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Conserved domains on  [gi|2738594402|ref|WP_348488360|]
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phage integrase N-terminal SAM-like domain-containing protein, partial [Parvibaculum sp.]

Protein Classification

tyrosine-type recombinase/integrase( domain architecture ID 11471964)

tyrosine-type recombinase/integrase cleaves 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.

Gene Ontology:  GO:0009009|GO:0006310
PubMed:  10047575|9278480

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
13-138 2.78e-19

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 81.19  E-value: 2.78e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2738594402  13 LRQRMQHDMLMRGLGSHTRQDYVRHVRYFAAFLG----RSPDTATPDDIRRFQLDQHEKGVGPATINGAVSALRFLFLVT 88
Cdd:COG4974     7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEelgkIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2738594402  89 LQRR----DLSRALVITRYHRKLPDVLSVEEAGRLLEAAP-----GLKYKAALGVAYGA 138
Cdd:COG4974    87 VREGlledNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDtetpeGLRDRALLLLLYAT 145
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
13-138 2.78e-19

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 81.19  E-value: 2.78e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2738594402  13 LRQRMQHDMLMRGLGSHTRQDYVRHVRYFAAFLG----RSPDTATPDDIRRFQLDQHEKGVGPATINGAVSALRFLFLVT 88
Cdd:COG4974     7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEelgkIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2738594402  89 LQRR----DLSRALVITRYHRKLPDVLSVEEAGRLLEAAP-----GLKYKAALGVAYGA 138
Cdd:COG4974    87 VREGlledNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDtetpeGLRDRALLLLLYAT 145
xerD PRK00283
tyrosine recombinase;
20-137 1.19e-12

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 62.90  E-value: 1.19e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2738594402  20 DMLM--RGLGSHTRQDYVRHVRYFAAFL---GRSPDTATPDDIRRFQLDQHEKGVGPATINGAVSALR--FLFLVTLQRR 92
Cdd:PRK00283   14 DALWveRGLAENTLSSYRRDLELFAEWLaarGLSLAEATRDDLQAFLAELAEGGYKATSSARRLSALRrfFQFLLREGLR 93

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2738594402  93 --DLSRALVITRYHRKLPDVLSVEEAGRLLEAAP-----GLKYKAALGVAYG 137
Cdd:PRK00283   94 edDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDidtplGLRDRAMLELLYA 145
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
13-91 3.20e-12

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 58.01  E-value: 3.20e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2738594402  13 LRQRMQHDMLMRGLGSHTRQDYVRHVRYFAAFL-GRSPDTATPDDIRRFQLD-QHEKGVGPATINGAVSALRFLFLVTLQ 90
Cdd:pfam13495   1 LLERFREALRLRGYAERTIKAYLRWIRRFLRFHdKKHPEELTEEDIEAYLSHlANERNVSASTQNQALNALSFFYRWVLE 80


                  .
gi 2738594402  91 R 91
Cdd:pfam13495  81 R 81
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 106-138 1.38e-04

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: 39.57  E-value: 1.38e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2738594402 106 KLPDVLSVEEAGRLLEAAPGLKYKAALGVAYGA 138
Cdd:cd01193     1 KLPVVLSPDEVRRILGALTELRHRLILSLLYGA 33
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
13-138 2.78e-19

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 81.19  E-value: 2.78e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2738594402  13 LRQRMQHDMLMRGLGSHTRQDYVRHVRYFAAFLG----RSPDTATPDDIRRFQLDQHEKGVGPATINGAVSALRFLFLVT 88
Cdd:COG4974     7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEelgkIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2738594402  89 LQRR----DLSRALVITRYHRKLPDVLSVEEAGRLLEAAP-----GLKYKAALGVAYGA 138
Cdd:COG4974    87 VREGlledNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDtetpeGLRDRALLLLLYAT 145
xerD PRK00283
tyrosine recombinase;
20-137 1.19e-12

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 62.90  E-value: 1.19e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2738594402  20 DMLM--RGLGSHTRQDYVRHVRYFAAFL---GRSPDTATPDDIRRFQLDQHEKGVGPATINGAVSALR--FLFLVTLQRR 92
Cdd:PRK00283   14 DALWveRGLAENTLSSYRRDLELFAEWLaarGLSLAEATRDDLQAFLAELAEGGYKATSSARRLSALRrfFQFLLREGLR 93

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2738594402  93 --DLSRALVITRYHRKLPDVLSVEEAGRLLEAAP-----GLKYKAALGVAYG 137
Cdd:PRK00283   94 edDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDidtplGLRDRAMLELLYA 145
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
24-137 1.49e-12

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 62.67  E-value: 1.49e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2738594402  24 RGLGSHTRQDYVRHVRYFAAFLG---RSPDTATPDDIRRFQLDQHEKGVGPATINGAVSALR--FLFLVTLQRRDLSRAL 98
Cdd:COG4973    18 RRLSPKTLEAYRRDLRRLIPLLGdadLPLEELTPADVRRFLARLHRRGLSPRTLNRRLSALRsfFNWAVREGLLEANPAA 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2738594402  99 VIT--RYHRKLPDVLSVEEAGRLLEAAP----GLKYKAALGVAYG 137
Cdd:COG4973    98 GVKapKAPRKLPRALTVDELAQLLDALAddplAVRDRAIVELLYS 142
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
13-91 3.20e-12

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 58.01  E-value: 3.20e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2738594402  13 LRQRMQHDMLMRGLGSHTRQDYVRHVRYFAAFL-GRSPDTATPDDIRRFQLD-QHEKGVGPATINGAVSALRFLFLVTLQ 90
Cdd:pfam13495   1 LLERFREALRLRGYAERTIKAYLRWIRRFLRFHdKKHPEELTEEDIEAYLSHlANERNVSASTQNQALNALSFFYRWVLE 80


                  .
gi 2738594402  91 R 91
Cdd:pfam13495  81 R 81
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 24-124 5.77e-10

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 55.55  E-value: 5.77e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2738594402  24 RGLGSHTRQDYVRHVRYFAAFL----GRSPDTATPDDIRRFQLDQHEKGVGPATINGAVSALRfLFLVTLQRRDL----- 94
Cdd:PRK00236   21 RGLSPHTLRAYRRDLRAFLAFLeehgISSLQDLDAADLRSFLARRRRQGLSARSLARRLSALR-SFYRWLVRRGLlkanp 99

                          90       100       110
                  ....*....|....*....|....*....|
gi 2738594402  95 SRALVITRYHRKLPDVLSVEEAGRLLEAAP 124
Cdd:PRK00236  100 AAGLRAPKIPKRLPKPLDVDQAKRLLDAID 129
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
24-85 3.87e-06

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 42.25  E-value: 3.87e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2738594402  24 RGLGSHTRQDYVRHVRYFAAFL---GRSPDTATPDDIRRFQLDQHEKGVGPATINGAVSALRFLF 85
Cdd:pfam02899  12 RGLSPHTLRAYRRDLLAFLKFLsegGSSLEQITTSDVRAFLAELRAQGLSASSLARRLSALRSFY 76
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 106-138 1.38e-04

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: 39.57  E-value: 1.38e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2738594402 106 KLPDVLSVEEAGRLLEAAPGLKYKAALGVAYGA 138
Cdd:cd01193     1 KLPVVLSPDEVRRILGALTELRHRLILSLLYGA 33
 
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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