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Conserved domains on  [gi|1088626007|gb|OHE40275|]
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MAG: site-specific tyrosine recombinase XerD [Tenericutes bacterium GWE2_38_8]

Protein Classification

site-specific tyrosine recombinase( domain architecture ID 11493903)

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

CATH:  1.10.443.10
Gene Ontology:  GO:0009037|GO:0003677|GO:0007049|GO:0051301|GO:0006313
PubMed:  10047575|9278480|10577069
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 7-295 8.98e-130

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: 370.37  E-value: 8.98e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   7 DFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEkyHEITKPKFIEKKHIEGFLKSMKRQ-VSTKSLARKLTAIKGFHHFLM 85
Cdd:TIGR02225   2 QFLDYLWVERGLSQNTLEAYRRDLEKFLEFLE--ERGIDLEEVDRGDIVDFLAELKEAgLSARSIARALSALRSFYRFLL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  86 IEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYV 165
Cdd:TIGR02225  80 REGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFV 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 166 IVKGKGNKERMVPISDMSIIALRNYIVKSREYLL-GDLKVN-FLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTL 243
Cdd:TIGR02225 160 RVRGKGNKERLVPLGEEAIEALERYLKEARPLLLkKKVKESdALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088626007 244 RHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYKDAHPRA 295
Cdd:TIGR02225 240 RHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291
 
Name Accession Description Interval E-value
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 7-295 8.98e-130

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: 370.37  E-value: 8.98e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   7 DFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEkyHEITKPKFIEKKHIEGFLKSMKRQ-VSTKSLARKLTAIKGFHHFLM 85
Cdd:TIGR02225   2 QFLDYLWVERGLSQNTLEAYRRDLEKFLEFLE--ERGIDLEEVDRGDIVDFLAELKEAgLSARSIARALSALRSFYRFLL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  86 IEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYV 165
Cdd:TIGR02225  80 REGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFV 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 166 IVKGKGNKERMVPISDMSIIALRNYIVKSREYLL-GDLKVN-FLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTL 243
Cdd:TIGR02225 160 RVRGKGNKERLVPLGEEAIEALERYLKEARPLLLkKKVKESdALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088626007 244 RHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYKDAHPRA 295
Cdd:TIGR02225 240 RHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291
xerD PRK00283
tyrosine recombinase;
1-295 2.78e-118

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 341.79  E-value: 2.78e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   1 MKYLLKDFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEKYHeiTKPKFIEKKHIEGFLKSMKRQ-VSTKSLARKLTAIKG 79
Cdd:PRK00283    5 DRALIEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARG--LSLAEATRDDLQAFLAELAEGgYKATSSARRLSALRR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  80 FHHFLMIEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIH 159
Cdd:PRK00283   83 FFQFLLREGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVS 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 160 LNQGYVIVKGKGNKERMVPISDMSIIALRNYIVKSREYLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTE-C 238
Cdd:PRK00283  163 LRQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGRPALLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPKkL 242

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1088626007 239 SPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYKDAHPRA 295
Cdd:PRK00283  243 SPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 299
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
1-293 1.87e-104

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 306.54  E-value: 1.87e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   1 MKYLLKDFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEKYHeITKPKFIEKKHIEGFLKSM-KRQVSTKSLARKLTAIKG 79
Cdd:COG4974     3 LADLLEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEELG-KIPLAEITPEDIRAYLNYLrERGLSPSTINRYLAALRS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  80 FHHFLMIEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIH 159
Cdd:COG4974    82 FFRYAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDID 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 160 LNQGYVIVK-GKGNKERMVPISDMSIIALRNYIVKSREYllgdlKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTEC 238
Cdd:COG4974   162 LDRGTIRVRrGKGGKERTVPLSPEALEALREYLEERRPR-----DSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRV 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1088626007 239 SPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYKDAHP 293
Cdd:COG4974   237 TPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 113-284 1.27e-86

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: 256.67  E-value: 1.27e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 113 IDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKGKGNKERMVPISDMSIIALRNYIV 192
Cdd:cd00798     1 VDEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 193 KSREYLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHEDIST 272
Cdd:cd00798    81 ERRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLST 160

                         170
                  ....*....|..
gi 1088626007 273 TQIYTHISQKRI 284
Cdd:cd00798   161 TQIYTHVSFERL 172
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 110-280 2.54e-53

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: 171.73  E-value: 2.54e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 110 VLSIDEVVSILeQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVK-GKGNKERMVPISDMSIIALR 188
Cdd:pfam00589   1 RLTEDEVERLL-DAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 189 NYIVKSreyLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHE 268
Cdd:pfam00589  80 EWLSKR---LLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|..
gi 1088626007 269 DISTTQIYTHIS 280
Cdd:pfam00589 157 SISTTQIYTHVA 168
 
Name Accession Description Interval E-value
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 7-295 8.98e-130

