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Conserved domains on  [gi|639847202|ref|WP_024750094|]
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MULTISPECIES: recombinase family protein [Methylosinus]

Protein Classification

recombinase family protein( domain architecture ID 10446406)

recombinase family protein is a serine recombinase that catalyzes the site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme

CATH:  3.40.50.1390
Gene Ontology:  GO:0000150|GO:0003677|GO:0006310|GO:0015074
PubMed:  21645851|26104451|11972771|16077726|9348666
SCOP:  3000065

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SpoIVCA super family cl34383
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 5-111 1.80e-19

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1961:

Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 82.77  E-value: 1.80e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202   5 RPaQLHRALA---AGKGDVLLVMRpprpLD------ADLLNTLDSIAKAEAGFRSLADTWsDITTLHGKLMLAVLGGHAE 75
Cdd:COG1961   54 RP-GLQRLLAdlrAGKFDTLVVWK----LDrlgrnlADLLELVEELKERGVRLISLTEGI-DTSTPMGRLLLTILAAFAE 127

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 639847202  76 FERELIRARTGEGRSRAKAQGVHMGRPPALNRHQRK 111
Cdd:COG1961  128 FERELISERTRAGLAAAKARGKYLGRPPYGYRDPKK 163
 
Name Accession Description Interval E-value
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 5-111 1.80e-19

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 82.77  E-value: 1.80e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202   5 RPaQLHRALA---AGKGDVLLVMRpprpLD------ADLLNTLDSIAKAEAGFRSLADTWsDITTLHGKLMLAVLGGHAE 75
Cdd:COG1961   54 RP-GLQRLLAdlrAGKFDTLVVWK----LDrlgrnlADLLELVEELKERGVRLISLTEGI-DTSTPMGRLLLTILAAFAE 127

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 639847202  76 FERELIRARTGEGRSRAKAQGVHMGRPPALNRHQRK 111
Cdd:COG1961  128 FERELISERTRAGLAAAKARGKYLGRPPYGYRDPKK 163
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 2-98 7.75e-18

Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796.


Pssm-ID: 425548 [Multi-domain]  Cd Length: 144  Bit Score: 74.61  E-value: 7.75e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202    2 TWLRPA--QLHRALAAGKGDVLLVMRpprpLD------ADLLNTLDSIAKAEAGFRSLADtWSDITTLHGKLMLAVLGGH 73
Cdd:pfam00239  45 KLDRPGlqRLLALLRAGKGDVLVVYK----LDrlgrslRDLLTLVEELREKGVDLVSLDE-GIDTSTPMGRLLLTILAAL 119

                          90       100
                  ....*....|....*....|....*
gi 639847202   74 AEFERELIRARTGEGRSRAKAQGVH 98
Cdd:pfam00239 120 AEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 5-98 2.46e-17

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 73.43  E-value: 2.46e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202     5 RPA--QLHRALAAGKGDVLLVMRpprpLD------ADLLNTLDSIAKAEAGFRSLADTWSDITTLHGKLMLAVLGGHAEF 76
Cdd:smart00857  51 RPGlqRLLADLRAGDIDVLVVYK----LDrlgrslRDLLALLELLEEKGVRLVSLKEGILDTSTPAGRLLLDILAALAEF 126

                           90       100
                   ....*....|....*....|..
gi 639847202    77 ERELIRARTGEGRSRAKAQGVH 98
Cdd:smart00857 127 ERELISERTKAGLARAAARGRW 148
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 5-88 3.79e-15

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 67.12  E-value: 3.79e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202   5 RPaQLHRALA-AGKGDVLLVMRpprpLD------ADLLNTLDSIAKAEAGFRSLADTWsDITTLHGKLMLAVLGGHAEFE 77
Cdd:cd03768   42 RP-ELQKLLEdLREGDTLVVTK----LDrlgrstKDLLEIVEELREKGVSLRSLTEGI-DTSTPSGKLMLTILGAFAEFE 115

                         90
                 ....*....|.
gi 639847202  78 RELIRARTGEG 88
Cdd:cd03768  116 RELIRERTKEG 126
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
74-102 3.97e-05

