NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|347520148|gb|EGY27287|]
View 

hypothetical protein DA2_0434 [Desulfovibrio sp. A2]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
TIGR02285 super family cl27684
conserved hypothetical protein; Members of this family are found in several Proteobacteria, ...
 15-194 4.25e-13

conserved hypothetical protein; Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown. [Hypothetical proteins, Conserved]


The actual alignment was detected with superfamily member TIGR02285:

Pssm-ID: 131338  Cd Length: 268  Bit Score: 66.73  E-value: 4.25e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   15 HEFKPMPAKRALERVERDPTAISIGWFRTEERERRFIFSRPIYTNRPPELLVLSSRVAEFRNHR----TFAGLMKDAFFR 90
Cdd:TIGR02285  59 HRFVRVSFARSLKELQGKGGVCTVNLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAGVRDEQdgdvDLKKLLASKKKR 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   91 LGTIVGHSEGEYCDAIIA----THAGDVYHLAGTrVQLVKMLRSYRIDGVLVPPEEVDALTEAAGIPRDEMTTIKLddip 166
Cdd:TIGR02285 139 LGVIASRSYGQQIDDILSdsgyQHNTRIIGNAAM-GNLFKMLEKGRVNYTLAYPPEKTYYEELNNGALPPLKFLPV---- 213

                         170       180       190
                  ....*....|....*....|....*....|...
gi 347520148  167 AGNARHI---IFNKNTNPG--VIATINAVIQSL 194
Cdd:TIGR02285 214 AGMPAHIsvwVACPKTEWGrkVIADIDQALSEL 246
 
Name Accession Description Interval E-value
TIGR02285 TIGR02285
conserved hypothetical protein; Members of this family are found in several Proteobacteria, ...
 15-194 4.25e-13

conserved hypothetical protein; Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown. [Hypothetical proteins, Conserved]


Pssm-ID: 131338  Cd Length: 268  Bit Score: 66.73  E-value: 4.25e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   15 HEFKPMPAKRALERVERDPTAISIGWFRTEERERRFIFSRPIYTNRPPELLVLSSRVAEFRNHR----TFAGLMKDAFFR 90
Cdd:TIGR02285  59 HRFVRVSFARSLKELQGKGGVCTVNLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAGVRDEQdgdvDLKKLLASKKKR 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   91 LGTIVGHSEGEYCDAIIA----THAGDVYHLAGTrVQLVKMLRSYRIDGVLVPPEEVDALTEAAGIPRDEMTTIKLddip 166
Cdd:TIGR02285 139 LGVIASRSYGQQIDDILSdsgyQHNTRIIGNAAM-GNLFKMLEKGRVNYTLAYPPEKTYYEELNNGALPPLKFLPV---- 213

                         170       180       190
                  ....*....|....*....|....*....|...
gi 347520148  167 AGNARHI---IFNKNTNPG--VIATINAVIQSL 194
Cdd:TIGR02285 214 AGMPAHIsvwVACPKTEWGrkVIADIDQALSEL 246
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
 4-196 2.96e-10

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: 58.07  E-value: 2.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   4 VKAVLEAARIRHEFKPMPAKRALERVERDPTAISIGWF-RTEERERRFIFSRPIYTNrPPELLVLSSRvAEFRNHRTFAG 82
Cdd:COG0834   29 ARAIAKRLGLKVEFVPVPWDRLIPALQSGKVDLIIAGMtITPEREKQVDFSDPYYTS-GQVLLVRKDN-SGIKSLADLKG 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148  83 LmkdaffRLGTIVGHSEGEYcdaIIATHAGDVYHLAGTRVQLVKMLRSYRIDGVLVPPEEVDALTEAAGIPRDEMTTIKL 162
Cdd:COG0834  107 K------TVGVQAGTTYEEY---LKKLGPNAEIVEFDSYAEALQALASGRVDAVVTDEPVAAYLLAKNPGDDLKIVGEPL 177

                        170       180       190
                 ....*....|....*....|....*....|....
gi 347520148 163 DDIPAGnarhIIFNKNtNPGVIATINAVIQSLED 196
Cdd:COG0834  178 SGEPYG----IAVRKG-DPELLEAVNKALAALKA 206
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
 4-194 3.03e-07

Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognizes Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 425719 [Multi-domain]  Cd Length: 221  Bit Score: 49.21  E-value: 3.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148    4 VKAVLEAARIRHEFKPMPAKRALERVER---DpTAISiGWFRTEERERRFIFSRPIYTNrPPELLVLSSrvAEFRNHRTF 80
Cdd:pfam00497  29 AKAIAKRLGVKVEFVPVSWDGLIPALQSgkvD-LIIA-GMTITPERAKQVDFSDPYYYS-GQVILVRKK--DSSKSIKSL 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   81 AGLmkdAFFRLGTIVGHSEGEYcdAIIATHAGDVYHLAGTRVQLVKMLRSYRIDGVLVPPEEVDALTEAAGIPRDEMTTI 160
Cdd:pfam00497 104 ADL---KGKTVGVQKGSTAEEL--LKNLKLPGAEIVEYDDDAEALQALANGRVDAVVADSPVAAYLIKKNPGLNLVVVGE 178

                         170       180       190
                  ....*....|....*....|....*....|....
gi 347520148  161 KLDDIPAGnarhIIFNKNtNPGVIATINAVIQSL 194
Cdd:pfam00497 179 PLSPEPYG----IAVRKG-DPELLAAVNKALAEL 207
PBP2_HisK_like_1 cd13706
Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This ...
 13-58 3.22e-06

Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This group includes periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space through their function as an initial high-affinity binding component. PBP2 typically comprises 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.