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: 370.37  E-value: 8.98e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   7 DFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEkyHEITKPKFIEKKHIEGFLKSMKRQ-VSTKSLARKLTAIKGFHHFLM 85
Cdd:TIGR02225   2 QFLDYLWVERGLSQNTLEAYRRDLEKFLEFLE--ERGIDLEEVDRGDIVDFLAELKEAgLSARSIARALSALRSFYRFLL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  86 IEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYV 165
Cdd:TIGR02225  80 REGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFV 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 166 IVKGKGNKERMVPISDMSIIALRNYIVKSREYLL-GDLKVN-FLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTL 243
Cdd:TIGR02225 160 RVRGKGNKERLVPLGEEAIEALERYLKEARPLLLkKKVKESdALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088626007 244 RHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYKDAHPRA 295
Cdd:TIGR02225 240 RHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291
xerD PRK00283
tyrosine recombinase;
1-295 2.78e-118

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 341.79  E-value: 2.78e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   1 MKYLLKDFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEKYHeiTKPKFIEKKHIEGFLKSMKRQ-VSTKSLARKLTAIKG 79
Cdd:PRK00283    5 DRALIEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARG--LSLAEATRDDLQAFLAELAEGgYKATSSARRLSALRR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  80 FHHFLMIEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIH 159
Cdd:PRK00283   83 FFQFLLREGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVS 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 160 LNQGYVIVKGKGNKERMVPISDMSIIALRNYIVKSREYLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTE-C 238
Cdd:PRK00283  163 LRQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGRPALLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPKkL 242

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1088626007 239 SPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYKDAHPRA 295
Cdd:PRK00283  243 SPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 299
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 4-295 2.97e-113

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 329.04  E-value: 2.97e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   4 LLKDFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEKyHEITKPKFIEKKHIEGFL-KSMKRQVSTKSLARKLTAIKGFHH 82
Cdd:PRK00236    9 ALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEE-HGISSLQDLDAADLRSFLaRRRRQGLSARSLARRLSALRSFYR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  83 FLMIEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQ 162
Cdd:PRK00236   88 WLVRRGLLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSELVGLDIDDLDLAS 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 163 GYVIVKGKGNKERMVPISDMSIIALRNYIvKSREYLLGDlkVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHT 242
Cdd:PRK00236  168 GTLRVLGKGNKERTVPLGRAAREALEAYL-ALRPLFLPD--DDALFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHK 244

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1088626007 243 LRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYKDAHPRA 295
Cdd:PRK00236  245 LRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPRA 297
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 6-297 5.89e-112

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: 325.72  E-value: 5.89e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   6 KDFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEKYHEITKPKFIEKKHIEGFL-KSMKRQVSTKSLARKLTAIKGFHHFL 84
Cdd:TIGR02224   1 EAFLEYLRLERNYSPHTVRAYRRDLEAFLEFLEEEGGLASLAEVTAADLRSFLaELHARGLSRRSLARKLSALRSFYRFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  85 MIEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTR--PLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQ 162
Cdd:TIGR02224  81 LRRGLIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEDDedWLALRDRAILELLYSSGLRVSELVGLDLSDLDLDF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 163 GYVIVKGKGNKERMVPISDMSIIALRNYIVKSREYLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHT 242
Cdd:TIGR02224 161 GEVRVRGKGNKERIVPFGPYARDALQAYLEARRSPLLASEGQDALFLNRRGGRLTPRGVQYRLQQLRAKAGLPKHVHPHA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1088626007 243 LRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYKDAHPRAKE 297
Cdd:TIGR02224 241 LRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHPRAKK 295
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
1-293 1.87e-104

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 306.54  E-value: 1.87e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   1 MKYLLKDFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEKYHeITKPKFIEKKHIEGFLKSM-KRQVSTKSLARKLTAIKG 79
Cdd:COG4974     3 LADLLEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEELG-KIPLAEITPEDIRAYLNYLrERGLSPSTINRYLAALRS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  80 FHHFLMIEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIH 159
Cdd:COG4974    82 FFRYAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDID 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 160 LNQGYVIVK-GKGNKERMVPISDMSIIALRNYIVKSREYllgdlKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTEC 238
Cdd:COG4974   162 LDRGTIRVRrGKGGKERTVPLSPEALEALREYLEERRPR-----DSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRV 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1088626007 239 SPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYKDAHP 293
Cdd:COG4974   237 TPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 113-284 1.27e-86

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: 256.67  E-value: 1.27e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 113 IDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKGKGNKERMVPISDMSIIALRNYIV 192
Cdd:cd00798     1 VDEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 193 KSREYLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHEDIST 272
Cdd:cd00798    81 ERRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLST 160

                         170
                  ....*....|..
gi 1088626007 273 TQIYTHISQKRI 284
Cdd:cd00798   161 TQIYTHVSFERL 172
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
8-289 1.55e-85

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 257.97  E-value: 1.55e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   8 FEYYL--KKEKGSSQNTIAAYLTDLNQYTLFLEKYHeiTKPKFIEKKHIEGFLKSMKRQ-VSTKSLARKLTAIKGFHHFL 84
Cdd:COG4973     8 LEAYLehLRERRLSPKTLEAYRRDLRRLIPLLGDAD--LPLEELTPADVRRFLARLHRRgLSPRTLNRRLSALRSFFNWA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  85 MIEKEVDADVAKAFSAPKVEKSLPQVLSIDEVVSILEQVDKTrPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGY 164
Cdd:COG4973    86 VREGLLEANPAAGVKAPKAPRKLPRALTVDELAQLLDALADD-PLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGE 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 165 VIVKGKGNKERMVPISDMSIIALRNYIVKSREYLLGDLkvNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLR 244
Cdd:COG4973   165 VRVRGKTGKSRTVPLGPKALAALREWLAVRPELAAPDE--GALFPSRRGTRLSPRNVQKRLRRLAKKAGLPKHVHPHDLR 242

