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Conserved domains on  [gi|738982286|ref|WP_036865144|]
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phage integrase SAM-like domain-containing protein, partial [Prevotella bivia]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XerD super family cl44177
Site-specific recombinase XerD [Replication, recombination and repair];
116-271 1.60e-12

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


The actual alignment was detected with superfamily member COG4974:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 66.17  E-value: 1.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738982286 116 YHSTRTHLQNFIKSRYKVSDLAFSQLTEQFIYDFQQYfMGICGFQESTFYNAATHLRTVCRLAYREGLADILLFDKVKVS 195
Cdd:COG4974   25 IKAYRRDLRRFLRFLEELGKIPLAEITPEDIRAYLNY-LRERGLSPSTINRYLAALRSFFRYAVREGLLEDNPAAKVKLP 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 738982286 196 KGDKKLPKALDRRSLDKLMNiqfGELEEEMETARD--LFVFACHTGAAYCDLMGLSKTHLvrdDEENLWMKFNRKKTG 271
Cdd:COG4974  104 KKPRKLPRVLTEEEIEALLE---ALDTETPEGLRDraLLLLLYATGLRVSELLGLKWSDI---DLDRGTIRVRRGKGG 175
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 1-76 1.82e-05

Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.


:

Pssm-ID: 465401  Cd Length: 87  Bit Score: 42.36  E-value: 1.82e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738982286    1 KAPIMGRITLGRSIAQFSCKLSCNPDLWNPRESRMGGKSREAVEVNGRLESLLLSVQATYQSLLSKGCPfDATDIK 76
Cdd:pfam17293  13 EAPLYLRIYKNGKRKYESLGLYITPEPWDKKKQKVKRKHPNALELNEQIDQERSKLEDIILELEQKGKL-SAELLK 87
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
116-271 1.60e-12

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 66.17  E-value: 1.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738982286 116 YHSTRTHLQNFIKSRYKVSDLAFSQLTEQFIYDFQQYfMGICGFQESTFYNAATHLRTVCRLAYREGLADILLFDKVKVS 195
Cdd:COG4974   25 IKAYRRDLRRFLRFLEELGKIPLAEITPEDIRAYLNY-LRERGLSPSTINRYLAALRSFFRYAVREGLLEDNPAAKVKLP 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 738982286 196 KGDKKLPKALDRRSLDKLMNiqfGELEEEMETARD--LFVFACHTGAAYCDLMGLSKTHLvrdDEENLWMKFNRKKTG 271
Cdd:COG4974  104 KKPRKLPRVLTEEEIEALLE---ALDTETPEGLRDraLLLLLYATGLRVSELLGLKWSDI---DLDRGTIRVRRGKGG 175
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 210-276 1.40e-10

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: 58.43  E-value: 1.40e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 738982286 210 LDKLMNIQFgELEEEMETARDLFVFACHTGAAYCDLMGLSKTHLVrDDEENLWMKFNRKKTGVLCRI 276
Cdd:cd01185    3 LKRLMALEL-SDTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIV-EASGRTWIRYRRKKTGKPVTV 67
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 88-194 6.16e-08

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 49.53  E-value: 6.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738982286   88 MLIERMDRLIKEKENHIGIDIKGqsifVYHSTRTHLQNFIKSrykvSDLAFSQLTEQFIYDFQQYFMGICGFQESTFYNA 167
Cdd:pfam13102   1 DFLDYFKEYIEELKKKGSKGTAR----NYKSTLKHLKKFLKK----KDITFEEITVDFLEKFEEYLKKKKGLSENTISKY 72

                          90       100
                  ....*....|....*....|....*..
gi 738982286  168 ATHLRTVCRLAYREGLADILLFDKVKV 194
Cdd:pfam13102  73 FRTLRAVLNKAIKEGIIKKNPYPKYKI 99
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 1-76 1.82e-05

Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.


