NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|639389087|ref|WP_024609211|]
View 

ABC transporter substrate-binding protein [Pseudoalteromonas arctica]

Protein Classification

substrate-binding periplasmic protein( domain architecture ID 11435556)

substrate-binding periplasmic protein similar to ABC transporter substrate-binding proteins, which function as the initial receptor in the ABC transport of a variety of substrates including amino acids and peptides, and to 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

PubMed:  15313245

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
30-239 9.74e-13

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: 65.39  E-value: 9.74e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087  30 IAASASIPPYVFVKTD---SGIHLNLIKAALKANGFaNINVQYMSNKRAEHQLHNKGVDILlnyAGGIS------AGIYP 100
Cdd:COG0834    3 VGVDPDYPPFSFRDEDgklVGFDVDLARAIAKRLGL-KVEFVPVPWDRLIPALQSGKVDLI---IAGMTitpereKQVDF 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087 101 SKTVLSYENVAITLKRNKyNIDKIEGMFNKNVLAFQNAT--AYLPPIFKR-NVKHFSSYQEVInqkaqvDKLLKGWVDVI 177
Cdd:COG0834   79 SDPYYTSGQVLLVRKDNS-GIKSLADLKGKTVGVQAGTTyeEYLKKLGPNaEIVEFDSYAEAL------QALASGRVDAV 151
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 639389087 178 VLDKRIFYYYYNQHKSPEAVQIYTLFPKAdrPAYF----NNFSLATEFDIGLALIKQNGTYKRIVD 239
Cdd:COG0834  152 VTDEPVAAYLLAKNPGDDLKIVGEPLSGE--PYGIavrkGDPELLEAVNKALAALKADGTLDKILE 215
 
Name Accession Description Interval E-value
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
30-239 9.74e-13

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: 65.39  E-value: 9.74e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087  30 IAASASIPPYVFVKTD---SGIHLNLIKAALKANGFaNINVQYMSNKRAEHQLHNKGVDILlnyAGGIS------AGIYP 100
Cdd:COG0834    3 VGVDPDYPPFSFRDEDgklVGFDVDLARAIAKRLGL-KVEFVPVPWDRLIPALQSGKVDLI---IAGMTitpereKQVDF 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087 101 SKTVLSYENVAITLKRNKyNIDKIEGMFNKNVLAFQNAT--AYLPPIFKR-NVKHFSSYQEVInqkaqvDKLLKGWVDVI 177
Cdd:COG0834   79 SDPYYTSGQVLLVRKDNS-GIKSLADLKGKTVGVQAGTTyeEYLKKLGPNaEIVEFDSYAEAL------QALASGRVDAV 151
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 639389087 178 VLDKRIFYYYYNQHKSPEAVQIYTLFPKAdrPAYF----NNFSLATEFDIGLALIKQNGTYKRIVD 239
Cdd:COG0834  152 VTDEPVAAYLLAKNPGDDLKIVGEPLSGE--PYGIavrkGDPELLEAVNKALAALKADGTLDKILE 215
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
25-239 4.15e-08