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1088626007 245 HSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIYK 289
Cdd:COG4973   243 HSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVYR 287
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 51-299 3.43e-56

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 185.33  E-value: 3.43e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  51 KKHIEGFLKSMKRQVSTKSLARKLTAIKGFHHFLMIEKEVDADVAKAFSAPKVEKSLP-QVLSIDEVVSILEQVDKTRPL 129
Cdd:PRK01287   76 QRYLYGYRKANGEPLSTRTQRTQLSPLRVWFRWLLKRHHILYNPAEDLELPKEEKRLPrQILSEAETEQVLASPDLTTLQ 155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 130 GLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYV-IVKGKGNKERMVPISDMSIIALRNYIVKSREYLLGDLKVNFLF 208
Cdd:PRK01287  156 GLRDRALLELLWSTGIRRGELARLDLYDVDASRGVVtVRQGKGNKDRVVPVGERALAWLQRYLQDVRPQLAVRPDSGALF 235

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 209 VNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRIKEIY 288
Cdd:PRK01287  236 VAMDGDGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAVH 315

                         250
                  ....*....|....
gi 1088626007 289 KDAHP---RAKEVL 299
Cdd:PRK01287  316 ASTHPaerKADEKL 329
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 110-280 2.54e-53

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: 171.73  E-value: 2.54e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 110 VLSIDEVVSILeQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVK-GKGNKERMVPISDMSIIALR 188
Cdd:pfam00589   1 RLTEDEVERLL-DAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 189 NYIVKSreyLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHE 268
Cdd:pfam00589  80 EWLSKR---LLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|..
gi 1088626007 269 DISTTQIYTHIS 280
Cdd:pfam00589 157 SISTTQIYTHVA 168
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 107-279 3.56e-52

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: 168.99  E-value: 3.56e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 107 LPQVLSIDEVVSILEQVDKtrplgLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVK-GKGNKERMVPISDMSII 185
Cdd:cd01193     2 LPVVLSPDEVRRILGALTE-----LRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRqGKGGKDRVVPLPEKLLE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 186 ALRNYIVKSR---EYLLGDLKVNFLFVNQNGNR---LSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLR 259
Cdd:cd01193    77 PLRRYLKSARpkeELDPAEGRAGVLDPRTGVERrhhISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIR 156

                         170       180
                  ....*....|....*....|
gi 1088626007 260 TLQTLLGHEDISTTQIYTHI 279
Cdd:cd01193   157 TIQELLGHSDLSTTMIYTHV 176
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 115-277 1.96e-45

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: 151.48  E-value: 1.96e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 115 EVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKGKG---NKERMVPISDMSIIALRNYI 191
Cdd:cd00397     1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkgGKERTVPLPKELAEELKEYL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 192 VKSRE---YLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKteCSPHTLRHSFATHLLENGMDLRTLQTLLGHE 268
Cdd:cd00397    81 KERRDkrgPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRK--ITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158


                  ....*....
gi 1088626007 269 DISTTQIYT 277
Cdd:cd00397   159 SISTTQRYL 167
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 16-279 4.12e-45

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: 155.24  E-value: 4.12e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  16 KGSSQNTIAAYLTDLNQYTLFLEKYHeitkPKFIEKKHIEGFLKSM--KRQVSTKSLARKLTAI-KGFHHFLMIEKEVDA 92
Cdd:TIGR02249  12 RHYAKRTEEAYLHWIKRFIRFHNKRH----PSTMGDTEVEAFLSDLavDGKVAASTQNQALNALlFLYKEILKTPLSLME 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  93 DVAKAfsapKVEKSLPQVLSIDEVVSILEQVDKTRPLglrnmaLLELIYGSGLRVSELLDIQMEDIHLNQGYVIVK-GKG 171
Cdd:TIGR02249  88 RFVRA----KRPRKLPVVLTREEVRRLLEHLEGKYRL------IAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRqGKG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 172 NKERMVPISDMSIIALRNYIVKSREYLLGDLKVNFLFV-----------NQN----------GNRLSR------------ 218
Cdd:TIGR02249 158 GKDRTVTLPKELIPPLREQIELARAYHEADLAEGYGGVylphalarkypNAPkewgwqylfpSHRLSRdpesgvirrhhi 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1088626007 219 --QGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHI 279
Cdd:TIGR02249 238 neTTIQRAVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHV 300
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 111-286 9.15e-45

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: 150.12  E-value: 9.15e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 111 LSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHL-NQGYVIVKGKGNKERMVPISDMSIIALRN 189
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLdDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 190 YIvksREYLLGDLKVN--FLFVNQNGNRLSRQGFFKILKKLSTDAgvKTEC-------SPHTLRHSFATHLLENGMDLRT 260
Cdd:cd01182    81 YL---QEFHLTPDPKQlfPLFPNRRGQPLTRDGVAYILNKYVALA--SNRCpslpkriTPHTLRHTKAMHLLQAGVDLTV 155