Pssm-ID: 270424 [Multi-domain]  Cd Length: 219  Bit Score: 46.40  E-value: 3.22e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 347520148  13 IRHEFKPMPAKRALERVERDPTAISIGWFRTEERERRFIFSRPIYT 58
Cdd:cd13706   41 IPVEFVLLDWNESLEAVRQGEADVHDGLFKSPEREKYLDFSQPIAT 86
 
Name Accession Description Interval E-value
TIGR02285 TIGR02285
conserved hypothetical protein; Members of this family are found in several Proteobacteria, ...
 15-194 4.25e-13

conserved hypothetical protein; Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown. [Hypothetical proteins, Conserved]


Pssm-ID: 131338  Cd Length: 268  Bit Score: 66.73  E-value: 4.25e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   15 HEFKPMPAKRALERVERDPTAISIGWFRTEERERRFIFSRPIYTNRPPELLVLSSRVAEFRNHR----TFAGLMKDAFFR 90
Cdd:TIGR02285  59 HRFVRVSFARSLKELQGKGGVCTVNLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAGVRDEQdgdvDLKKLLASKKKR 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   91 LGTIVGHSEGEYCDAIIA----THAGDVYHLAGTrVQLVKMLRSYRIDGVLVPPEEVDALTEAAGIPRDEMTTIKLddip 166
Cdd:TIGR02285 139 LGVIASRSYGQQIDDILSdsgyQHNTRIIGNAAM-GNLFKMLEKGRVNYTLAYPPEKTYYEELNNGALPPLKFLPV---- 213

                         170       180       190
                  ....*....|....*....|....*....|...
gi 347520148  167 AGNARHI---IFNKNTNPG--VIATINAVIQSL 194
Cdd:TIGR02285 214 AGMPAHIsvwVACPKTEWGrkVIADIDQALSEL 246
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
 4-196 2.96e-10

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: 58.07  E-value: 2.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   4 VKAVLEAARIRHEFKPMPAKRALERVERDPTAISIGWF-RTEERERRFIFSRPIYTNrPPELLVLSSRvAEFRNHRTFAG 82
Cdd:COG0834   29 ARAIAKRLGLKVEFVPVPWDRLIPALQSGKVDLIIAGMtITPEREKQVDFSDPYYTS-GQVLLVRKDN-SGIKSLADLKG 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148  83 LmkdaffRLGTIVGHSEGEYcdaIIATHAGDVYHLAGTRVQLVKMLRSYRIDGVLVPPEEVDALTEAAGIPRDEMTTIKL 162
Cdd:COG0834  107 K------TVGVQAGTTYEEY---LKKLGPNAEIVEFDSYAEALQALASGRVDAVVTDEPVAAYLLAKNPGDDLKIVGEPL 177

                        170       180       190
                 ....*....|....*....|....*....|....
gi 347520148 163 DDIPAGnarhIIFNKNtNPGVIATINAVIQSLED 196
Cdd:COG0834  178 SGEPYG----IAVRKG-DPELLEAVNKALAALKA 206
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
 4-194 3.03e-07

Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognizes Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 425719 [Multi-domain]  Cd Length: 221  Bit Score: 49.21  E-value: 3.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148    4 VKAVLEAARIRHEFKPMPAKRALERVER---DpTAISiGWFRTEERERRFIFSRPIYTNrPPELLVLSSrvAEFRNHRTF 80
Cdd:pfam00497  29 AKAIAKRLGVKVEFVPVSWDGLIPALQSgkvD-LIIA-GMTITPERAKQVDFSDPYYYS-GQVILVRKK--DSSKSIKSL 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   81 AGLmkdAFFRLGTIVGHSEGEYcdAIIATHAGDVYHLAGTRVQLVKMLRSYRIDGVLVPPEEVDALTEAAGIPRDEMTTI 160
Cdd:pfam00497 104 ADL---KGKTVGVQKGSTAEEL--LKNLKLPGAEIVEYDDDAEALQALANGRVDAVVADSPVAAYLIKKNPGLNLVVVGE 178

                         170       180       190
                  ....*....|....*....|....*....|....
gi 347520148  161 KLDDIPAGnarhIIFNKNtNPGVIATINAVIQSL 194
Cdd:pfam00497 179 PLSPEPYG----IAVRKG-DPELLAAVNKALAEL 207
PBP2_HisK_like_1 cd13706
Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This ...
 13-58 3.22e-06

Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This group includes periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space through their function as an initial high-affinity binding component. PBP2 typically comprises 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.


Pssm-ID: 270424 [Multi-domain]  Cd Length: 219  Bit Score: 46.40  E-value: 3.22e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 347520148  13 IRHEFKPMPAKRALERVERDPTAISIGWFRTEERERRFIFSRPIYT 58
Cdd:cd13706   41 IPVEFVLLDWNESLEAVRQGEADVHDGLFKSPEREKYLDFSQPIAT 86
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
 4-60 5.59e-06

The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding fold protein; This subfamily includes the periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space through their function as an initial high-affinity binding component. PBP2 typically comprises 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.


Pssm-ID: 270422 [Multi-domain]  Cd Length: 220  Bit Score: 45.65  E-value: 5.59e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 347520148   4 VKAVLEAARIRHEFKPMP---AKRALERVERDptaISIGWFRTEERERRFIFSRPIYTNR 60
Cdd:cd13704   32 LRAIAEEMGLKVEIRLGPwseVLQALENGEID---VLIGMAYSEERAKLFDFSDPYLEVS 88
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH