDSLWLEDGLAKNTLAAYRQDMHAFIEFLQRERpAVSVFTVKAEDIQAWLAQMHVET-KPSTANRRLATLRRFYAW 84
Cdd:COG4974     7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEELG-KIPLAEITPEDIRAYLNYLRERGlSPSTINRYLAALRSFFRY 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  85 AMQHHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREG 164
Cdd:COG4974    86 AVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRG 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 165 FLRVVEAKGSKERIVPLGEEALYWLERYLLEARPellkgRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHV 244
Cdd:COG4974   166 TIRVRRGKGGKERTVPLSPEALEALREYLEERRP-----RDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHS 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1081141252 245 LRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHP 295
Cdd:COG4974   241 LRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 114-286 1.85e-91

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: 268.61  E-value: 1.85e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 114 ESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVeAKGSKERIVPLGEEALYWLERYL 193
Cdd:cd00798     1 VDEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVT-GKGNKERLVPFGSYAVEALEEYL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 194 LEARPELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADIS 273
Cdd:cd00798    80 EERRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLS 159

                         170
                  ....*....|...
gi 1081141252 274 TTQIYTHVARERL 286
Cdd:cd00798   160 TTQIYTHVSFERL 172
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 112-282 2.79e-57

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: 181.75  E-value: 2.79e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 112 LSESQVELLLAAPDlKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEALYWLER 191
Cdd:pfam00589   2 LTEDEVERLLDAAE-TGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 192 YLLEARPELLKgrlDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHAD 271
Cdd:pfam00589  81 WLSKRLLEAPK---SDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSS 157

                         170
                  ....*....|.
gi 1081141252 272 ISTTQIYTHVA 282
Cdd:pfam00589 158 ISTTQIYTHVA 168
 
Name Accession Description Interval E-value
xerD PRK00283
tyrosine recombinase;
6-297 2.08e-147

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 415.36  E-value: 2.08e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   6 LSAFLDSLWLEDGLAKNTLAAYRQDMHAFIEFLQRERpaVSVFTVKAEDIQAWLAQMHVET-KPSTANRRLATLRRFYAW 84
Cdd:PRK00283    9 IEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARG--LSLAEATRDDLQAFLAELAEGGyKATSSARRLSALRRFFQF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  85 AMQHHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREG 164
Cdd:PRK00283   87 LLREGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQG 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 165 FLRVVeAKGSKERIVPLGEEALYWLERYLLEARPELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQV-PLSPH 243
Cdd:PRK00283  167 VVRVT-GKGNKERLVPLGEEAVYAIERYLERGRPALLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPkKLSPH 245

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1081141252 244 VLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHPRA 297
Cdd:PRK00283  246 VLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 299
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 9-297 1.81e-143

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


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 405.04  E-value: 1.81e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   9 FLDSLWLEDGLAKNTLAAYRQDMHAFIEFLqrERPAVSVFTVKAEDIQAWLAQMHVETK-PSTANRRLATLRRFYAWAMQ 87
Cdd:TIGR02225   3 FLDYLWVERGLSQNTLEAYRRDLEKFLEFL--EERGIDLEEVDRGDIVDFLAELKEAGLsARSIARALSALRSFYRFLLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  88 HHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLR 167
Cdd:TIGR02225  81 EGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 168 VvEAKGSKERIVPLGEEALYWLERYLLEARPELLKGRL--DDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVL 245
Cdd:TIGR02225 161 V-RGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVkeSDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1081141252 246 RHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHPRA 297
Cdd:TIGR02225 240 RHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
6-295 2.07e-106

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 311.16  E-value: 2.07e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   6 LSAFLDSLWLEDGLAKNTLAAYRQDMHAFIEFLQRERpAVSVFTVKAEDIQAWLAQMHVET-KPSTANRRLATLRRFYAW 84
Cdd:COG4974     7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEELG-KIPLAEITPEDIRAYLNYLRERGlSPSTINRYLAALRSFFRY 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  85 AMQHHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREG 164
Cdd:COG4974    86 AVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRG 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 165 FLRVVEAKGSKERIVPLGEEALYWLERYLLEARPellkgRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHV 244
Cdd:COG4974   166 TIRVRRGKGGKERTVPLSPEALEALREYLEERRP-----RDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHS 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1081141252 245 LRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHP 295
Cdd:COG4974   241 LRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 8-297 1.14e-101

tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 299.14  E-value: 1.14e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   8 AFLDSLWLEDGLAKNTLAAYRQDMHAFIEFLQRERPAVSVFTVKAEDIQAWLAQMHVET-KPSTANRRLATLRRFYAWAM 86
Cdd:TIGR02224   2 AFLEYLRLERNYSPHTVRAYRRDLEAFLEFLEEEGGLASLAEVTAADLRSFLAELHARGlSRRSLARKLSALRSFYRFLL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  87 QHHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAP--DLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREG 164
Cdd:TIGR02224  82 RRGLIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPeeDDEDWLALRDRAILELLYSSGLRVSELVGLDLSDLDLDFG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 165 FLRVVeAKGSKERIVPLGEEALYWLERYLLEARPELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHV 244
Cdd:TIGR02224 162 EVRVR-GKGNKERIVPFGPYARDALQAYLEARRSPLLASEGQDALFLNRRGGRLTPRGVQYRLQQLRAKAGLPKHVHPHA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1081141252 245 LRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHPRA 297
Cdd:TIGR02224 241 LRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHPRA 293
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 3-297 1.07e-98

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 291.67  E-value: 1.07e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   3 ENELSAFLDSLWLEDGLAKNTLAAYRQDMHAFIEFLQRERPAvSVFTVKAEDIQAWLAQMHVE-TKPSTANRRLATLRRF 81
Cdd:PRK00236    7 PAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGIS-SLQDLDAADLRSFLARRRRQgLSARSLARRLSALRSF 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  82 YAWAMQHHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLAL 161
Cdd:PRK00236   86 YRWLVRRGLLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSELVGLDIDDLDL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 162 REGFLRVVeAKGSKERIVPLGEEALYWLERYLlEARPELLKGrlDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLS 241
Cdd:PRK00236  166 ASGTLRVL-GKGNKERTVPLGRAAREALEAYL-ALRPLFLPD--DDALFLGARGGRLSPRVVQRRVKKLGKKAGLPSHIT 241

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1081141252 242 PHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHPRA 297
Cdd:PRK00236  242 PHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPRA 297
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 114-286 1.85e-91

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: 268.61  E-value: 1.85e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 114 ESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVeAKGSKERIVPLGEEALYWLERYL 193
Cdd:cd00798     1 VDEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVT-GKGNKERLVPFGSYAVEALEEYL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 194 LEARPELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADIS 273
Cdd:cd00798    80 EERRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLS 159

                         170
                  ....*....|...
gi 1081141252 274 TTQIYTHVARERL 286
Cdd:cd00798   160 TTQIYTHVSFERL 172
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
3-286 9.00e-80

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 243.33  E-value: 9.00e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   3 ENELSAFLDSLwLEDGLAKNTLAAYRQDMHAFIEFLQRERPAVSvfTVKAEDIQAWLAQMHVE-TKPSTANRRLATLRRF 81
Cdd:COG4973     5 AEALEAYLEHL-RERRLSPKTLEAYRRDLRRLIPLLGDADLPLE--ELTPADVRRFLARLHRRgLSPRTLNRRLSALRSF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  82 YAWAMQHHRMEEDPCLHIKAVRQAARFPKSLSESQVELLLAAPDlKTPGGLRDRAMLETLYATGLRVSELIALRVFHLAL 161
Cdd:COG4973    82 FNWAVREGLLEANPAAGVKAPKAPRKLPRALTVDELAQLLDALA-DDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 162 REGFLRVVeAKGSKERIVPLGEEALYWLERYLlEARPELLKGRlDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLS 241
Cdd:COG4973   161 DAGEVRVR-GKTGKSRTVPLGPKALAALREWL-AVRPELAAPD-EGALFPSRRGTRLSPRNVQKRLRRLAKKAGLPKHVH 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1081141252 242 PHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERL 286
Cdd:COG4973   238 PHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHL 282
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 6-295 7.55e-62