                         170       180
                  ....*....|....*....|....*.
gi 1088626007 261 LQTLLGHEDISTTQIYTHISQKRIKE 286
Cdd:cd01182   156 IRDWLGHESVETTQIYAEADLEMKRE 181
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 9-286 3.46e-32

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 121.95  E-value: 3.46e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   9 EYY-LKKEKGSSQNTIAAYLTDLNQYT--LFLEKYHEITKPKFIE--------KKHIEGFL-----------KSMKRQVS 66
Cdd:PRK05084   23 EYYqSKLATPYSPTTLYEYLTEYRRFFnwLISEGLSDASKIKDIPlstlenltKKDVEAFIlylrerpllngHSTKKGNS 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  67 TKSLARKLTAIKGFHHFLMIEKE-------VDADVAKAFSAPKVEKSLP--------QVLSIDEVVSILEQVDKTRPLGL 131
Cdd:PRK05084  103 QTTINRTLSALKSLFKYLTEEAEnedgepyFYRNVMKKIELKKKKETLAarahnlkqKLFLGDEDYEFLDFIDNEYEQKL 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 132 -------------RNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKGKGNKERMVPISDMSIIALRNYIVKSREYL 198
Cdd:PRK05084  183 snralssfkknkeRDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEYLKIRASRY 262

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 199 LGDLKVNFLFV---NQNGNRLSRQGFFKILKKLSTDAGVKTecSPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQI 275
Cdd:PRK05084  263 KAEKQEKALFLtkyRGKPNRISARAIEKMVAKYSEAFGVRL--TPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDL 340

                         330
                  ....*....|.
gi 1088626007 276 YTHISQKRIKE 286
Cdd:PRK05084  341 YTHIVNDEQKE 351
PRK15417 PRK15417
integron integrase;
39-283 3.99e-32

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 121.69  E-value: 3.99e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  39 KYHEITKPKFIEKKHIEGFLKSM--KRQVSTKSLARKLTAIKGFHHFLMIekeVDADVAKAFSAPKVEKSLPQVLSIDEV 116
Cdd:PRK15417   46 RFHGVRHPATLGSSEVEAFLSWLanERKVSVSTHRQALAALLFFYGKVLC---TDLPWLQEIGRPRPSRRLPVVLTPDEV 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 117 VSILEQVDKTRPLglrnmaLLELIYGSGLRVSELLDIQMEDIHLNQGYVIVK-GKGNKERMVPISDMSIIALRNYIVKSR 195
Cdd:PRK15417  123 VRILGFLEGEHRL------FAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKDRALMLPESLAPSLREQLSRAR 196

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 196 EYLLGDLKVN------------------------FLFVNQNGNRLSRQG-----------FFKILKKLSTDAGVKTECSP 240
Cdd:PRK15417  197 AWWLKDQAEGrsgvalpdalerkypraghswpwfWVFAQHTHSTDPRSGvvrrhhmydqtFQRAFKRAVEQAGITKPATP 276

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1088626007 241 HTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKR 283
Cdd:PRK15417  277 HTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVG 319
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 111-278 1.33e-28

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: 108.55  E-value: 1.33e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 111 LSIDEVVSILEQVDKTRPL-GLRN--MA-LLELIYGSGLRVSELLDIQMEDIHLNQGYVIVK-GKGNKERMVPISDMSII 185
Cdd:cd00797     1 YTDAEIRRLLAAADQLPPEsPLRPltYAtLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRqTKFGKSRLVPLHPSTVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 186 ALRNYIvKSREYLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECS-----PHTLRHSFATHLL----ENGM 256
Cdd:cd00797    81 ALRDYL-ARRDRLLPSPSSSYFFVSQQGGRLTGGGVYRVFRRLLRRIGLRGAGDgrgprLHDLRHTFAVNRLtrwyREGA 159

                         170       180
                  ....*....|....*....|....*.
gi 1088626007 257 D----LRTLQTLLGHEDISTTQIYTH 278
Cdd:cd00797   160 DverkLPVLSTYLGHVNVTDTYWYLT 185
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 115-287 8.56e-26

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: 100.66  E-value: 8.56e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 115 EVVSILEQVDKTRpLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKG-KGNKERMVPISDMSIIALRNYIvK 193
Cdd:cd01197    11 EVQALLQAACRGR-TPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRlKNGFSTTHPLRFDEREALEAWL-K 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 194 SREYLLGDlKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTT 273
Cdd:cd01197    89 ERANWKGA-DTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGHRNIRHT 167

                         170
                  ....*....|....
gi 1088626007 274 QIYTHISQKRIKEI 287
Cdd:cd01197   168 VIYTASNAARFANL 181
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 112-287 1.38e-25

