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Conserved domains on  [gi|1832552642|ref|WP_168443593|]
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MULTISPECIES: helix-turn-helix domain-containing protein, partial [Enterobacteriaceae]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
mpi super family cl32873
master DNA invertase Mpi family serine-type recombinase;
4-78 2.37e-14

master DNA invertase Mpi family serine-type recombinase;


The actual alignment was detected with superfamily member PRK13413:

Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 64.35  E-value: 2.37e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1832552642   4 AEFERDLISERVKSGLAVAKARGKRLGRQAGVRPKSDRLLPK---VVAMRAEGRSYRWIARELGISKNTVADIVQRHR 78
Cdd:PRK13413  120 AEIERNLISQRTKEALARKKAEGVTLGRPKGSTPKKYKLTGKeekIKKLLDKGTSKSEIARKLGVSRTTLARFLKTRG 197
 
Name Accession Description Interval E-value
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
4-78 2.37e-14

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 64.35  E-value: 2.37e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1832552642   4 AEFERDLISERVKSGLAVAKARGKRLGRQAGVRPKSDRLLPK---VVAMRAEGRSYRWIARELGISKNTVADIVQRHR 78
Cdd:PRK13413  120 AEIERNLISQRTKEALARKKAEGVTLGRPKGSTPKKYKLTGKeekIKKLLDKGTSKSEIARKLGVSRTTLARFLKTRG 197
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
1-76 3.44e-11

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 56.96  E-value: 3.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832552642   1 SGIAEFERDLISERVKSGLAVAKARGKRLGRQAG---------VRPKSDRLLPKVVAMRAEGRSYRWIAREL---GI--- 65
Cdd:COG1961   123 AAFAEFERELISERTRAGLAAAKARGKYLGRPPYgyrdpkklvIDEEEAEVVRRIFELYLEGKSLREIARELnerGIptw 202
                          90
                  ....*....|.
gi 1832552642  66 SKNTVADIVQR 76
Cdd:COG1961   203 SRSTVYRILKN 213
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
1-28 2.31e-06

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: 42.26  E-value: 2.31e-06
                          10        20
                  ....*....|....*....|....*...
gi 1832552642   1 SGIAEFERDLISERVKSGLAVAKARGKR 28
Cdd:pfam00239 117 AALAEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
1-28 4.96e-05

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: 38.76  E-value: 4.96e-05
                           10        20
                   ....*....|....*....|....*...
gi 1832552642    1 SGIAEFERDLISERVKSGLAVAKARGKR 28
Cdd:smart00857 121 AALAEFERELISERTKAGLARAAARGRW 148
transpos_IS630 NF033545
IS630 family transposase;
45-79 2.03e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 37.62  E-value: 2.03e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1832552642  45 KVVAMRAEGRSYRWIARELGISKNTVADIVQRHRA 79
Cdd:NF033545    4 RILLLAAEGLSITEIAERLGVSRSTVYRWLKRFNE 38
transpos_IS21 NF033546
IS21 family transposase;
49-76 3.38e-04

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 37.19  E-value: 3.38e-04
                          10        20
                  ....*....|....*....|....*...
gi 1832552642  49 MRAEGRSYRWIARELGISKNTVADIVQR 76
Cdd:NF033546    4 LFRQGLSIREIARELGISRNTVRKYLRR 31
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
1-18 1.04e-03

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: 35.15  E-value: 1.04e-03
                          10
                  ....*....|....*...
gi 1832552642   1 SGIAEFERDLISERVKSG 18
Cdd:cd03768   109 GAFAEFERELIRERTKEG 126
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
45-70 4.97e-03

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 33.30  E-value: 4.97e-03
                          10        20
                  ....*....|....*....|....*..
gi 1832552642  45 KVVAM-RAEGRSYRWIARELGISKNTV 70
Cdd:TIGR02985 120 EIFILsRFEGLSNKEIAEELGISVKTV 146
 
Name Accession Description Interval E-value
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
4-78 2.37e-14

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 64.35  E-value: 2.37e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1832552642   4 AEFERDLISERVKSGLAVAKARGKRLGRQAGVRPKSDRLLPK---VVAMRAEGRSYRWIARELGISKNTVADIVQRHR 78
Cdd:PRK13413  120 AEIERNLISQRTKEALARKKAEGVTLGRPKGSTPKKYKLTGKeekIKKLLDKGTSKSEIARKLGVSRTTLARFLKTRG 197
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
1-76 3.44e-11

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 56.96  E-value: 3.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832552642   1 SGIAEFERDLISERVKSGLAVAKARGKRLGRQAG---------VRPKSDRLLPKVVAMRAEGRSYRWIAREL---GI--- 65
Cdd:COG1961   123 AAFAEFERELISERTRAGLAAAKARGKYLGRPPYgyrdpkklvIDEEEAEVVRRIFELYLEGKSLREIARELnerGIptw 202
                          90
                  ....*....|.
gi 1832552642  66 SKNTVADIVQR 76
Cdd:COG1961   203 SRSTVYRILKN 213
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
1-28 2.31e-06

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: 42.26  E-value: 2.31e-06
                          10        20
                  ....*....|....*....|....*...
gi 1832552642   1 SGIAEFERDLISERVKSGLAVAKARGKR 28
Cdd:pfam00239 117 AALAEFERALIRERTRAGLAAAAARGKL 144
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
6-81 3.94e-05

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 39.31  E-value: 3.94e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1832552642   6 FERDLISERVKSGLAVAKARGKRLGRQAGVRPKSDRLLPK---VVAMRAEGRSYRWIARELGISKNTvadiVQRHRANA 81
Cdd:COG4566   102 FDDQALLDAVRRALARDRARRAERARRAELRARLASLTPRereVLDLVVAGLSNKQIARELGISPRT----VEVHRANV 176
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
1-28 4.96e-05

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: 38.76  E-value: 4.96e-05
                           10        20
                   ....*....|....*....|....*...
gi 1832552642    1 SGIAEFERDLISERVKSGLAVAKARGKR 28
Cdd:smart00857 121 AALAEFERELISERTKAGLARAAARGRW 148
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
45-76 1.41e-04

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 38.28  E-value: 1.41e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1832552642  45 KVVAMRAEGRSYRWIARELGISKNTVADIVQR 76
Cdd:COG4584     9 EIRRLLREGLSIREIARELGISRNTVRKYLRR 40
transpos_IS630 NF033545
IS630 family transposase;
45-79 2.03e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 37.62  E-value: 2.03e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1832552642  45 KVVAMRAEGRSYRWIARELGISKNTVADIVQRHRA 79
Cdd:NF033545    4 RILLLAAEGLSITEIAERLGVSRSTVYRWLKRFNE 38
transpos_IS21 NF033546
IS21 family transposase;
49-76 3.38e-04

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 37.19  E-value: 3.38e-04
                          10        20
                  ....*....|....*....|....*...
gi 1832552642  49 MRAEGRSYRWIARELGISKNTVADIVQR 76
Cdd:NF033546    4 LFRQGLSIREIARELGISRNTVRKYLRR 31
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
1-18 1.04e-03

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: 35.15  E-value: 1.04e-03
                          10
                  ....*....|....*...
gi 1832552642   1 SGIAEFERDLISERVKSG 18
Cdd:cd03768   109 GAFAEFERELIRERTKEG 126
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
45-70 4.97e-03

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 33.30  E-value: 4.97e-03
                          10        20
                  ....*....|....*....|....*..
gi 1832552642  45 KVVAM-RAEGRSYRWIARELGISKNTV 70
Cdd:TIGR02985 120 EIFILsRFEGLSNKEIAEELGISVKTV 146
InsA COG3677
Transposase InsA [Mobilome: prophages, transposons];
45-78 9.78e-03

Transposase InsA [Mobilome: prophages, transposons];


Pssm-ID: 442893 [Multi-domain]  Cd Length: 241  Bit Score: 32.92  E-value: 9.78e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1832552642  45 KVVAMRAEGRSYRWIARELGISKNTVADIVQRHR 78
Cdd:COG3677    67 QAIRLLLNGISLRQIARVLGVSYKTVWRWLHRIR 100
 
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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