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 199.59  E-value: 7.55e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   6 LSAFLDSLwLEDGLAKNTLAAYRQDMHAFIEFLQrER-----PAVSVFTVkaEDIQAWLAQMH-VETKPSTAN---RRLA 76
Cdd:PRK01287   25 LERFLAWL-QERNWSERTLKVYTEHLYPFILWCE-ERglyyaADVTLPVL--ERYQRYLYGYRkANGEPLSTRtqrTQLS 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  77 TLRRFYAWAMQHHRMEEDPCLHIKAVRQAARFPKS-LSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALR 155
Cdd:PRK01287  101 PLRVWFRWLLKRHHILYNPAEDLELPKEEKRLPRQiLSEAETEQVLASPDLTTLQGLRDRALLELLWSTGIRRGELARLD 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 156 VFHLALREGFLRVVEAKGSKERIVPLGEEALYWLERYLLEARPELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQD 235
Cdd:PRK01287  181 LYDVDASRGVVTVRQGKGNKDRVVPVGERALAWLQRYLQDVRPQLAVRPDSGALFVAMDGDGLARNTLTNMVGRYIRAAG 260

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 236 IQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKTLHQKHHP 295
Cdd:PRK01287  261 IEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAVHASTHP 320
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 112-282 2.79e-57

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: 181.75  E-value: 2.79e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 112 LSESQVELLLAAPDlKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEALYWLER 191
Cdd:pfam00589   2 LTEDEVERLLDAAE-TGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 192 YLLEARPELLKgrlDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHAD 271
Cdd:pfam00589  81 WLSKRLLEAPK---SDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSS 157

                         170
                  ....*....|.
gi 1081141252 272 ISTTQIYTHVA 282
Cdd:pfam00589 158 ISTTQIYTHVA 168
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 107-281 3.56e-49

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: 161.29  E-value: 3.56e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 107 RFPKSLSESQVELLL-AAPDLktpgglRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEA 185
Cdd:cd01193     1 KLPVVLSPDEVRRILgALTEL------RHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 186 LYWLERYLLEAR------PELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGAD 259
Cdd:cd01193    75 LEPLRRYLKSARpkeeldPAEGRAGVLDPRTGVERRHHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTD 154

                         170       180
                  ....*....|....*....|..
gi 1081141252 260 LRVVQMLLGHADISTTQIYTHV 281
Cdd:cd01193   155 IRTIQELLGHSDLSTTMIYTHV 176
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 116-279 6.82e-44

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: 147.24  E-value: 6.82e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 116 QVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVE--AKGSKERIVPLGEEALYWLERYL 193
Cdd:cd00397     1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGkkTKGGKERTVPLPKELAEELKEYL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 194 LEAR---PELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKqqDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHA 270
Cdd:cd00397    81 KERRdkrGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGI--EAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158


                  ....*....
gi 1081141252 271 DISTTQIYT 279
Cdd:cd00397   159 SISTTQRYL 167
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 112-279 3.04e-39

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: 135.87  E-value: 3.04e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 112 LSESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEALYWLER 191
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 192 YLLEARPElLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVP-----LSPHVLRHAFATHLLNHGADLRVVQML 266
Cdd:cd01182    81 YLQEFHLT-PDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPslpkrITPHTLRHTKAMHLLQAGVDLTVIRDW 159

                         170
                  ....*....|...
gi 1081141252 267 LGHADISTTQIYT 279
Cdd:cd01182   160 LGHESVETTQIYA 172
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 113-289 4.98e-34

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: 122.35  E-value: 4.98e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 113 SESQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEALYWLERY 192
Cdd:cd01188     1 SPDEVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPLTEPVGEALADY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 193 LLEARPEllkgRLDDAVFITR---LGSAMSRQAFWQLVKKYAKQQDIQVPL-SPHVLRHAFATHLLNHGADLRVVQMLLG 268
Cdd:cd01188    81 LRDGRPR----TDSREVFLRArapYRPLSSTSQISSIVRRYLRKAGIEPSHrGTHSLRHSLATRMLRAGTSLKVIADLLG 156

                         170       180
                  ....*....|....*....|.
gi 1081141252 269 HADISTTQIYTHVARERLKTL 289
Cdd:cd01188   157 HRSIETTAIYAKIDVDDLREV 177
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 18-281 1.62e-29