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 41.63  E-value: 3.97e-05
                         10        20
                 ....*....|....*....|....*....
gi 639847202  74 AEFERELIRARTGEGRSRAKAQGVHMGRP 102
Cdd:PRK13413 120 AEIERNLISQRTKEALARKKAEGVTLGRP 148
 
Name Accession Description Interval E-value
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 5-111 1.80e-19

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 82.77  E-value: 1.80e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202   5 RPaQLHRALA---AGKGDVLLVMRpprpLD------ADLLNTLDSIAKAEAGFRSLADTWsDITTLHGKLMLAVLGGHAE 75
Cdd:COG1961   54 RP-GLQRLLAdlrAGKFDTLVVWK----LDrlgrnlADLLELVEELKERGVRLISLTEGI-DTSTPMGRLLLTILAAFAE 127

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 639847202  76 FERELIRARTGEGRSRAKAQGVHMGRPPALNRHQRK 111
Cdd:COG1961  128 FERELISERTRAGLAAAKARGKYLGRPPYGYRDPKK 163
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 2-98 7.75e-18

Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796.


Pssm-ID: 425548 [Multi-domain]  Cd Length: 144  Bit Score: 74.61  E-value: 7.75e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202    2 TWLRPA--QLHRALAAGKGDVLLVMRpprpLD------ADLLNTLDSIAKAEAGFRSLADtWSDITTLHGKLMLAVLGGH 73
Cdd:pfam00239  45 KLDRPGlqRLLALLRAGKGDVLVVYK----LDrlgrslRDLLTLVEELREKGVDLVSLDE-GIDTSTPMGRLLLTILAAL 119

                          90       100
                  ....*....|....*....|....*
gi 639847202   74 AEFERELIRARTGEGRSRAKAQGVH 98
Cdd:pfam00239 120 AEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 5-98 2.46e-17

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 73.43  E-value: 2.46e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202     5 RPA--QLHRALAAGKGDVLLVMRpprpLD------ADLLNTLDSIAKAEAGFRSLADTWSDITTLHGKLMLAVLGGHAEF 76
Cdd:smart00857  51 RPGlqRLLADLRAGDIDVLVVYK----LDrlgrslRDLLALLELLEEKGVRLVSLKEGILDTSTPAGRLLLDILAALAEF 126

                           90       100
                   ....*....|....*....|..
gi 639847202    77 ERELIRARTGEGRSRAKAQGVH 98
Cdd:smart00857 127 ERELISERTKAGLARAAARGRW 148
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 5-88 3.79e-15

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 67.12  E-value: 3.79e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202   5 RPaQLHRALA-AGKGDVLLVMRpprpLD------ADLLNTLDSIAKAEAGFRSLADTWsDITTLHGKLMLAVLGGHAEFE 77
Cdd:cd03768   42 RP-ELQKLLEdLREGDTLVVTK----LDrlgrstKDLLEIVEELREKGVSLRSLTEGI-DTSTPSGKLMLTILGAFAEFE 115

                         90
                 ....*....|.
gi 639847202  78 RELIRARTGEG 88
Cdd:cd03768  116 RELIRERTKEG 126
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 5-88 1.82e-05

Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are proteins with N-terminal DNA binding domains similar to IS607- and IS1535-transposases from Helicobacter and Mycobacterium.


Pssm-ID: 238206 [Multi-domain]  Cd Length: 137  Bit Score: 41.86  E-value: 1.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639847202   5 RPA--QLHRALAAGKGDVLLVMRPPRpL---DADLLNTLDSIAKAEAGFRSLADTWsDITTLHGKLMLAVLGGHAEFERE 79
Cdd:cd00338   51 RPGlqRLLADVKAGKIDVVLVEKLDR-LsrnLVDLLELLELLEAHGVRVVTADGEI-DLDSEDGRLMLGILAAMAEEESK 128


                 ....*....
gi 639847202  80 LIRARTGEG 88
Cdd:cd00338  129 LISERTKRG 137
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
74-102 3.97e-05

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 41.63  E-value: 3.97e-05
                         10        20
                 ....*....|....*....|....*....
gi 639847202  74 AEFERELIRARTGEGRSRAKAQGVHMGRP 102
Cdd:PRK13413 120 AEIERNLISQRTKEALARKKAEGVTLGRP 148
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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