hypothetical protein CLDAP_29760 [Caldilinea aerophila DSM 14535 = NBRC 104270]
Protein Classification
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 ... |
70-303 | 1.04e-105 | ||||
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: 307.67 E-value: 1.04e-105
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| HTH_ARSR super family | cl46857 | Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ... |
19-66 | 1.80e-11 | ||||
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: 58.27 E-value: 1.80e-11
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| 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 ... |
70-303 | 1.04e-105 | |||||
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: 307.67 E-value: 1.04e-105
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| YhfZ_full | NF041241 | GntR family transcriptional regulator YhfZ; Full-length homologs of the transcriptional ... |
1-303 | 2.23e-105 | |||||
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: 309.47 E-value: 2.23e-105
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| PBP2_Yhfz | cd13533 | Substrate-binding domain of uncharacterized protein Yhfz from Shigella Flexneri; the type 2 ... |
70-292 | 2.01e-70 | |||||
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: 217.53 E-value: 2.01e-70
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| HTH_41 | pfam14502 | Helix-turn-helix domain; |
19-66 | 1.80e-11 | |||||
Helix-turn-helix domain; Pssm-ID: 433997 [Multi-domain] Cd Length: 48 Bit Score: 58.27 E-value: 1.80e-11
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| TauA | COG0715 | ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ... |
67-270 | 2.00e-08 | |||||
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 440479 [Multi-domain] Cd Length: 297 Bit Score: 54.63 E-value: 2.00e-08
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| YhcF | COG1725 | DNA-binding transcriptional regulator YhcF, GntR family [Transcription]; |
19-68 | 6.02e-06 | |||||
DNA-binding transcriptional regulator YhcF, GntR family [Transcription]; Pssm-ID: 441331 [Multi-domain] Cd Length: 114 Bit Score: 44.40 E-value: 6.02e-06
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| WHTH_GntR | cd07377 | Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ... |
19-67 | 2.98e-05 | |||||
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: 41.28 E-value: 2.98e-05
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| HTH_GNTR | smart00345 | helix_turn_helix gluconate operon transcriptional repressor; |
19-66 | 2.42e-03 | |||||
helix_turn_helix gluconate operon transcriptional repressor; Pssm-ID: 197669 [Multi-domain] Cd Length: 60 Bit Score: 35.63 E-value: 2.42e-03
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| 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 ... |
70-303 | 1.04e-105 | |||||
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: 307.67 E-value: 1.04e-105
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| YhfZ_full | NF041241 | GntR family transcriptional regulator YhfZ; Full-length homologs of the transcriptional ... |
1-303 | 2.23e-105 | |||||
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: 309.47 E-value: 2.23e-105
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| PBP2_Yhfz | cd13533 | Substrate-binding domain of uncharacterized protein Yhfz from Shigella Flexneri; the type 2 ... |
70-292 | 2.01e-70 | |||||
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: 217.53 E-value: 2.01e-70
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| HTH_41 | pfam14502 | Helix-turn-helix domain; |
19-66 | 1.80e-11 | |||||
Helix-turn-helix domain; Pssm-ID: 433997 [Multi-domain] Cd Length: 48 Bit Score: 58.27 E-value: 1.80e-11
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| TauA | COG0715 | ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ... |
67-270 | 2.00e-08 | |||||
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 440479 [Multi-domain] Cd Length: 297 Bit Score: 54.63 E-value: 2.00e-08
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| YhcF | COG1725 | DNA-binding transcriptional regulator YhcF, GntR family [Transcription]; |
19-68 | 6.02e-06 | |||||
DNA-binding transcriptional regulator YhcF, GntR family [Transcription]; Pssm-ID: 441331 [Multi-domain] Cd Length: 114 Bit Score: 44.40 E-value: 6.02e-06
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| WHTH_GntR | cd07377 | Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ... |
19-67 | 2.98e-05 | |||||
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: 41.28 E-value: 2.98e-05
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| HisJ | COG0834 | ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ... |
98-231 | 8.89e-05 | |||||
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms]; Pssm-ID: 440596 [Multi-domain] Cd Length: 223 Bit Score: 43.04 E-value: 8.89e-05
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| PBP2_SsuA_like_6 | cd13563 | Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 ... |
106-231 | 1.11e-04 | |||||
Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270281 [Multi-domain] Cd Length: 208 Bit Score: 42.61 E-value: 1.11e-04
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| Periplasmic_Binding_Protein_Type_2 | cd00648 | Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ... |
83-259 | 1.42e-04 | |||||
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), 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 origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences. Pssm-ID: 270214 [Multi-domain] Cd Length: 196 Bit Score: 42.18 E-value: 1.42e-04
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| GntR | pfam00392 | Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ... |
19-66 | 2.08e-04 | |||||
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: 38.75 E-value: 2.08e-04
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| ARO8 | COG1167 | DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ... |
9-68 | 8.56e-04 | |||||
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain [Transcription, Amino acid transport and metabolism]; DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain is part of the Pathway/BioSystem: Lysine biosynthesis Pssm-ID: 440781 [Multi-domain] Cd Length: 471 Bit Score: 40.58 E-value: 8.56e-04
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| HTH_GNTR | smart00345 | helix_turn_helix gluconate operon transcriptional repressor; |
19-66 | 2.42e-03 | |||||
helix_turn_helix gluconate operon transcriptional repressor; Pssm-ID: 197669 [Multi-domain] Cd Length: 60 Bit Score: 35.63 E-value: 2.42e-03
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| PBP2_NrtA_SsuA_CpmA_like | cd01008 | Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ... |
106-251 | 2.69e-03 | |||||
Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily; This family represents the periplasmic binding proteins involved in nitrate, alkanesulfonate, and bicarbonate transport. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. Other closest homologs involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB) are also included in this family. After binding their ligand with high affinity, they 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. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Pssm-ID: 270229 [Multi-domain] Cd Length: 212 Bit Score: 38.42 E-value: 2.69e-03
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| MngR | COG2188 | DNA-binding transcriptional regulator, GntR family [Transcription]; |
19-68 | 7.67e-03 | |||||
DNA-binding transcriptional regulator, GntR family [Transcription]; Pssm-ID: 441791 [Multi-domain] Cd Length: 238 Bit Score: 37.15 E-value: 7.67e-03
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| Blast search parameters | ||||
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