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: 114.03  E-value: 1.62e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  18 GLAKNTLAAYRQDMHAFIEFLQRERPAvsvfTVKAEDIQAWLAQMHVETK--PSTANRRLATLRRFYAWAMQhhrMEEDP 95
Cdd:TIGR02249  13 HYAKRTEEAYLHWIKRFIRFHNKRHPS----TMGDTEVEAFLSDLAVDGKvaASTQNQALNALLFLYKEILK---TPLSL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  96 CLHIKAVRQAARFPKSLSESQVELLLAA--PDLKTPGGLrdramletLYATGLRVSELIALRVFHLALREGFLRVVEAKG 173
Cdd:TIGR02249  86 MERFVRAKRPRKLPVVLTREEVRRLLEHleGKYRLIAKL--------LYGSGMRLMECLRLRIQDIDFDYGEIRIRQGKG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 174 SKERIVPLGEEALYWLERYLLEAR----------------PELLKGRLDDA--------VFITRLGSA-----------M 218
Cdd:TIGR02249 158 GKDRTVTLPKELIPPLREQIELARayheadlaegyggvylPHALARKYPNApkewgwqyLFPSHRLSRdpesgvirrhhI 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1081141252 219 SRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHV 281
Cdd:TIGR02249 238 NETTIQRAVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHV 300
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 110-289 3.28e-28

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


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 107.21  E-value: 3.28e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 110 KSLSESQVELLLAAPDlKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEALYWL 189
Cdd:cd01197     5 KYLTGKEVQALLQAAC-RGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDEREAL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 190 ERYLLEARPelLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGH 269
Cdd:cd01197    84 EAWLKERAN--WKGADTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGH 161

                         170       180
                  ....*....|....*....|
gi 1081141252 270 ADISTTQIYTHVARERLKTL 289
Cdd:cd01197   162 RNIRHTVIYTASNAARFANL 181
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 133-287 1.32e-26

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 106.93  E-value: 1.32e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 133 RDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEaKGSKERIVPLGEEALYWLERYLlEARPELLK-GRLDDAVFI 211
Cdd:PRK05084  196 RDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTR-KGGKRDSVNIAPFALPYLEEYL-KIRASRYKaEKQEKALFL 273

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1081141252 212 TR---LGSAMSRQAFWQLVKKYAKqqDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLK 287
Cdd:PRK05084  274 TKyrgKPNRISARAIEKMVAKYSE--AFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQK 350
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 110-280 2.43e-24

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


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 96.24  E-value: 2.43e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 110 KSLSESQVELLLAAPDLKTPGGLRDRAMLetLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEAlywl 189
Cdd:cd00796     3 RFLTEDEEARLLAALEESTNPHLRLIVLL--ALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEA---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 190 eRYLLEARPELLKGRLDDAVFITRLGSAMSRQAFWQLVKKYAKQQDiqvpLSPHVLRHAFATHLLNHGADLRVVQMLLGH 269
Cdd:cd00796    77 -IAILKELKRKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLED----LRFHDLRHTFASRLVQAGVPIKTVAKILGH 151

                         170
                  ....*....|.
gi 1081141252 270 ADISTTQIYTH 280
Cdd:cd00796   152 SSIKMTMRYAH 162
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 112-280 5.98e-24

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: 95.52  E-value: 5.98e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 112 LSESQVELLLAA-PDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRV-VEAKG--SKERIVPLGEEALY 187
Cdd:cd01194     1 LTLEQARQLLASlPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILyVQGKGktSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 188 WLERYLlEARPELlkgRLDDAVFIT----RLGSAMSRQAFWQLVKKYAKQQDIQVP-LSPHVLRHAFATHLLNHGADLRV 262
Cdd:cd01194    81 ALQAYL-KARGKL---DFEEPLFTSlsnnSKGQRLTTRSIRRIIKKYLRKAGLDDDrLTAHSLRHTAGTLALKAGKSLRE 156

                         170
                  ....*....|....*...
gi 1081141252 263 VQMLLGHADISTTQIYTH 280
Cdd:cd01194   157 VQQLLRHSDPNTTMIYAH 174
PRK15417 PRK15417
integron integrase;
23-285 1.49e-23

