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Conserved domains on  [gi|1941773775|gb|QPO58626|]
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helix-turn-helix domain-containing protein [Enterobacter hormaechei]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RobA_TF super family cl41266
MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as ...
 7-106 1.52e-39

MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as a Right side Origin of replication Binding protein A (robA) may be misleading. Characterizations in large numbers of papers since then treat RobA as a transcriptional activator of the AcrAB antibiotic efflux pump.


The actual alignment was detected with superfamily member NF012228:

Pssm-ID: 467958 [Multi-domain]  Cd Length: 286  Bit Score: 133.10  E-value: 1.52e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQ 86
Cdd:NF012228    5 IRDLLVWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGQAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFDSQQ 84

                          90       100
                  ....*....|....*....|
gi 1941773775  87 SFNRSFKRQYGQAPGAWRRS 106
Cdd:NF012228   85 TFTRAFKKQFNQTPALYRRS 104
 
Name Accession Description Interval E-value
RobA_TF NF012228
MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as ...
 7-106 1.52e-39

MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as a Right side Origin of replication Binding protein A (robA) may be misleading. Characterizations in large numbers of papers since then treat RobA as a transcriptional activator of the AcrAB antibiotic efflux pump.


Pssm-ID: 467958 [Multi-domain]  Cd Length: 286  Bit Score: 133.10  E-value: 1.52e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQ 86
Cdd:NF012228    5 IRDLLVWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGQAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFDSQQ 84

                          90       100
                  ....*....|....*....|
gi 1941773775  87 SFNRSFKRQYGQAPGAWRRS 106
Cdd:NF012228   85 TFTRAFKKQFNQTPALYRRS 104
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
1-106 1.34e-38

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 130.90  E-value: 1.34e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   1 MNTGAFIHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIAL 80
Cdd:PRK15121    1 MDQAGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQY 80

                          90       100
                  ....*....|....*....|....*.
gi 1941773775  81 GFDSQQSFNRSFKRQYGQAPGAWRRS 106
Cdd:PRK15121   81 RFDSQQTFTRAFKKQFAQTPALYRRS 106
ramA_TF NF012144
RamA family antibiotic efflux transcriptional regulator;
7-105 8.57e-35

RamA family antibiotic efflux transcriptional regulator;


Pssm-ID: 411085 [Multi-domain]  Cd Length: 108  Bit Score: 115.57  E-value: 8.57e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQ 86
Cdd:NF012144    7 IDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQKVYDICLKYGFDSQQ 86

                          90
                  ....*....|....*....
gi 1941773775  87 SFNRSFKRQYGQAPGAWRR 105
Cdd:NF012144   87 TFTRIFTRTFNQPPGAYRK 105
MarA_TF NF012198
MDR efflux pump AcrAB transcriptional activator MarA;
7-104 1.90e-32

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 411088  Cd Length: 124  Bit Score: 110.23  E-value: 1.90e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQ 86
Cdd:NF012198   11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQ 90

                          90
                  ....*....|....*...
gi 1941773775  87 SFNRSFKRQYGQAPGAWR 104
Cdd:NF012198   91 TLTRTFKNYFDVPPHKYR 108
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
21-104 1.90e-27

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 96.08  E-value: 1.90e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   21 RLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQSFNRSFKRQYGQAP 100
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1941773775  101 GAWR 104
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
4-106 3.50e-27

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 100.62  E-value: 3.50e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   4 GAFIHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFD 83
Cdd:COG2207   151 LLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFS 230

                          90       100
                  ....*....|....*....|...
gi 1941773775  84 SQQSFNRSFKRQYGQAPGAWRRS 106
Cdd:COG2207   231 SQSHFSRAFKKRFGVTPSEYRKR 253
HTH_18 pfam12833
Helix-turn-helix domain;
27-106 5.77e-24

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 87.26  E-value: 5.77e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775  27 VSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQ-SDEPILNVAIALGFDSQQSFNRSFKRQYGQAPGAWRR 105
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 1941773775 106 S 106
Cdd:pfam12833  81 R 81
V_AnPalA_UmRIM20_like cd09236
Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and ...
 51-105 4.74e-03

Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins; This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas PalA binds a nonviral YPXnL motif (tandem YPXL/I motifs within PacC). The Alix V-domain is also a dimerization domain. In addition to this V-domain, members of the V_Alix_like superfamily also have an N-terminal Bro1-like domain, which has been shown to bind CHMP4/Snf7, a component of the ESCRT-III complex.


