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Conserved domains on  [gi|1394072659|gb|PWW59712|]
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helix-turn-helix protein [Eubacterium limosum]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YhfZ_C pfam14503
YhfZ C-terminal domain; This domain is often found in association with the helix-turn-helix ...
 75-308 1.27e-103

YhfZ C-terminal domain; This domain is often found in association with the helix-turn-helix domain HTH_41 (pfam14502). It includes YhfZ proteins from Escherichia coli and Shigella flexneri.


:

Pssm-ID: 433998  Cd Length: 236  Bit Score: 302.66  E-value: 1.27e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659  75 DYEKLYPYTNWGSLTGTMPVPMTISFSSLTTAICEEMEKSPFPFSFAYVTGSEKRLAALKEMIYDFIIVSKSSAERYLSE 154
Cdd:pfam14503   1 DYKKLWELAGLGNLVGAMPLPYSRRYEGLATGLKAQFEDLGIPFNFAYMRGADVRLEALKEGRYDFAVVSRLAAERYLAE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 155 NDFLERAIELTGCVYSEPYVLYFLDDQKTEIEDGMRMAVDCNSIDQYTISQKLCEGKDVAFVQTPYASFSELLVKKNVDC 234
Cdd:pfam14503  81 GPGLEIALELGPGTYVSAHVLLLRDGEKTEIKDGMRVGIDSNSADQRILTEAEFEGKDVEFVEIPYMQLLELLLAGDIDA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 235 FIYRRDgwynNFQPDLNQRVVELPGYPL------EEVTTPVILVNRENYGFKKLLCQYITVEKTHEIQEKVISGECAVKF 308
Cdd:pfam14503 161 VVWNLD----EVQDPLELGLRALPLTSLdarpivEQASEAVLVIRKDNPGLKALLRNLIDVEAVLEIQKKVLEGERIPSY 236
HTH_ARSR super family cl46857
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 24-71 1.45e-10

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


The actual alignment was detected with superfamily member pfam14502:

Pssm-ID: 481197 [Multi-domain]  Cd Length: 48  Bit Score: 55.58  E-value: 1.45e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1394072659  24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNGVKGTFV 71
Cdd:pfam14502   1 KAGERLPTISEYSHKFELSVGTVQKALKKLEDMKAIQLERRGHNGTYL 48
 
Name Accession Description Interval E-value
YhfZ_C pfam14503
YhfZ C-terminal domain; This domain is often found in association with the helix-turn-helix ...
 75-308 1.27e-103

YhfZ C-terminal domain; This domain is often found in association with the helix-turn-helix domain HTH_41 (pfam14502). It includes YhfZ proteins from Escherichia coli and Shigella flexneri.


Pssm-ID: 433998  Cd Length: 236  Bit Score: 302.66  E-value: 1.27e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659  75 DYEKLYPYTNWGSLTGTMPVPMTISFSSLTTAICEEMEKSPFPFSFAYVTGSEKRLAALKEMIYDFIIVSKSSAERYLSE 154
Cdd:pfam14503   1 DYKKLWELAGLGNLVGAMPLPYSRRYEGLATGLKAQFEDLGIPFNFAYMRGADVRLEALKEGRYDFAVVSRLAAERYLAE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 155 NDFLERAIELTGCVYSEPYVLYFLDDQKTEIEDGMRMAVDCNSIDQYTISQKLCEGKDVAFVQTPYASFSELLVKKNVDC 234
Cdd:pfam14503  81 GPGLEIALELGPGTYVSAHVLLLRDGEKTEIKDGMRVGIDSNSADQRILTEAEFEGKDVEFVEIPYMQLLELLLAGDIDA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 235 FIYRRDgwynNFQPDLNQRVVELPGYPL------EEVTTPVILVNRENYGFKKLLCQYITVEKTHEIQEKVISGECAVKF 308
Cdd:pfam14503 161 VVWNLD----EVQDPLELGLRALPLTSLdarpivEQASEAVLVIRKDNPGLKALLRNLIDVEAVLEIQKKVLEGERIPSY 236
YhfZ_full NF041241
GntR family transcriptional regulator YhfZ; Full-length homologs of the transcriptional ...
 5-304 6.82e-88

GntR family transcriptional regulator YhfZ; Full-length homologs of the transcriptional regulator YhfZ from Escherichia coli, with an N-terminal GntR-like domain, are quite divergent. See PF14503 (YhfZ_C) for the broader family. This HMM identifies a subset in which the motif MPLPYxxxYEGLA and the C-terminal PxY motifs are both well conserved, suggesting orthology with conserved function.


