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Conserved domains on  [gi|289526971]
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Chain D, Two-component response regulator yesN

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11454391)

helix-turn-helix (HTH) domain-containing protein with an AraC family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.60
Gene Ontology:  GO:0003700|GO:0003677
PubMed:  10473770|15808743|8831795

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
5-102 9.68e-20

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 80.59  E-value: 9.68e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971   5 ELIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVN 84
Cdd:COG2207  154 LLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQS 233

                         90
                 ....*....|....*...
gi 289526971  85 YFITKFKKYYQITPKQYR 102
Cdd:COG2207  234 HFSRAFKKRFGVTPSEYR 251
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
5-102 9.68e-20

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 80.59  E-value: 9.68e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971   5 ELIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVN 84
Cdd:COG2207  154 LLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQS 233

                         90
                 ....*....|....*...
gi 289526971  85 YFITKFKKYYQITPKQYR 102
Cdd:COG2207  234 HFSRAFKKRFGVTPSEYR 251
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
21-102 2.03e-19

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 75.28  E-value: 2.03e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971    21 TLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQITPKQ 100
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   ..
gi 289526971   101 YR 102
Cdd:smart00342  83 YR 84
HTH_18 pfam12833
Helix-turn-helix domain;
25-103 6.98e-17

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 68.77  E-value: 6.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971   25 LSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKN-YEIAEQVGFEDVNYFITKFKKYYQITPKQYRE 103
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTGLSvAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
20-102 1.43e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 44.66  E-value: 1.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971  20 FTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQITPK 99
Cdd:PRK13502 193 FALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPS 272


                 ...
gi 289526971 100 QYR 102
Cdd:PRK13502 273 QWR 275
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 21-102 1.23e-05

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 41.97  E-value: 1.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971   21 TLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNyEIAEQVGFEDVNYFITKFKKYYQITPKQ 100
Cdd:TIGR04094 303 KVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRSQIPVS-EVSNELGFYDLSHFSRTFKKHTGVSPKQ 381


                  ..
gi 289526971  101 YR 102
Cdd:TIGR04094 382 YQ 383
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
5-102 9.68e-20

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 80.59  E-value: 9.68e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971   5 ELIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVN 84
Cdd:COG2207  154 LLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQS 233

                         90
                 ....*....|....*...
gi 289526971  85 YFITKFKKYYQITPKQYR 102
Cdd:COG2207  234 HFSRAFKKRFGVTPSEYR 251
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
21-102 2.03e-19

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 75.28  E-value: 2.03e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971    21 TLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQITPKQ 100
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   ..
gi 289526971   101 YR 102
Cdd:smart00342  83 YR 84
HTH_18 pfam12833
Helix-turn-helix domain;
25-103 6.98e-17

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 68.77  E-value: 6.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971   25 LSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKN-YEIAEQVGFEDVNYFITKFKKYYQITPKQYRE 103
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTGLSvAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 10-103 1.99e-10

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];


Pssm-ID: 441772 [Multi-domain]  Cd Length: 358  Bit Score: 55.83  E-value: 1.99e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971  10 IIEESYTDsQFTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNyEIAEQVGFEDVNYFITK 89
Cdd:COG2169   92 LIEAGAED-RPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGLSVT-DAAYAAGFGSLSRFYEA 169

                         90
                 ....*....|....
gi 289526971  90 FKKYYQITPKQYRE 103
Cdd:COG2169  170 FKKLLGMTPSAYRR 183
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 7-103 1.30e-07

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 47.46  E-value: 1.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971   7 IQNIIEESYTDSqFTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYF 86
Cdd:COG4977  215 AQAWMEANLEEP-LSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHF 293

                         90
                 ....*....|....*..
gi 289526971  87 ITKFKKYYQITPKQYRE 103
Cdd:COG4977  294 RRAFRRRFGVSPSAYRR 310
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
20-102 1.43e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 44.66  E-value: 1.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971  20 FTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQITPK 99
Cdd:PRK13502 193 FALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPS 272


                 ...
gi 289526971 100 QYR 102
Cdd:PRK13502 273 QWR 275
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
20-103 3.37e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 43.74  E-value: 3.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971  20 FTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQITPK 99
Cdd:PRK13501 193 FDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPR 272


                 ....
gi 289526971 100 QYRE 103
Cdd:PRK13501 273 DYRQ 276
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 73-102 5.04e-06

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 40.21  E-value: 5.04e-06
                          10        20        30
                  ....*....|....*....|....*....|
gi 289526971   73 EIAEQVGFeDVNYFITKFKKYYQITPKQYR 102
Cdd:pfam00165  13 DIADELGF-SRSYFSRLFKKYTGVTPSQYR 41
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
18-102 1.05e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 42.40  E-value: 1.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971  18 SQFTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQIT 97
Cdd:PRK13500 221 SPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMT 300


                 ....*
gi 289526971  98 PKQYR 102
Cdd:PRK13500 301 PSQWR 305
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 21-102 1.23e-05

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 41.97  E-value: 1.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971   21 TLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNyEIAEQVGFEDVNYFITKFKKYYQITPKQ 100
Cdd:TIGR04094 303 KVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRSQIPVS-EVSNELGFYDLSHFSRTFKKHTGVSPKQ 381


                  ..
gi 289526971  101 YR 102
Cdd:TIGR04094 382 YQ 383
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
25-102 4.34e-05

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 40.43  E-value: 4.34e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 289526971  25 LSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQITPKQYR 102
Cdd:PRK13503 193 LADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRDIR 270
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
13-102 2.42e-04

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 37.39  E-value: 2.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971  13 ESYTDSQFTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKK 92
Cdd:PRK11511  19 EDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKN 98

                         90
                 ....*....|
gi 289526971  93 YYQITPKQYR 102
Cdd:PRK11511  99 YFDVPPHKYR 108
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 4-101 2.45e-04

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 38.44  E-value: 2.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971   4 KELIQNIIEESyTDSQFTLSVLSEKLDLSSGYLSI*FKKNfGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDV 83
Cdd:PRK15185 208 KERVYNIISSS-PSRQWKLTDVADHIFMSTSTLKRKLAEE-GTSFSDIYLSARMNQAAKLLRIGNHNVNAVALKCGYDST 285

                         90
                 ....*....|....*...
gi 289526971  84 NYFITKFKKYYQITPKQY 101
Cdd:PRK15185 286 SYFIQCFKKYFKTTPSTF 303
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 19-103 5.74e-04

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 37.21  E-value: 5.74e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971  19 QFTLSVLSEKLDLSSGYLSI*FKKNfGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQITP 98
Cdd:PRK09978 158 EWTLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTP 236


                 ....*
gi 289526971  99 KQYRE 103
Cdd:PRK09978 237 TEYQE 241
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 73-102 6.58e-04

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 36.93  E-value: 6.58e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 289526971  73 EIAEQVGFEDVNYFITKFKKYYQITPKQYR 102
Cdd:PRK09685 269 SIAYKWGFSDSSHFSTAFKQRFGVSPGEYR 298
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
18-103 7.63e-04

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 36.88  E-value: 7.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971  18 SQFTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQIT 97
Cdd:PRK10572 198 SEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGAS 277


                 ....*.
gi 289526971  98 PKQYRE 103
Cdd:PRK10572 278 PSEFRA 283
PRK10371 PRK10371
transcriptional regulator MelR;
11-102 3.49e-03

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 35.18  E-value: 3.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 289526971  11 IEESYtDSQFTLSVLSEKLDLSSGYLSI*FKKNFGIPFQDYLLQKR*EKAKLLLLTTELKNYEIAEQVGFEDVNYFITKF 90
Cdd:PRK10371 200 IAENY-DQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSRFYSTF 278

                         90
                 ....*....|..
gi 289526971  91 KKYYQITPKQYR 102
Cdd:PRK10371 279 GKYVGMSPQQYR 290
 
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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