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: 52.20  E-value: 4.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087  25 EREVMIAASASIPPYVFVKTD---SGIHLNLIKAALKANGFaNINVQYMSNKRAEHQLHNKGVDILlnyaggisAGIYPS 101
Cdd:cd13704    1 ARTVIVGGDKNYPPYEFLDENgnpTGFNVDLLRAIAEEMGL-KVEIRLGPWSEVLQALENGEIDVL--------IGMAYS 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087 102 ----KTVL-----SYENVAITLKRNKYNIDKIEGMFNKNVLAFQNATAY---LPPIFKRNVKHFSSYQEVInqkaqvDKL 169
Cdd:cd13704   72 eeraKLFDfsdpyLEVSVSIFVRKGSSIINSLEDLKGKKVAVQRGDIMHeylKERGLGINLVLVDSPEEAL------RLL 145
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 639389087 170 LKGWVDVIVLDKRIFYYYYNQHKSPEaVQIyTLFPKADRPAYF----NNFSLATEFDIGLALIKQNGTYKRIVD 239
Cdd:cd13704  146 ASGKVDAAVVDRLVGLYLIKELGLTN-VKI-VGPPLLPLKYCFavrkGNPELLAKLNEGLAILKASGEYDEIYE 217
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
28-239 1.88e-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: 50.37  E-value: 1.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087   28 VMIAASASIPPYVFVKTD---SGIHLNLIKAALKANGFaNINVQYMSNKRAEHQLHNKGVDIllnyaggISAGIYPS--- 101
Cdd:pfam00497   1 LRVGTDGDYPPFEYVDENgklVGFDVDLAKAIAKRLGV-KVEFVPVSWDGLIPALQSGKVDL-------IIAGMTITper 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087  102 -KTVL-------SYENVAITLKRNKYNIDKIEGMFNKNVlAFQNATAY-----LPPIFKRNVKHFSSYQEVINQkaqvdk 168
Cdd:pfam00497  73 aKQVDfsdpyyySGQVILVRKKDSSKSIKSLADLKGKTV-GVQKGSTAeellkNLKLPGAEIVEYDDDAEALQA------ 145
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 639389087  169 LLKGWVDVIVLDKRIFYYYynQHKSPEAVQIYTLFPKADRPAYF----NNFSLATEFDIGLALIKQNGTYKRIVD 239
Cdd:pfam00497 146 LANGRVDAVVADSPVAAYL--IKKNPGLNLVVVGEPLSPEPYGIavrkGDPELLAAVNKALAELKADGTLAKIYE 218
 
Name Accession Description Interval E-value
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
30-239 9.74e-13

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: 65.39  E-value: 9.74e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087  30 IAASASIPPYVFVKTD---SGIHLNLIKAALKANGFaNINVQYMSNKRAEHQLHNKGVDILlnyAGGIS------AGIYP 100
Cdd:COG0834    3 VGVDPDYPPFSFRDEDgklVGFDVDLARAIAKRLGL-KVEFVPVPWDRLIPALQSGKVDLI---IAGMTitpereKQVDF 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087 101 SKTVLSYENVAITLKRNKyNIDKIEGMFNKNVLAFQNAT--AYLPPIFKR-NVKHFSSYQEVInqkaqvDKLLKGWVDVI 177
Cdd:COG0834   79 SDPYYTSGQVLLVRKDNS-GIKSLADLKGKTVGVQAGTTyeEYLKKLGPNaEIVEFDSYAEAL------QALASGRVDAV 151
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 639389087 178 VLDKRIFYYYYNQHKSPEAVQIYTLFPKAdrPAYF----NNFSLATEFDIGLALIKQNGTYKRIVD 239
Cdd:COG0834  152 VTDEPVAAYLLAKNPGDDLKIVGEPLSGE--PYGIavrkGDPELLEAVNKALAALKADGTLDKILE 215
PBP2_HisK cd13704
The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding ...
25-239 4.15e-08

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: 52.20  E-value: 4.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087  25 EREVMIAASASIPPYVFVKTD---SGIHLNLIKAALKANGFaNINVQYMSNKRAEHQLHNKGVDILlnyaggisAGIYPS 101
Cdd:cd13704    1 ARTVIVGGDKNYPPYEFLDENgnpTGFNVDLLRAIAEEMGL-KVEIRLGPWSEVLQALENGEIDVL--------IGMAYS 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087 102 ----KTVL-----SYENVAITLKRNKYNIDKIEGMFNKNVLAFQNATAY---LPPIFKRNVKHFSSYQEVInqkaqvDKL 169
Cdd:cd13704   72 eeraKLFDfsdpyLEVSVSIFVRKGSSIINSLEDLKGKKVAVQRGDIMHeylKERGLGINLVLVDSPEEAL------RLL 145
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 639389087 170 LKGWVDVIVLDKRIFYYYYNQHKSPEaVQIyTLFPKADRPAYF----NNFSLATEFDIGLALIKQNGTYKRIVD 239
Cdd:cd13704  146 ASGKVDAAVVDRLVGLYLIKELGLTN-VKI-VGPPLLPLKYCFavrkGNPELLAKLNEGLAILKASGEYDEIYE 217
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
30-239 6.98e-08

Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1, 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 PBP2 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: 270248 [Multi-domain]  Cd Length: 217  Bit Score: 51.48  E-value: 6.98e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087  30 IAASASIPPYVFVKTD---SGIHLNLIKAALKANGFaNINVQYMSNKRAEHQLHNKGVDIllnyaggISAGIYPS----K 102
Cdd:cd13530    4 VGTDADYPPFEYIDKNgklVGFDVDLANAIAKRLGV-KVEFVDTDFDGLIPALQSGKIDV-------AISGMTITperaK 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087 103 TVL-----SYENVAITLKRNKYNIDKIEGMFNKNV------LAFQNATAYLPPIfkrNVKHFSSYQEVINQkaqvdkLLK 171
Cdd:cd13530   76 VVDfsdpyYYTGQVLVVKKDSKITKTVADLKGKKVgvqagtTGEDYAKKNLPNA---EVVTYDNYPEALQA------LKA 146
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 639389087 172 GWVDVIVLDKRIFYYYYNQHKSPEAVQIYTLFPKadrPAYF----NNFSLATEFDIGLALIKQNGTYKRIVD 239
Cdd:cd13530  147 GRIDAVITDAPVAKYYVKKNGPDLKVVGEPLTPE---PYGIavrkGNPELLDAINKALAELKADGTLDKLLE 215
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
28-239 1.88e-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: 50.37  E-value: 1.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087   28 VMIAASASIPPYVFVKTD---SGIHLNLIKAALKANGFaNINVQYMSNKRAEHQLHNKGVDIllnyaggISAGIYPS--- 101
Cdd:pfam00497   1 LRVGTDGDYPPFEYVDENgklVGFDVDLAKAIAKRLGV-KVEFVPVSWDGLIPALQSGKVDL-------IIAGMTITper 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087  102 -KTVL-------SYENVAITLKRNKYNIDKIEGMFNKNVlAFQNATAY-----LPPIFKRNVKHFSSYQEVINQkaqvdk 168
Cdd:pfam00497  73 aKQVDfsdpyyySGQVILVRKKDSSKSIKSLADLKGKTV-GVQKGSTAeellkNLKLPGAEIVEYDDDAEALQA------ 145
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 639389087  169 LLKGWVDVIVLDKRIFYYYynQHKSPEAVQIYTLFPKADRPAYF----NNFSLATEFDIGLALIKQNGTYKRIVD 239
Cdd:pfam00497 146 LANGRVDAVVADSPVAAYL--IKKNPGLNLVVVGEPLSPEPYGIavrkGDPELLAAVNKALAELKADGTLAKIYE 218
PBP2_Arg_Lys_His cd13624
Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 ...
149-239 7.95e-03

Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 periplasmic binding protein fold; This group includes the periplasmic substrate-binding protein ArtJ of the ATP-binding cassette (ABC) transport system from the thermophilic bacterium Geobacillus stearothermophilus, which is specific for arginine, lysine, and histidine. ArtJ 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 as a primary receptor. 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. 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 receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270342 [Multi-domain]  Cd Length: 219  Bit Score: 36.70  E-value: 7.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639389087 149 NVKHFSSYQEVINQkaqvdkLLKGWVDVIVLDKRIFYYYYNQHKSPEAVQIYTLFPKAdrpaYF------NNFSLATEFD 222
Cdd:cd13624  130 KVKRFDTIPLAFLE------LKNGGVDAVVNDNPVAAYYVKQNPDKKLKIVGDPLTSE----YYgiavrkGNKELLDKIN 199
                         90
                 ....*....|....*..
gi 639389087 223 IGLALIKQNGTYKRIVD 239
Cdd:cd13624  200 KALKKIKENGTYDKIYK 216
 
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