Pssm-ID: 469143 [Multi-domain]  Cd Length: 304  Bit Score: 265.17  E-value: 6.82e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659   5 FYKKTGLATINIARDFYTMQAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNGVKGTFVTGIDYEKLYPYTN 84
Cdd:NF041241    3 FLKKNGLAIIKLARELLSLKEGDRIPTISELAEKFGVSRGTVQNALKYLEESGAIKLESRGHLGTFLVKIDYKKLLELAG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659  85 WGSLTGTMPVPMTISFSSLTTAICEEMEKSPFPFSFAYVTGSEKRLAALKEMIYDFIIVSKSSAERYLSENDFLERAIEL 164
Cdd:NF041241   83 IGTIVGAMPLPYSRLYEGLATGLYAAFEKAGIPLNLAYMRGAKVRIEALLNGRYDFAVVSKLAAEQYIEEGEDLEIALDF 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 165 TGCVYSEPYVLYFLDDQKTEIEDGMRMAVDCNSIDQYTISQKLCEGKDVAFVQTPYASFSELLVKKNVDCFIyrrdgWYN 244
Cdd:NF041241  163 GPGSYVSEHVLLFRDGEKKEIRDGMRVGIDSSSLDQKILTEAEFEGKDVELVELSYNQLLDALAKGEIDAAV-----WNL 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1394072659 245 NFQPDLNQ--RVVELPGYPLEEV-TTPVILVNRENYGFKKLLCQYITVEKTHEIQEKVISGEC 304
Cdd:NF041241  238 DEIKDKKLglNYQPLKSEKANKDaSEAVIVVRKDNEEIKALLRKLIDVEKVLAIQKKVLEGEI 300
PBP2_Yhfz cd13533
Substrate-binding domain of uncharacterized protein Yhfz from Shigella Flexneri; the type 2 ...
 75-296 4.09e-49

Substrate-binding domain of uncharacterized protein Yhfz from Shigella Flexneri; the type 2 periplasmic-binding protein fold; This subfamily contains periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBPII proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 270251  Cd Length: 222  Bit Score: 162.83  E-value: 4.09e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659  75 DYEKLYPYTNWGSLTGTMPVPMTISFSSLTTAICEEMEKSPFPFSFAYVTGSEKRLAALKEMIYDFIIVSKSSAERYLSE 154
Cdd:cd13533     1 DYKKLLEIAGIGSLVGAMPLPYSRRYEGLATGLYAQFEELKIPFNLAYMRGADNRIEALLEGRYDFAVVSRLAAEQAVDE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 155 NDFLERAIELTGCVYSEPYVLYFLDDQKTEIEDGMRMAVDCNSIDQYTISQKLCEGKDVAFVQTPYASFSELLVKKNVDC 234
Cdd:cd13533    81 GKDIEIVLELGPGTYVSQHVLLFRDPEDKEIQDGMRVGIDPSSADQRILTHRECEGKKVELVEINYNQLLQLLKSGEIDA 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1394072659 235 FIYRRD----GWYNnfqpdLNQRVVELPGYPLEEVTTPVILVNRENYGFKKLLCQYITVEKTHEIQ 296
Cdd:cd13533   161 AIWNLDeiqsKNLG-----LNYVPLKDEDARALRATEAVIVIRKGNPFLKRLLRALIDFPEVLEIQ 221
HTH_41 pfam14502
Helix-turn-helix domain;
24-71 1.45e-10

Helix-turn-helix domain;


Pssm-ID: 433997 [Multi-domain]  Cd Length: 48  Bit Score: 55.58  E-value: 1.45e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1394072659  24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNGVKGTFV 71
Cdd:pfam14502   1 KAGERLPTISEYSHKFELSVGTVQKALKKLEDMKAIQLERRGHNGTYL 48
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 24-72 1.61e-08

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 50.52  E-value: 1.61e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1394072659  24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNgvKGTFVT 72
Cdd:cd07377    20 KPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPG--RGTFVA 66
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
24-71 8.05e-08

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 48.34  E-value: 8.05e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1394072659   24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNgvKGTFV 71
Cdd:smart00345  15 RPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPG--SGTFV 60
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
24-72 7.82e-07

DNA-binding transcriptional regulator, GntR family [Transcription];


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 49.09  E-value: 7.82e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1394072659  24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKnGvKGTFVT 72
Cdd:COG2188    24 PPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQ-G-RGTFVA 70
PRK11402 PRK11402
transcriptional regulator PhoB;
15-115 1.64e-04

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 42.13  E-value: 1.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659  15 NIARDFYtmQAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNgvKGTFVTGIDYEK----LYPYTNWGSLTG 90
Cdd:PRK11402   21 DIAQGVY--QAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQG--KGTFVQSQKVENalltVSGFTDFGVSQG 96

                          90       100
                  ....*....|....*....|....*.
gi 1394072659  91 TMPVPMTISFSSLTTA-ICEEMEKSP 115
Cdd:PRK11402   97 KATKEKVIEQERVSAApFCEKLNIPG 122
 
Name Accession Description Interval E-value
YhfZ_C pfam14503
YhfZ C-terminal domain; This domain is often found in association with the helix-turn-helix ...
 75-308 1.27e-103

YhfZ C-terminal domain; This domain is often found in association with the helix-turn-helix domain HTH_41 (pfam14502). It includes YhfZ proteins from Escherichia coli and Shigella flexneri.


Pssm-ID: 433998  Cd Length: 236  Bit Score: 302.66  E-value: 1.27e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659  75 DYEKLYPYTNWGSLTGTMPVPMTISFSSLTTAICEEMEKSPFPFSFAYVTGSEKRLAALKEMIYDFIIVSKSSAERYLSE 154
Cdd:pfam14503   1 DYKKLWELAGLGNLVGAMPLPYSRRYEGLATGLKAQFEDLGIPFNFAYMRGADVRLEALKEGRYDFAVVSRLAAERYLAE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 155 NDFLERAIELTGCVYSEPYVLYFLDDQKTEIEDGMRMAVDCNSIDQYTISQKLCEGKDVAFVQTPYASFSELLVKKNVDC 234
Cdd:pfam14503  81 GPGLEIALELGPGTYVSAHVLLLRDGEKTEIKDGMRVGIDSNSADQRILTEAEFEGKDVEFVEIPYMQLLELLLAGDIDA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 235 FIYRRDgwynNFQPDLNQRVVELPGYPL------EEVTTPVILVNRENYGFKKLLCQYITVEKTHEIQEKVISGECAVKF 308
Cdd:pfam14503 161 VVWNLD----EVQDPLELGLRALPLTSLdarpivEQASEAVLVIRKDNPGLKALLRNLIDVEAVLEIQKKVLEGERIPSY 236
YhfZ_full NF041241
GntR family transcriptional regulator YhfZ; Full-length homologs of the transcriptional ...
 5-304 6.82e-88

GntR family transcriptional regulator YhfZ; Full-length homologs of the transcriptional regulator YhfZ from Escherichia coli, with an N-terminal GntR-like domain, are quite divergent. See PF14503 (YhfZ_C) for the broader family. This HMM identifies a subset in which the motif MPLPYxxxYEGLA and the C-terminal PxY motifs are both well conserved, suggesting orthology with conserved function.


Pssm-ID: 469143 [Multi-domain]  Cd Length: 304  Bit Score: 265.17  E-value: 6.82e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659   5 FYKKTGLATINIARDFYTMQAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNGVKGTFVTGIDYEKLYPYTN 84
Cdd:NF041241    3 FLKKNGLAIIKLARELLSLKEGDRIPTISELAEKFGVSRGTVQNALKYLEESGAIKLESRGHLGTFLVKIDYKKLLELAG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659  85 WGSLTGTMPVPMTISFSSLTTAICEEMEKSPFPFSFAYVTGSEKRLAALKEMIYDFIIVSKSSAERYLSENDFLERAIEL 164
Cdd:NF041241   83 IGTIVGAMPLPYSRLYEGLATGLYAAFEKAGIPLNLAYMRGAKVRIEALLNGRYDFAVVSKLAAEQYIEEGEDLEIALDF 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 165 TGCVYSEPYVLYFLDDQKTEIEDGMRMAVDCNSIDQYTISQKLCEGKDVAFVQTPYASFSELLVKKNVDCFIyrrdgWYN 244
Cdd:NF041241  163 GPGSYVSEHVLLFRDGEKKEIRDGMRVGIDSSSLDQKILTEAEFEGKDVELVELSYNQLLDALAKGEIDAAV-----WNL 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1394072659 245 NFQPDLNQ--RVVELPGYPLEEV-TTPVILVNRENYGFKKLLCQYITVEKTHEIQEKVISGEC 304
Cdd:NF041241  238 DEIKDKKLglNYQPLKSEKANKDaSEAVIVVRKDNEEIKALLRKLIDVEKVLAIQKKVLEGEI 300
PBP2_Yhfz cd13533
Substrate-binding domain of uncharacterized protein Yhfz from Shigella Flexneri; the type 2 ...
 75-296 4.09e-49

