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Conserved domains on  [gi|2157295329|ref|WP_230467915|]
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extracellular solute-binding protein, partial [Lujinxingia vulgaris]

Protein Classification

type 2 periplasmic-binding domain-containing protein( domain architecture ID 229383)

type 2 periplasmic-binding protein (PBP2) is typically comprised of two globular subdomains connected by a flexible hinge; it binds its ligand in the cleft between these domains in a manner resembling a Venus flytrap; similar to the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UgpB super family cl43481
ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport ...
 23-124 2.11e-11

ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism];


The actual alignment was detected with superfamily member COG1653:

Pssm-ID: 441259 [Multi-domain]  Cd Length: 363  Bit Score: 59.29  E-value: 2.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2157295329  23 CSGGGDT----DGKITLDVWTFGG---MGLDEAFATYQEENPNIILKVTNAGgSDEQAQALTTALAGGKGPDVAAIEVGY 95
Cdd:COG1653    19 CGGGGSGaaaaAGKVTLTVWHTGGgeaAALEALIKEFEAEHPGIKVEVESVP-YDDYRTKLLTALAAGNAPDVVQVDSGW 97

                          90       100
                  ....*....|....*....|....*....
gi 2157295329  96 MSQFKAQPQnFVDLrtlgSDDIESSFLDW 124
Cdd:COG1653    98 LAEFAAAGA-LVPL----DDLLDDDGLDK 121
 
Name Accession Description Interval E-value
UgpB COG1653
ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport ...
 23-124 2.11e-11

ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism];


Pssm-ID: 441259 [Multi-domain]  Cd Length: 363  Bit Score: 59.29  E-value: 2.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2157295329  23 CSGGGDT----DGKITLDVWTFGG---MGLDEAFATYQEENPNIILKVTNAGgSDEQAQALTTALAGGKGPDVAAIEVGY 95
Cdd:COG1653    19 CGGGGSGaaaaAGKVTLTVWHTGGgeaAALEALIKEFEAEHPGIKVEVESVP-YDDYRTKLLTALAAGNAPDVVQVDSGW 97

                          90       100
                  ....*....|....*....|....*....
gi 2157295329  96 MSQFKAQPQnFVDLrtlgSDDIESSFLDW 124
Cdd:COG1653    98 LAEFAAAGA-LVPL----DDLLDDDGLDK 121
PBP2_UgpB cd14748
The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; ...
 34-124 2.12e-09

The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; possesses type 2 periplasmic binding fold; This group includes the periplasmic component of an ABC transport system specific for sn-glycerol-3-phosphate (G3P) and closely related proteins from archaea and bacteria. Under phophate starvation conditions, Escherichia coli can utilize G3P as phosphate source when exclusively imported by an ATP-binding cassette (ABC) transporter composed of the periplasmic binding protein, UgpB, the transmembrane subunits, UgpA and UgpE, and a homodimer of the nucleotide binding subunit, UgpC. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are 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.


Pssm-ID: 270451 [Multi-domain]  Cd Length: 385  Bit Score: 53.84  E-value: 2.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2157295329  34 TLDVWTFG----GMGLDEAFATYQEENPNIILKVTNAGGSDEQAQALTTALAGGKGPDVAAIEVGYMSQFKAQPQnFVDL 109
Cdd:cd14748     1 EITFWHGMsgpdGKALEELVDEFNKSHPDIKVKAVYQGSYDDTLTKLLAALAAGTAPDVAQVDASWVAQLADSGA-LEPL 79

                          90
                  ....*....|....*
gi 2157295329 110 rtlgSDDIESSFLDW 124
Cdd:cd14748    80 ----DDYIDKDGVDD 90
SBP_bac_1 pfam01547
Bacterial extracellular solute-binding protein; This family also includes the bacterial ...
 44-102 2.28e-05

Bacterial extracellular solute-binding protein; This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.