C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; Recombinases RitA (also known as pAE1), RitB, and RitC are encoded by three adjacent and overlapping genes. Collectively they are known as the Recombinase in Trio (RIT). This RitA family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 100.01  E-value: 1.38e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 112 SIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKG-KGNKERMVPISDMSIIALRNY 190
Cdd:cd01188     1 SPDEVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQkKTGRPVELPLTEPVGEALADY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 191 IVKSREYLlgDLKVNFLFVNQNGNRLSRQ-GFFKILKKLSTDAGVKTEC-SPHTLRHSFATHLLENGMDLRTLQTLLGHE 268
Cdd:cd01188    81 LRDGRPRT--DSREVFLRARAPYRPLSSTsQISSIVRRYLRKAGIEPSHrGTHSLRHSLATRMLRAGTSLKVIADLLGHR 158

                         170
                  ....*....|....*....
gi 1088626007 269 DISTTQIYTHISQKRIKEI 287
Cdd:cd01188   159 SIETTAIYAKIDVDDLREV 177
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 112-278 4.65e-25

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: 98.31  E-value: 4.65e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 112 SIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKGKGNKER-MVPISDMSIIALRNY 190
Cdd:cd01195     1 SREEARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQReVVTLPPTTREALAAW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 191 IVKSREYLlGDLKVNFlFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDL-RTLQTLLGHED 269
Cdd:cd01195    81 LAARGEAE-GPLFVSL-DRASRGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGLiRKVQDFSRHAD 158


                  ....*....
gi 1088626007 270 ISTTQIYTH 278
Cdd:cd01195   159 LRTLQVYDD 167
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 109-278 9.51e-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: 94.70  E-value: 9.51e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 109 QVLSIDEVVSILEQVDKTRPLGLRNMALLELiyGSGLRVSELLDIQMEDIHLNQGYVIVKG-KGNKERMVPISDMSIIAL 187
Cdd:cd00796     3 RFLTEDEEARLLAALEESTNPHLRLIVLLAL--YTGARRGEILSLRWDDIDLEVGLIVLPEtKNGKPRTVPLSDEAIAIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 188 RNYIVKSREYLLgdlkvnflFVNQNGNRLSRQGFFKILKKLSTDAGVkTECSPHTLRHSFATHLLENGMDLRTLQTLLGH 267
Cdd:cd00796    81 KELKRKRGKDGF--------FVDGRFFGIPIASLRRAFKKARKRAGL-EDLRFHDLRHTFASRLVQAGVPIKTVAKILGH 151

                         170
                  ....*....|.
gi 1088626007 268 EDISTTQIYTH 278
Cdd:cd00796   152 SSIKMTMRYAH 162
PRK09871 PRK09871
tyrosine recombinase; Provisional
 111-293 1.03e-21

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 90.43  E-value: 1.03e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 111 LSIDEVVSILEQVdKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKGKGNKERMV-PISDMSIIALRN 189
Cdd:PRK09871    7 LTGKEVQAMMQAV-CYGATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVhPLRFDEREAVER 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 190 YiVKSREYLLGDLKVNFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHED 269
Cdd:PRK09871   86 W-TQERANWKGADRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRN 164

                         170       180
                  ....*....|....*....|....
gi 1088626007 270 ISTTQIYTHISQKRIKEIYKDAHP 293
Cdd:PRK09871  165 IRHTVRYTASNAARFAGLWERNNL 188
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 130-278 1.45e-21

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: 89.36  E-value: 1.45e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 130 GLRNMALLELIYGSGLRVSELLDIQMEDIHLNQG----YVIVKGKGNKERMVPISDMSIIALRNYIvKSREYLLgdlKVN 205
Cdd:cd01194    21 GLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEgtilYVQGKGKTSKDDFVYLRPDVLKALQAYL-KARGKLD---FEE 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088626007 206 FLFV----NQNGNRLSRQGFFKILKKLSTDAGVKTE-CSPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTH 278
Cdd:cd01194    97 PLFTslsnNSKGQRLTTRSIRRIIKKYLRKAGLDDDrLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIYAH 174
PRK09870 PRK09870
tyrosine recombinase; Provisional
 111-294 5.72e-21

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 88.46  E-value: 5.72e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 111 LSIDEVVSILEQVDkTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYV-IVKGKGNKERMVPISDMSIIALRN 189
Cdd:PRK09870   13 LTHSEIESLLKAAN-TGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIyIHRLKKGFSTTHPLLNKEIQALKN 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 190 YIVKSREYLLGDLKvnFLFVNQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHED 269
Cdd:PRK09870   92 WLSIRTSYPHAESE--WVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRN 169

                         170       180
                  ....*....|....*....|....*
gi 1088626007 270 ISTTQIYTHISQKRIKEIYKDAHPR 294
Cdd:PRK09870  170 IRHTVWYTASNAGRFYGIWDRARGR 194
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 144-284 1.38e-19

Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain; IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271185 [Multi-domain]  Cd Length: 161  Bit Score: 83.47  E-value: 1.38e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 144 GLRVSELLDIQMEDI-HLNQGYVIVK--GKGNKERMVPISD--MSIIALRNYIVKSReyllgdlKVNFLFVNQNGNRlsr 218
Cdd:cd01185    31 GLRFSDLKNLTWKNIvEASGRTWIRYrrKKTGKPVTVPLLPvaREILEKYKDDRSEG-------KLFPVLSNQKINR--- 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1088626007 219 qgffkILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYTHISQKRI 284
Cdd:cd01185   101 -----YLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVDSKK 161
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 112-276 1.50e-19