Substrate-binding domain of uncharacterized protein Yhfz from Shigella Flexneri; the type 2 periplasmic-binding protein fold; This subfamily contains periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBPII proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 270251  Cd Length: 222  Bit Score: 162.83  E-value: 4.09e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659  75 DYEKLYPYTNWGSLTGTMPVPMTISFSSLTTAICEEMEKSPFPFSFAYVTGSEKRLAALKEMIYDFIIVSKSSAERYLSE 154
Cdd:cd13533     1 DYKKLLEIAGIGSLVGAMPLPYSRRYEGLATGLYAQFEELKIPFNLAYMRGADNRIEALLEGRYDFAVVSRLAAEQAVDE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659 155 NDFLERAIELTGCVYSEPYVLYFLDDQKTEIEDGMRMAVDCNSIDQYTISQKLCEGKDVAFVQTPYASFSELLVKKNVDC 234
Cdd:cd13533    81 GKDIEIVLELGPGTYVSQHVLLFRDPEDKEIQDGMRVGIDPSSADQRILTHRECEGKKVELVEINYNQLLQLLKSGEIDA 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1394072659 235 FIYRRD----GWYNnfqpdLNQRVVELPGYPLEEVTTPVILVNRENYGFKKLLCQYITVEKTHEIQ 296
Cdd:cd13533   161 AIWNLDeiqsKNLG-----LNYVPLKDEDARALRATEAVIVIRKGNPFLKRLLRALIDFPEVLEIQ 221
HTH_41 pfam14502
Helix-turn-helix domain;
24-71 1.45e-10

Helix-turn-helix domain;


Pssm-ID: 433997 [Multi-domain]  Cd Length: 48  Bit Score: 55.58  E-value: 1.45e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1394072659  24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNGVKGTFV 71
Cdd:pfam14502   1 KAGERLPTISEYSHKFELSVGTVQKALKKLEDMKAIQLERRGHNGTYL 48
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 24-72 1.61e-08

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 50.52  E-value: 1.61e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1394072659  24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNgvKGTFVT 72
Cdd:cd07377    20 KPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPG--RGTFVA 66
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
24-71 8.05e-08

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 48.34  E-value: 8.05e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1394072659   24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNgvKGTFV 71
Cdd:smart00345  15 RPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPG--SGTFV 60
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
24-72 7.82e-07

DNA-binding transcriptional regulator, GntR family [Transcription];


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 49.09  E-value: 7.82e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1394072659  24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKnGvKGTFVT 72
Cdd:COG2188    24 PPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQ-G-RGTFVA 70
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 25-71 3.48e-05

Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.


Pssm-ID: 306822 [Multi-domain]  Cd Length: 64  Bit Score: 41.06  E-value: 3.48e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1394072659  25 AGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNgvKGTFV 71
Cdd:pfam00392  20 PGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQG--RGTFV 64
YhcF COG1725
DNA-binding transcriptional regulator YhcF, GntR family [Transcription];
22-72 4.44e-05

DNA-binding transcriptional regulator YhcF, GntR family [Transcription];


Pssm-ID: 441331 [Multi-domain]  Cd Length: 114  Bit Score: 42.09  E-value: 4.44e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1394072659  22 TMQAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNgvKGTFVT 72
Cdd:COG1725    27 ELKPGDRLPSVRELAAELGVNPNTVAKAYRELEDEGLIETRRG--KGTFVA 75
PRK11402 PRK11402
transcriptional regulator PhoB;
15-115 1.64e-04

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 42.13  E-value: 1.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1394072659  15 NIARDFYtmQAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNgvKGTFVTGIDYEK----LYPYTNWGSLTG 90
Cdd:PRK11402   21 DIAQGVY--QAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQG--KGTFVQSQKVENalltVSGFTDFGVSQG 96

                          90       100
                  ....*....|....*....|....*.
gi 1394072659  91 TMPVPMTISFSSLTTA-ICEEMEKSP 115
Cdd:PRK11402   97 KATKEKVIEQERVSAApFCEKLNIPG 122
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
24-72 1.03e-03

DNA-binding transcriptional regulator, FadR family [Transcription];


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 39.92  E-value: 1.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1394072659  24 QAGDRVPTIAEYTQRFEVSRGIVQKAIATLEEDACIQTQKNGvkGTFVT 72
Cdd:COG2186    26 KPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGG--GTFVR 72
 
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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