Pssm-ID: 465401  Cd Length: 87  Bit Score: 42.36  E-value: 1.82e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738982286    1 KAPIMGRITLGRSIAQFSCKLSCNPDLWNPRESRMGGKSREAVEVNGRLESLLLSVQATYQSLLSKGCPfDATDIK 76
Cdd:pfam17293  13 EAPLYLRIYKNGKRKYESLGLYITPEPWDKKKQKVKRKHPNALELNEQIDQERSKLEDIILELEQKGKL-SAELLK 87
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
116-271 1.60e-12

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 66.17  E-value: 1.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738982286 116 YHSTRTHLQNFIKSRYKVSDLAFSQLTEQFIYDFQQYfMGICGFQESTFYNAATHLRTVCRLAYREGLADILLFDKVKVS 195
Cdd:COG4974   25 IKAYRRDLRRFLRFLEELGKIPLAEITPEDIRAYLNY-LRERGLSPSTINRYLAALRSFFRYAVREGLLEDNPAAKVKLP 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 738982286 196 KGDKKLPKALDRRSLDKLMNiqfGELEEEMETARD--LFVFACHTGAAYCDLMGLSKTHLvrdDEENLWMKFNRKKTG 271
Cdd:COG4974  104 KKPRKLPRVLTEEEIEALLE---ALDTETPEGLRDraLLLLLYATGLRVSELLGLKWSDI---DLDRGTIRVRRGKGG 175
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 210-276 1.40e-10

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: 58.43  E-value: 1.40e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 738982286 210 LDKLMNIQFgELEEEMETARDLFVFACHTGAAYCDLMGLSKTHLVrDDEENLWMKFNRKKTGVLCRI 276
Cdd:cd01185    3 LKRLMALEL-SDTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIV-EASGRTWIRYRRKKTGKPVTV 67
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 88-194 6.16e-08

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 49.53  E-value: 6.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738982286   88 MLIERMDRLIKEKENHIGIDIKGqsifVYHSTRTHLQNFIKSrykvSDLAFSQLTEQFIYDFQQYFMGICGFQESTFYNA 167
Cdd:pfam13102   1 DFLDYFKEYIEELKKKGSKGTAR----NYKSTLKHLKKFLKK----KDITFEEITVDFLEKFEEYLKKKKGLSENTISKY 72

                          90       100
                  ....*....|....*....|....*..
gi 738982286  168 ATHLRTVCRLAYREGLADILLFDKVKV 194
Cdd:pfam13102  73 FRTLRAVLNKAIKEGIIKKNPYPKYKI 99
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
120-259 5.16e-06

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 46.88  E-value: 5.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738982286 120 RTHLQNFIKsRYKVSDLAFSQLTEQFIYDF-QQYFMGicGFQESTFYNAATHLRTVCRLAYREGLADILLFDKVKVSKGD 198
Cdd:COG4973   29 RRDLRRLIP-LLGDADLPLEELTPADVRRFlARLHRR--GLSPRTLNRRLSALRSFFNWAVREGLLEANPAAGVKAPKAP 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 738982286 199 KKLPKALDRRSLDKLMNIQFGELEEemETARDLFVFACHTGAAYCDLMGLSKTHLVRDDEE 259
Cdd:COG4973  106 RKLPRALTVDELAQLLDALADDPLA--VRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGE 164
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 1-76 1.82e-05

Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.


Pssm-ID: 465401  Cd Length: 87  Bit Score: 42.36  E-value: 1.82e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738982286    1 KAPIMGRITLGRSIAQFSCKLSCNPDLWNPRESRMGGKSREAVEVNGRLESLLLSVQATYQSLLSKGCPfDATDIK 76
Cdd:pfam17293  13 EAPLYLRIYKNGKRKYESLGLYITPEPWDKKKQKVKRKHPNALELNEQIDQERSKLEDIILELEQKGKL-SAELLK 87
 
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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