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: 84.07  E-value: 1.50e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 112 SIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHL--NQGYVIVKGKGNKERMVPISDMSIIALRN 189
Cdd:cd01196     1 TAPEARRLLESIDSTHPVGLRDRALIALMVYSFARIGAVLAMRVEDVYDqgRRLWVRLAEKGGKQHEMPCHHDLEEYLRA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 190 YIVKSReyLLGDLKVNFLFVNQNG------NRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQT 263
Cdd:cd01196    81 YLEAAE--IEEDPKGPLFRTTRGGtrklthNPLTQANAYRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTLEDAQN 158

                         170
                  ....*....|...
gi 1088626007 264 LLGHEDISTTQIY 276
Cdd:cd01196   159 MANHASTRTTQLY 171
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 109-287 8.30e-19

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: 81.95  E-value: 8.30e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 109 QVLSIDEVVSILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKGKGNKERMVPISDMSIIALR 188
Cdd:cd01192     2 IVEPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVTNKDKLSIKEQKTGKQKTFPLNPTLVKALK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 189 NYIvKSREYLLGDLKVNFLFVNQNGNrLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHE 268
Cdd:cd01192    82 EYI-DDLDLKRNDYLFKSLKQGPEKP-ISRKQAYKILKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHS 159

                         170
                  ....*....|....*....
gi 1088626007 269 DISTTQIYTHISQKRIKEI 287
Cdd:cd01192   160 SPSITLRYLGIDQEDVDKA 178
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 113-278 8.61e-19

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: 81.07  E-value: 8.61e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 113 IDEVVSILEQVDKTrplGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKG---------------KGNK-ERM 176
Cdd:cd01189     1 PEELKKLLEALKKR---GDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRtlvrkkkggyvikppKTKSsIRT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 177 VPISDMSIIALRNYIVksreyllgdlkvnflfvnqngnrlsrqgFFKILKKlstdAGVKTeCSPHTLRHSFATHLLENGM 256
Cdd:cd01189    78 IPLPDELIELLKELKA----------------------------FKKLLKK----AGLPR-ITPHDLRHTFASLLLEAGV 124

                         170       180
                  ....*....|....*....|...
gi 1088626007 257 DLRTLQTLLGHEDISTT-QIYTH 278
Cdd:cd01189   125 PLKVIAERLGHSDISTTlDVYAH 147
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 9-278 2.55e-16

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 78.54  E-value: 2.55e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   9 EYYLKKEKGSSQNTIAAYLTDLNQYTL-FLEKY--HEITKPkfiekkHIEGFLKSMKRQVSTKSLARKLTAIKGFHHFLM 85
Cdd:COG0582   105 EWLEEKKPEWKEKTAAQVRRTLEKHIFpVLGDRpiAEITPP------DLLAVLRPIEARGAPETARRVRQRLRQVFRYAV 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  86 IEKEVD----ADVAKAFSAPKVEKslPQVLSIDEVVSILEQVDKTRplGLRNMAL-LELIYGSGLRVSELLDIQMEDIHL 160
Cdd:COG0582   179 ARGLIErnpaADLKGALPKPKVKH--HPALTPEELPELLRALDAYR--GSPVTRLaLRLLLLTGVRPGELRGARWSEIDL 254

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 161 NQGYVIV---KGKGNKERMVPISDMSIIALRNYIVKSREYllgdlkvNFLFVNQNGNR--LSRQGFFKILKKLstdaGVK 235
Cdd:COG0582   255 EAALWTIpaeRMKTRRPHIVPLSRQALEILKELKPLTGDS-------EYVFPSRRGPKkpMSENTLNKALRRM----GYG 323

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1088626007 236 tECSPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQ-IYTH 278
Cdd:COG0582   324 -RFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaAYNR 366
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 118-277 2.85e-16

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: 75.41  E-value: 2.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 118 SILEQVDKTRPLGLRNMALLELIYGSGLRVSELLDIQMEDI--HLNQGYVIV--KGKGN---KERMVPISDMSII----A 186
Cdd:cd00799     3 AMLATLDDTTLRGLRDRALLLLGFAGALRRSELVALRVEDLtrFVDGGLLIRlrRSKTDqdgEGEIKALPYGPETcpvrA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 187 LRNYIVKSReyllgdLKVNFLF--VNQNGN----RLSRQGFFKILKKLSTDAGV-KTECSPHTLRHSFATHLLENGMDLR 259
Cdd:cd00799    83 LRAWLEAAG------IPSGPLFrrIRRGGSvgttRLSDRSVARIVKRRAALAGLdPGDFSGHSLRRGFATEAARAGASLP 156