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 98.19  E-value: 1.49e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  23 TLAAYRQDMHAFIEFLQRERPAvsvfTVKAEDIQAWLAQMHVETKPSTANRR--LATLRRFYAWAMqhhrMEEDPCLH-I 99
Cdd:PRK15417   33 TEQAYVHWVRAFIRFHGVRHPA----TLGSSEVEAFLSWLANERKVSVSTHRqaLAALLFFYGKVL----CTDLPWLQeI 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 100 KAVRQAARFPKSLSESQVelllaapdLKTPGGLR--DRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKER 177
Cdd:PRK15417  105 GRPRPSRRLPVVLTPDEV--------VRILGFLEgeHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDR 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 178 IVPLGEEALYWLERYLLEARPELLK----GR----LDDA----------------VFITRLGSA-----------MSRQA 222
Cdd:PRK15417  177 ALMLPESLAPSLREQLSRARAWWLKdqaeGRsgvaLPDAlerkypraghswpwfwVFAQHTHSTdprsgvvrrhhMYDQT 256

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1081141252 223 FWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARER 285
Cdd:PRK15417  257 FQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVG 319
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 50-280 5.58e-23

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 97.42  E-value: 5.58e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  50 VKAEDIQAWLAQMHVETKPSTANRRLATLRRFYAWAMQHHRMEEDPCLHIKAVRQAARFPK--SLSESQVELLLAAPDlK 127
Cdd:COG0582   142 ITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHhpALTPEELPELLRALD-A 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 128 TPGGLRDRAMLETLYATGLRVSELIALRV--FHLALREGFLRVVEAKGSKERIVPLGEEALYWLERYLLEARPELLkgrl 205
Cdd:COG0582   221 YRGSPVTRLALRLLLLTGVRPGELRGARWseIDLEAALWTIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEY---- 296

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 206 ddaVFITRLGSA--MSRQAFWQLVKK--YAKqqdiqvpLSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQ-IYTH 280
Cdd:COG0582   297 ---VFPSRRGPKkpMSENTLNKALRRmgYGR-------FTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaAYNR 366
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 120-280 1.19e-22

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


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 92.15  E-value: 1.19e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 120 LLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVeAKGSKER-IVPLGEEALYWLERYL--LEA 196
Cdd:cd01195     8 RLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRIL-GKGKKQReVVTLPPTTREALAAWLaaRGE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 197 RPELLKGRLDDAVFITRLgsamSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADL-RVVQMLLGHADISTT 275
Cdd:cd01195    87 AEGPLFVSLDRASRGRRL----SPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGLiRKVQDFSRHADLRTL 162


                  ....*
gi 1081141252 276 QIYTH 280
Cdd:cd01195   163 QVYDD 167
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 114-280 2.88e-20

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: 84.92  E-value: 2.88e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 114 ESQVELLLAAPDLKtpgGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEA--------------K-GSKERI 178
Cdd:cd01189     1 PEELKKLLEALKKR---GDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTlvrkkkggyvikppKtKSSIRT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 179 VPLGEEALYWLERyllearpellkgrlddavfitrlgsamsrqafWQLVKKYAKQQDIQvPLSPHVLRHAFATHLLNHGA 258
Cdd:cd01189    78 IPLPDELIELLKE--------------------------------LKAFKKLLKKAGLP-RITPHDLRHTFASLLLEAGV 124

                         170       180
                  ....*....|....*....|...
gi 1081141252 259 DLRVVQMLLGHADISTT-QIYTH 280
Cdd:cd01189   125 PLKVIAERLGHSDISTTlDVYAH 147
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 115-281 3.29e-20

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: 85.01  E-value: 3.29e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 115 SQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHL--ALREGFLRVVEAKGSKERIVPLGEEALYWLERY 192
Cdd:cd01185     1 EELKRLMALELSDTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIveASGRTWIRYRRKKTGKPVTVPLLPVAREILEKY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 193 LlearpellKGRLDDAVFitrlgSAMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADI 272
Cdd:cd01185    81 K--------DDRSEGKLF-----PVLSNQKINRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSI 147


                  ....*....
gi 1081141252 273 STTQIYTHV 281
Cdd:cd01185   148 KTTQIYAKI 156
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 112-287 6.74e-19

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: 82.74  E-value: 6.74e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 112 LSESQVELLLAAPDLKTPGGLRDRAMLET----LYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEALY 187
Cdd:cd00797     1 YTDAEIRRLLAAADQLPPESPLRPLTYATlfglLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 188 WLERYLLEaRPELLKGRLDDAVFI----TRLGSAMSRQAFWQLVKKYA-KQQDIQVPLSPHVLRHAFATHLLNH----GA 258
Cdd:cd00797    81 ALRDYLAR-RDRLLPSPSSSYFFVsqqgGRLTGGGVYRVFRRLLRRIGlRGAGDGRGPRLHDLRHTFAVNRLTRwyreGA 159

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1081141252 259 D----LRVVQMLLGHADISTTQIYTHVARERLK 287
Cdd:cd00797   160 DverkLPVLSTYLGHVNVTDTYWYLTATPELME 192
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 126-287 7.24e-19

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: 82.08  E-value: 7.24e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 126 LKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVE---------AKGSKERIVPLGEEALYWLERYLLEA 196
Cdd:cd01186    11 INACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPredntnearAKSMRERRIPVSQDLIDLYADYLTYI 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 197 RPELLKgrLDDAVFIT----RLGSAMSRQAFWQLVKKYAKQQDIQVplSPHVLRHAFATHLLNHGADLRVVQMLLGHADI 272
Cdd:cd01186    91 YCEEAE--FSITVFVNvkggNQGKAMNYSDVYDLVRRLKKRTGIDF--TPHMFRHTHATALIRAGWSIEVVARRLGHAHV 166

                         170
                  ....*....|....*.
gi 1081141252 273 STT-QIYTHVARERLK 287
Cdd:cd01186   167 QTTlNTYGHLSEEDIR 182
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 115-278 3.33e-18

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: 80.22  E-value: 3.33e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 115 SQVELLLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRV--FHLALREGFLRVVEaKGSKERIVPLGEEALYWLERY 192
Cdd:cd01196     3 PEARRLLESIDSTHPVGLRDRALIALMVYSFARIGAVLAMRVedVYDQGRRLWVRLAE-KGGKQHEMPCHHDLEEYLRAY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 193 LLEAR-PELLKGRLddaVFITRLGS------AMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQM 265
Cdd:cd01196    82 LEAAEiEEDPKGPL---FRTTRGGTrklthnPLTQANAYRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTLEDAQN 158

                         170
                  ....*....|...
gi 1081141252 266 LLGHADISTTQIY 278
Cdd:cd01196   159 MANHASTRTTQLY 171
PRK09871 PRK09871
tyrosine recombinase; Provisional
 129-295 2.31e-17

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 78.49  E-value: 2.31e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 129 PGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEALYWLERYLLEaRPELLKGRLDDA 208
Cdd:PRK09871   23 ATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFDEREAVERWTQE-RANWKGADRTDA 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 209 VFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKT 288
Cdd:PRK09871  102 IFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTASNAARFAG 181


                  ....*..
gi 1081141252 289 LHQKHHP 295
Cdd:PRK09871  182 LWERNNL 188
int PHA02601
integrase; Provisional
 67-286 1.71e-16

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 78.23  E-value: 1.71e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  67 KPSTANRRLATLR-------RFYAWAMQHhrmeedPCLHIKAVRQAARFPKSLSESQVELLLAAPDLKTPGGLRDRAMLe 139
Cdd:PHA02601  127 KPATVNRELAYLSavfneliKLGKWSGPN------PLDGIRPFKEAEPELAFLTKEEIERLLDACDGSRSPDLGLIAKI- 199

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 140 tLYATGLRVSEliALRVFHLALREGFLRVVEAKGSKERIVPLGEealyWLERYLLEARpellkGRL-DDAvfitrlgsam 218
Cdd:PHA02601  200 -CLATGARWSE--AETLKRSQISPYKITFVKTKGKKNRTVPISE----ELYKMLPKRR-----GRLfKDA---------- 257

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 219 sRQAFwqlvKKYAKQQDIQVPL--SPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERL 286
Cdd:PHA02601  258 -YESF----ERAVKRAGIDLPEgqATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAHFAPDHL 322
PRK09870 PRK09870
tyrosine recombinase; Provisional
 112-279 3.25e-16

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 75.36  E-value: 3.25e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 112 LSESQVELLLAAPDlKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEAKGSKERIVPLGEEALYWLER 191
Cdd:PRK09870   13 LTHSEIESLLKAAN-TGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEIQALKN 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 192 YLlearpellKGRLD------DAVFITRLGSAMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQM 265
Cdd:PRK09870   92 WL--------SIRTSyphaesEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQD 163

                         170
                  ....*....|....
gi 1081141252 266 LLGHADISTTQIYT 279
Cdd:PRK09870  164 YLGHRNIRHTVWYT 177
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 120-279 3.96e-15

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: 71.95  E-value: 3.96e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 120 LLAAPDLKTPGGLRDRAMLETLYATGLRVSELIALRVFHL--ALREGFL-RVVEAKG---SKERIVPLGEEALY------ 187
Cdd:cd00799     4 MLATLDDTTLRGLRDRALLLLGFAGALRRSELVALRVEDLtrFVDGGLLiRLRRSKTdqdGEGEIKALPYGPETcpvral 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 188 --WLERYLLEARPellkgrlddaVF--ITRLGSAMSRQAFWQ----LVKKYAKQQDIQV-PLSPHVLRHAFATHLLNHGA 258
Cdd:cd00799    84 raWLEAAGIPSGP----------LFrrIRRGGSVGTTRLSDRsvarIVKRRAALAGLDPgDFSGHSLRRGFATEAARAGA 153

                         170       180
                  ....*....|....*....|.
gi 1081141252 259 DLRVVQMLLGHADISTTQIYT 279
Cdd:cd00799   154 SLPEIMAQGGHKSVATVMRYI 174
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 131-289 1.17e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 70.40  E-value: 1.17e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 131 GLRDRAMLETLYATGLRVSELIALRVFHLaLREGFLRVVEAKGSKERIVPLGEEALYWLERYLLEARPEllkgRLDDAVF 210
Cdd:cd01192    23 NPRNYLLFIVGINTGLRISDLLSLKVEDV-TNKDKLSIKEQKTGKQKTFPLNPTLVKALKEYIDDLDLK----RNDYLFK 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 211 ITRLGS--AMSRQAFWQLVKKYAKQQDIQVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTHVARERLKT 288
Cdd:cd01192    98 SLKQGPekPISRKQAYKILKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYLGIDQEDVDK 177


                  .
gi 1081141252 289 L 289
Cdd:cd01192   178 A 178
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 141-278 5.61e-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: 271191  Cd Length: 176  Bit Score: 68.60  E-value: 5.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 141 LYATGLRVSELIALRVFHLalREGFLRVVEAKGSKERI-VP--LGEEALYWLERyllearpellKGRLDDAVFITRLGSA 217
Cdd:cd01191    29 LAATGARVSELIKIKVEHV--ELGYFDIYSKGGKLRRLyIPkkLRNEALEWLKS----------TNRKSGYIFLNRFGER 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1081141252 218 MSRQAFWQLVKKYAKQQDI-QVPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIY 278
Cdd:cd01191    97 ITTRGIAQQLKNYARKYGLnPKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY 158
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
6-87 1.06e-10

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 56.88  E-value: 1.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   6 LSAFLDSLWLEDGLAKNTLAAYRQDMHAFIEFLQRERPavSVFTVKAEDIQAWLAQMHVETKP-STANRRLATLRRFYAW 84
Cdd:pfam02899   1 IDQFLEYLSLERGLSPHTLRAYRRDLLAFLKFLSEGGS--SLEQITTSDVRAFLAELRAQGLSaSSLARRLSALRSFYQF 78


                  ...
gi 1081141252  85 AMQ 87
Cdd:pfam02899  79 LIR 81
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 113-271 1.94e-08

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


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 53.04  E-value: 1.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 113 SESQVELLLAAPDlKTPGGLRDRAMLETLYATGLRVSELIALRVFHLALREGFLRVVEA--KGSKERIVPLGEEALYWLE 190
Cdd:cd00801     1 SPDELPELWRALD-TANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAErtKNKRPHRVPLSDQALEILE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 191 ryllEARPELLKGRLddaVFITRLGSA--MSRQAFWQLVKKYAKQQDIQvplSPHVLRHAFATHLLNHGADLRVVQMLLG 268
Cdd:cd00801    80 ----ELKEFTGDSGY---LFPSRRKKKkpISENTINKALKRLGYKGKEF---TPHDLRRTFSTLLNELGIDPEVIERLLN 149


                  ...
gi 1081141252 269 HAD 271
Cdd:cd00801   150 HVL 152
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 141-280 7.26e-07

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: 48.46  E-value: 7.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 141 LYaTGLRVSELIALRVFHLALREG--FLRVVEAKGSKE-------RIVPLGEEA-----LYWLERylLEARPELLKGRLD 206
Cdd:cd01184    33 LY-TGARLNEICQLRVDDIKEEDGiwCIDINDDAEGRRlktkasrRLVPIHPRLielgfLDYVEA--LRADGKLFLFPEK 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1081141252 207 DAVFITRlGSAMSRQaFWQLVKKYAKQQDIQVPLspHVLRHAFATHLLNHGADLRVVQMLLGHA-DISTTQIYTH 280
Cdd:cd01184   110 RDKDGKY-SKAASKW-FNRLLRKLGIKDDERKSF--HSFRHTFITALKRAGVPEELIAQIVGHSrGGVTHDTYGK 180
xerD PRK02436
site-specific tyrosine recombinase XerD;
4-278 4.39e-05

site-specific tyrosine recombinase XerD;


Pssm-ID: 235038 [Multi-domain]  Cd Length: 245  Bit Score: 43.82  E-value: 4.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252   4 NELSAFLDSlwleDGLAKNTLAAYRQDMHAFIEFLQRErpavsVFTVKAEDIQAWLAqmhvETKPSTANRRLATLRRFYA 83
Cdd:PRK02436    3 NYIEPFLAS----KQLSENSQKSYRYDLQQFLQLVGER-----VSQEKLKLYQQSLA----NLKPSAQKRKISAVNQFLY 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252  84 WAMQHHRMEedpclHIKAVRQAARFPKSLSESQVELLLAAPDLKTP---GGLRDRAMLETlyatGLRVSELIALRVFHLA 160
Cdd:PRK02436   70 FLYQKGELD-----SFFKLKETAKLPESKKEKLEILDLSSFYQETPfpeGQLIALLILEL----GLTPSEIAGLKVADID 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 161 LREGFLRVveAKGSKERIVPLGEEALYWLERYLlearpellkgrLDDAVFiTRLGSAMSRQAFWQLVKKYAKQQDIQvPL 240
Cdd:PRK02436  141 LDFQVLTI--EKAGGKRVLTLPEALLPFLEAIL-----------NQTYLF-EHKGKPYSRQWFFNQLKSFVKSIGYP-GL 205

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1081141252 241 SPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIY 278
Cdd:PRK02436  206 SAQKLREQFILKQKEAGKSIYELARLLGLKSPVTLEKY 243
INT_StrepXerD_C_like cd01190
Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; ...
 145-279 1.86e-04

Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; This family includes a putative XerD recombinase in Streptococcus pneumonia and similar tyrosine recombinases. However, the members of this family contain unusual active site motifs from the XerD from Escherichia coli. E. coli XerD and homologous enzymes show four conserved amino acids R-H-R-H that are spaced along the C-terminal domain. The putative S. pneumoniae XerD contains three unique replacements at the conserved positions resulting in L-Q-R-L. Severe growth defects in a loss-of-function xerD mutant demonstrate an important in vivo function of the S. pneumoniae XerD protein. 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: 271190  Cd Length: 150  Bit Score: 40.79  E-value: 1.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081141252 145 GLRVSELIALRVFHLALREGFLRVveAKGSKERIVPLGEEALywleryllearPELLKGRLDDAVFITRLGSAMSRQAFW 224
Cdd:cd01190    30 GLTPSEIANLKWADFDLDFQVLTI--EKGGIKRVLPLPKKLL-----------PFLEQHIKADYLEFDHEGKAYSRQWLF 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1081141252 225 QLVKKYAKQQDIQvPLSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYT 279
Cdd:cd01190    97 NQLKKFLNSIGLS-GLTAQKLREQYILKQKEAGKSIYELAKLLGLKSPVTLEKYY 150
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 240-280 4.90e-04

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


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 39.72  E-value: 4.90e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1081141252 240 LSPHVLRHAFATHLLNHGADLRVVQMLLGHADISTTQIYTH 280
Cdd:cd01187   102 FHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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