Pssm-ID: 185749 [Multi-domain]  Cd Length: 353  Bit Score: 35.02  E-value: 4.74e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1941773775  51 AEYIRAQ----KLQKS---VERLAQSDEPILNVAIALgFDSQQSFNRSFKRQYGQAPgaWRR 105
Cdd:cd09236    64 AEEIRQEdgleRIRASlddVARLAASDRAILEEAMDI-LDDEASEDESLRRKFGTDR--WTR 122
 
Name Accession Description Interval E-value
RobA_TF NF012228
MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as ...
 7-106 1.52e-39

MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as a Right side Origin of replication Binding protein A (robA) may be misleading. Characterizations in large numbers of papers since then treat RobA as a transcriptional activator of the AcrAB antibiotic efflux pump.


Pssm-ID: 467958 [Multi-domain]  Cd Length: 286  Bit Score: 133.10  E-value: 1.52e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQ 86
Cdd:NF012228    5 IRDLLVWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGQAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFDSQQ 84

                          90       100
                  ....*....|....*....|
gi 1941773775  87 SFNRSFKRQYGQAPGAWRRS 106
Cdd:NF012228   85 TFTRAFKKQFNQTPALYRRS 104
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
1-106 1.34e-38

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 130.90  E-value: 1.34e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   1 MNTGAFIHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIAL 80
Cdd:PRK15121    1 MDQAGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQY 80

                          90       100
                  ....*....|....*....|....*.
gi 1941773775  81 GFDSQQSFNRSFKRQYGQAPGAWRRS 106
Cdd:PRK15121   81 RFDSQQTFTRAFKKQFAQTPALYRRS 106
ramA_TF NF012144
RamA family antibiotic efflux transcriptional regulator;
7-105 8.57e-35

RamA family antibiotic efflux transcriptional regulator;


Pssm-ID: 411085 [Multi-domain]  Cd Length: 108  Bit Score: 115.57  E-value: 8.57e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQ 86
Cdd:NF012144    7 IDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQKVYDICLKYGFDSQQ 86

                          90
                  ....*....|....*....
gi 1941773775  87 SFNRSFKRQYGQAPGAWRR 105
Cdd:NF012144   87 TFTRIFTRTFNQPPGAYRK 105
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
7-107 1.49e-34

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 115.02  E-value: 1.49e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQ 86
Cdd:PRK10219    7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQ 86

                          90       100
                  ....*....|....*....|.
gi 1941773775  87 SFNRSFKRQYGQAPGAWRRSI 107
Cdd:PRK10219   87 TFSRVFRRQFDRTPSDYRHRL 107
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
2-104 2.66e-34

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 115.20  E-value: 2.66e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   2 NTGAFIHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALG 81
Cdd:PRK11511    6 TDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYG 85

                          90       100
                  ....*....|....*....|...
gi 1941773775  82 FDSQQSFNRSFKRQYGQAPGAWR 104
Cdd:PRK11511   86 FESQQTLTRTFKNYFDVPPHKYR 108
MarA_TF NF012198
MDR efflux pump AcrAB transcriptional activator MarA;
7-104 1.90e-32

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 411088  Cd Length: 124  Bit Score: 110.23  E-value: 1.90e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQ 86
Cdd:NF012198   11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQ 90

                          90
                  ....*....|....*...
gi 1941773775  87 SFNRSFKRQYGQAPGAWR 104
Cdd:NF012198   91 TLTRTFKNYFDVPPHKYR 108
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
21-104 1.90e-27

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 96.08  E-value: 1.90e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   21 RLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQSFNRSFKRQYGQAP 100
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1941773775  101 GAWR 104
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
4-106 3.50e-27

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 100.62  E-value: 3.50e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   4 GAFIHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFD 83
Cdd:COG2207   151 LLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFS 230

                          90       100
                  ....*....|....*....|...
gi 1941773775  84 SQQSFNRSFKRQYGQAPGAWRRS 106
Cdd:COG2207   231 SQSHFSRAFKKRFGVTPSEYRKR 253
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 7-113 5.96e-27

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: 101.00  E-value: 5.96e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQ 86
Cdd:COG4977   212 LARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSAS 291

                          90       100
                  ....*....|....*....|....*..
gi 1941773775  87 SFNRSFKRQYGQAPGAWRRSIGCRGSR 113
Cdd:COG4977   292 HFRRAFRRRFGVSPSAYRRRFRARAAA 318
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 3-105 4.11e-24

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: 93.96  E-value: 4.11e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   3 TGAFIHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTG-SPLAeYIRAQKLQKSVERLaQSDEPILNVAIALG 81
Cdd:COG2169    82 RADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGvTPKA-YARARRLLRARQLL-QTGLSVTDAAYAAG 159

                          90       100
                  ....*....|....*....|....
gi 1941773775  82 FDSQQSFNRSFKRQYGQAPGAWRR 105
Cdd:COG2169   160 FGSLSRFYEAFKKLLGMTPSAYRR 183
HTH_18 pfam12833
Helix-turn-helix domain;
27-106 5.77e-24