                         170
                  ....*....|....*...
gi 1088626007 260 TLQTLLGHEDISTTQIYT 277
Cdd:cd00799   157 EIMAQGGHKSVATVMRYI 174
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 143-276 2.41e-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: 69.76  E-value: 2.41e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 143 SGLRVSELLDIQMEdiHLNQGYVIVKGKGNKERMVPISdmsiIALRNyivKSREYLLG-DLKVNFLFVNQNGNRLSRQGF 221
Cdd:cd01191    32 TGARVSELIKIKVE--HVELGYFDIYSKGGKLRRLYIP----KKLRN---EALEWLKStNRKSGYIFLNRFGERITTRGI 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1088626007 222 FKILKKLSTDAGVKTEC-SPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIY 276
Cdd:cd01191   103 AQQLKNYARKYGLNPKVvYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY 158
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 110-286 5.74e-14

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: 68.98  E-value: 5.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 110 VLSIDEVVSILEQVDKtrplgLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIVKGKGN----------KERMVPI 179
Cdd:cd01186     1 VLTPREVQELINACNN-----LRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPREDntnearaksmRERRIPV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 180 SDMSIIALRNYIVKsrEYLLGDLKVNFLFVNqngnrLSRQGFFKILKKLSTDAGVKT-------ECSPHTLRHSFATHLL 252
Cdd:cd01186    76 SQDLIDLYADYLTY--IYCEEAEFSITVFVN-----VKGGNQGKAMNYSDVYDLVRRlkkrtgiDFTPHMFRHTHATALI 148

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1088626007 253 ENGMDLRTLQTLLGHEDISTT-QIYTHISQKRIKE 286
Cdd:cd01186   149 RAGWSIEVVARRLGHAHVQTTlNTYGHLSEEDIRR 183
int PHA02601
integrase; Provisional
 102-280 8.82e-14

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 70.53  E-value: 8.82e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 102 KVEKSLPQVLSIDEVVSILEQVDKTRPLGLRNMALLELiyGSGLRVSELLDIQMEDIHLNQgYVIVKGKGNKERMVPISD 181
Cdd:PHA02601  164 KEAEPELAFLTKEEIERLLDACDGSRSPDLGLIAKICL--ATGARWSEAETLKRSQISPYK-ITFVKTKGKKNRTVPISE 240

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 182 msiiALRNYIVKSREYLLGDlkvnflfvnqngnrlSRQGFFKILKKLSTD--AGVKTecspHTLRHSFATHLLENGMDLR 259
Cdd:PHA02601  241 ----ELYKMLPKRRGRLFKD---------------AYESFERAVKRAGIDlpEGQAT----HVLRHTFASHFMMNGGNIL 297

                         170       180
                  ....*....|....*....|.
gi 1088626007 260 TLQTLLGHEDISTTQIYTHIS 280
Cdd:PHA02601  298 VLQRILGHATIEMTMAYAHFA 318
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
5-88 3.20e-12

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 61.12  E-value: 3.20e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007   5 LKDFEYYLKKEKGSSQNTIAAYLTDLNQYTLFLEkyHEITKPKFIEKKHIEGFLKSMKRQ-VSTKSLARKLTAIKGFHHF 83
Cdd:pfam02899   1 IDQFLEYLSLERGLSPHTLRAYRRDLLAFLKFLS--EGGSSLEQITTSDVRAFLAELRAQgLSASSLARRLSALRSFYQF 78


                  ....*
gi 1088626007  84 LMIEK 88
Cdd:pfam02899  79 LIREG 83
xerD PRK02436
site-specific tyrosine recombinase XerD;
15-276 3.93e-11

site-specific tyrosine recombinase XerD;


Pssm-ID: 235038 [Multi-domain]  Cd Length: 245  Bit Score: 61.93  E-value: 3.93e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  15 EKGSSQNTIAAYLTDLNQYTLFLEkyHEITKPKfiekkhiegfLKSMKRQVSTKSLA---RKLTAIKGFHHFLMIEKEVD 91
Cdd:PRK02436   11 SKQLSENSQKSYRYDLQQFLQLVG--ERVSQEK----------LKLYQQSLANLKPSaqkRKISAVNQFLYFLYQKGELD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007  92 aDVAKAFSAPKVEKSLPQVLSIDEVvSILEQvDKTRPLGlRNMALLelIYGSGLRVSELLDIQMEDIHLNQGYVIVKGKG 171
Cdd:PRK02436   79 -SFFKLKETAKLPESKKEKLEILDL-SSFYQ-ETPFPEG-QLIALL--ILELGLTPSEIAGLKVADIDLDFQVLTIEKAG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 172 NKeRMVPISDMSIialrnyivksrEYLLGDLKVNFLFVNqNGNRLSRQGFFKILKKLSTDAGvKTECSPHTLRHSFATHL 251
Cdd:PRK02436  153 GK-RVLTLPEALL-----------PFLEAILNQTYLFEH-KGKPYSRQWFFNQLKSFVKSIG-YPGLSAQKLREQFILKQ 218

                         250       260
                  ....*....|....*....|....*
gi 1088626007 252 LENGMDLRTLQTLLGHEDISTTQIY 276
Cdd:PRK02436  219 KEAGKSIYELARLLGLKSPVTLEKY 243
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 137-277 2.55e-08

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: 52.35  E-value: 2.55e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 137 LELIYGSGLRVSELLDIQMEDIHlNQGYVIVKGKGNKERMVPISDmsiiALRNYIVKSREYLLGdlKVNFLFVNQNGNRL 216
Cdd:cd00800    18 MELALLTGQRQGDLLRLKWSDIT-DGGLLVEQSKTGKKLLIPWTP----SLRALVDRIRALPRK--RSEYLINSRKGGPL 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088626007 217 SRQGFFKILKKLSTDAGVKTECSP---HTLRHSFATHLLENGmDLRTLQTLLGHEDISTTQIYT 277
Cdd:cd00800    91 SYDTLKSAWRRARKAAGLKGETEGftfHDLRAKAATDYAEQG-GSTDAQALLGHKSDAMTERYT 153
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 112-283 4.29e-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: 51.89  E-value: 4.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 112 SIDEVVSILEQVDKTRpLGLRNMALLELIYGSGLRVSELLDIQMEDIHLNQGYVIV---KGKGNKERMVPISDMSIIALR 188
Cdd:cd00801     1 SPDELPELWRALDTAN-LSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIpaeRTKNKRPHRVPLSDQALEILE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 189 NY--IVKSREYLLGdlkvnflfvnQNGNRLSRQGFFKILKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLG 266
Cdd:cd00801    80 ELkeFTGDSGYLFP----------SRRKKKKPISENTINKALKRLGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLN 149

                         170       180
                  ....*....|....*....|.
gi 1088626007 267 HEDIS-TTQIY---THISQKR 283
Cdd:cd00801   150 HVLGGvVRAAYnryDYLEERR 170
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 143-278 7.29e-08

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


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 51.54  E-value: 7.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 143 SGLRVSELLDIQMEDIHLNQG-YVI----------VKGKgNKERMVPISDMSI-IALRNYiVKSR--EYLLGDLKVNFLF 208
Cdd:cd01184    35 TGARLNEICQLRVDDIKEEDGiWCIdinddaegrrLKTK-ASRRLVPIHPRLIeLGFLDY-VEALraDGKLFLFPEKRDK 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1088626007 209 VNQNGNRLSRQgFFKILKKL--STDAGVktecSPHTLRHSFATHLLENGMDLRTLQTLLGHE-DISTTQIYTH 278
Cdd:cd01184   113 DGKYSKAASKW-FNRLLRKLgiKDDERK----SFHSFRHTFITALKRAGVPEELIAQIVGHSrGGVTHDTYGK 180
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 119-278 8.21e-08

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: 50.51  E-value: 8.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 119 ILEQVDKTRplglRNMALLELIYGSGLRVSELLDIQMEDIHLNQG-------YVIVKGKGNKERMVPISDMSIIALRNYi 191
Cdd:cd01187     5 NLAALDLLP----QPIPVVQAAVFTGARASELATLKFGCLHAQTSddgtflyWLKWENKGGKQLDIPISKKVAELIKTI- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 192 vksREYLlgdlkvnflfvnqngNRLSRqgffkiLKKLSTDAGVKTECSPHTLRHSFATHLLENGMDLRTLQTLLGHEDIS 271
Cdd:cd01187    80 ---NWTL---------------NELSE------LKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPE 135


                  ....*..
gi 1088626007 272 TTQIYTH 278
Cdd:cd01187   136 MTLRYAL 142
INT_StrepXerD_C_like cd01190
Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; ...
 139-277 8.06e-07

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: 47.73  E-value: 8.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 139 LIYGSGLRVSELLDIQMEDIHLNQGYVIVKgKGNKERMVPISDMSIIalrnyivksreYLLGDLKVNFLFVNQNGNRLSR 218
Cdd:cd01190    25 LILELGLTPSEIANLKWADFDLDFQVLTIE-KGGIKRVLPLPKKLLP-----------FLEQHIKADYLEFDHEGKAYSR 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1088626007 219 QGFFKILKKLSTDAGVKtECSPHTLRHSFATHLLENGMDLRTLQTLLGHEDISTTQIYT 277
Cdd:cd01190    93 QWLFNQLKKFLNSIGLS-GLTAQKLREQYILKQKEAGKSIYELAKLLGLKSPVTLEKYY 150
Integrase_1 pfam12835
Integrase; This is a family of DNA-binding prophage integrases found in Proteobacteria.
 113-248 4.63e-05

Integrase; This is a family of DNA-binding prophage integrases found in Proteobacteria.


Pssm-ID: 432820  Cd Length: 149  Bit Score: 42.83  E-value: 4.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626007 113 IDEVVSILEQVDKtrplGLrnMALLELIYGSGLRVSELL----DIQMEDIHLNQGY---VIVKG-KGNKERMVPISDmsI 184
Cdd:pfam12835  19 YQSVLRKAEEIDA----GV--AAALQLARVLGLRSEEAVqcaaSLKTWEKALERGDetlRIVFGtKGGRPRETRILE--R 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088626007 185 IALRNYIvksrEYLLGDLKVNFLFVNQNGNRLSRQGFFKilkKLSTDAGVKTECSPHTLRHSFA 248
Cdd:pfam12835  91 EALKNAV----RLAIKIAKERNGKLIDKPDLHLAPNRYR---NILRRLGLTGPYSPHSLRYAYA 147
 
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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