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 87.26  E-value: 5.77e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775  27 VSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQ-SDEPILNVAIALGFDSQQSFNRSFKRQYGQAPGAWRR 105
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 1941773775 106 S 106
Cdd:pfam12833  81 R 81
ftrA PRK09393
transcriptional activator FtrA; Provisional
 10-108 5.25e-13

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 63.44  E-value: 5.25e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775  10 LLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQSFN 89
Cdd:PRK09393  223 LIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLR 302

                          90
                  ....*....|....*....
gi 1941773775  90 RSFKRQYGQAPGAWRRSIG 108
Cdd:PRK09393  303 HHFRRRAATSPAAYRKRFG 321
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 14-106 1.41e-11

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 59.27  E-value: 1.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775  14 IDNNLDS-RLDIETVSRRAGYSKWHLQRIFKEHtGSPLAEYIRAQKLQKSVERL--AQSDEPILNVAIALGFDSQQSFNR 90
Cdd:PRK09685  206 IDQSIQEeILRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRNRRLDRCADDLrpAADDEKITSIAYKWGFSDSSHFST 284

                          90
                  ....*....|....*.
gi 1941773775  91 SFKRQYGQAPGAWRRS 106
Cdd:PRK09685  285 AFKQRFGVSPGEYRRK 300
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
2-104 1.13e-10

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 56.61  E-value: 1.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   2 NTGAFIHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALG 81
Cdd:PRK13503  168 NSDARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCG 247

                          90       100
                  ....*....|....*....|...
gi 1941773775  82 FDSQQSFNRSFKRQYGQAPGAWR 104
Cdd:PRK13503  248 FGDSNHFSTLFRREFSWSPRDIR 270
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
7-112 1.73e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 56.14  E-value: 1.73e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   7 IHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEY------IRAQKLqksverLAQSDEPILNVAIAL 80
Cdd:PRK10572  185 VREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWredqriSRAKLL------LQTTRMPIATIGRNV 258

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1941773775  81 GFDSQQSFNRSFKRQYGQAPGAWRRSIGCRGS 112
Cdd:PRK10572  259 GYDDQLYFSRVFKKCTGASPSEFRARCEEKNN 290
PRK10371 PRK10371
transcriptional regulator MelR;
6-105 4.19e-08

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 49.43  E-value: 4.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775   6 FIHDLLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQ 85
Cdd:PRK10371  192 YVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSS 271

                          90       100
                  ....*....|....*....|
gi 1941773775  86 QSFNRSFKRQYGQAPGAWRR 105
Cdd:PRK10371  272 SRFYSTFGKYVGMSPQQYRK 291
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
38-105 3.94e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 44.12  E-value: 3.94e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1941773775  38 LQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQSFNRSFKRQYGQAPGAWRR 105
Cdd:PRK13501  209 LKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQ 276
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 67-105 6.82e-05

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: 37.52  E-value: 6.82e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1941773775  67 AQSDEPILNVAIALGFdSQQSFNRSFKRQYGQAPGAWRR 105
Cdd:pfam00165   5 LSTNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
10-104 1.69e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 39.27  E-value: 1.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775  10 LLDWIDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQSFN 89
Cdd:PRK13502  181 LITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFS 260

                          90
                  ....*....|....*
gi 1941773775  90 RSFKRQYGQAPGAWR 104
Cdd:PRK13502  261 VVFTRETGMTPSQWR 275
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
17-104 2.96e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 38.54  E-value: 2.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1941773775  17 NLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIRAQKLQKSVERLAQSDEPILNVAIALGFDSQQSFNRSFKRQY 96
Cdd:PRK13500  218 SLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRET 297


                  ....*...
gi 1941773775  97 GQAPGAWR 104
Cdd:PRK13500  298 GMTPSQWR 305
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 14-55 8.24e-04

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: 34.82  E-value: 8.24e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1941773775  14 IDNNLDSRLDIETVSRRAGYSKWHLQRIFKEHTGSPLAEYIR 55
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
V_AnPalA_UmRIM20_like cd09236
Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and ...
 51-105 4.74e-03

Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins; This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas PalA binds a nonviral YPXnL motif (tandem YPXL/I motifs within PacC). The Alix V-domain is also a dimerization domain. In addition to this V-domain, members of the V_Alix_like superfamily also have an N-terminal Bro1-like domain, which has been shown to bind CHMP4/Snf7, a component of the ESCRT-III complex.


Pssm-ID: 185749 [Multi-domain]  Cd Length: 353  Bit Score: 35.02  E-value: 4.74e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1941773775  51 AEYIRAQ----KLQKS---VERLAQSDEPILNVAIALgFDSQQSFNRSFKRQYGQAPgaWRR 105
Cdd:cd09236    64 AEEIRQEdgleRIRASlddVARLAASDRAILEEAMDI-LDDEASEDESLRRKFGTDR--WTR 122
 
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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