Pssm-ID: 460248 [Multi-domain]  Cd Length: 294  Bit Score: 42.02  E-value: 2.28e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2157295329  44 GLDEAFATYQEENPNIilKVT-NAGGSDEQAQALTTALAGGKGP-DVAAIEVGYMSQFKAQ 102
Cdd:pfam01547   9 ALQALVKEFEKEHPGI--KVEvESVGSGSLAQKLTTAIAAGDGPaDVFASDNDWIAELAKA 67
 
Name Accession Description Interval E-value
UgpB COG1653
ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport ...
 23-124 2.11e-11

ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism];


Pssm-ID: 441259 [Multi-domain]  Cd Length: 363  Bit Score: 59.29  E-value: 2.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2157295329  23 CSGGGDT----DGKITLDVWTFGG---MGLDEAFATYQEENPNIILKVTNAGgSDEQAQALTTALAGGKGPDVAAIEVGY 95
Cdd:COG1653    19 CGGGGSGaaaaAGKVTLTVWHTGGgeaAALEALIKEFEAEHPGIKVEVESVP-YDDYRTKLLTALAAGNAPDVVQVDSGW 97

                          90       100
                  ....*....|....*....|....*....
gi 2157295329  96 MSQFKAQPQnFVDLrtlgSDDIESSFLDW 124
Cdd:COG1653    98 LAEFAAAGA-LVPL----DDLLDDDGLDK 121
PBP2_UgpB cd14748
The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; ...
 34-124 2.12e-09

The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; possesses type 2 periplasmic binding fold; This group includes the periplasmic component of an ABC transport system specific for sn-glycerol-3-phosphate (G3P) and closely related proteins from archaea and bacteria. Under phophate starvation conditions, Escherichia coli can utilize G3P as phosphate source when exclusively imported by an ATP-binding cassette (ABC) transporter composed of the periplasmic binding protein, UgpB, the transmembrane subunits, UgpA and UgpE, and a homodimer of the nucleotide binding subunit, UgpC. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are 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.


Pssm-ID: 270451 [Multi-domain]  Cd Length: 385  Bit Score: 53.84  E-value: 2.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2157295329  34 TLDVWTFG----GMGLDEAFATYQEENPNIILKVTNAGGSDEQAQALTTALAGGKGPDVAAIEVGYMSQFKAQPQnFVDL 109
Cdd:cd14748     1 EITFWHGMsgpdGKALEELVDEFNKSHPDIKVKAVYQGSYDDTLTKLLAALAAGTAPDVAQVDASWVAQLADSGA-LEPL 79

                          90
                  ....*....|....*
gi 2157295329 110 rtlgSDDIESSFLDW 124
Cdd:cd14748    80 ----DDYIDKDGVDD 90
PBP2_TMBP_like cd13585
The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and ...
 34-102 3.47e-07

The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and similar oligosaccharides; possess type 2 periplasmic binding fold; This family includes the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is 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.


Pssm-ID: 270303 [Multi-domain]  Cd Length: 383  Bit Score: 47.40  E-value: 3.47e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2157295329  34 TLDVWTFGGMGLDEAF----ATYQEENPNIilKVTNAGGSDEQA-QALTTALAGGKGPDVAAIEVGYMSQFKAQ 102
Cdd:cd13585     1 TLTFWDWGQPAETAALkkliDAFEKENPGV--KVEVVPVPYDDYwTKLTTAAAAGTAPDVFYVDGPWVPEFASN 72
PBP2_MalE cd14747
Maltose-binding protein MalE; possesses type 2 periplasmic binding fold; This group includes ...
 34-127 6.82e-07

Maltose-binding protein MalE; possesses type 2 periplasmic binding fold; This group includes the periplasmic maltose-binding component of an ABC transport system from the phytopathogen Xanthomonas citri and its related bacterial proteins. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are 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.


Pssm-ID: 270450 [Multi-domain]  Cd Length: 386  Bit Score: 46.54  E-value: 6.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2157295329  34 TLDVWTFGGMGLDEAF----ATYQEENPNIILKVTNAGGSDEQaQALTTALAGGKGPDVAAIEVGYMSQFKAQpQNFVDL 109
Cdd:cd14747     1 TLTVWAMGNSAEAELLkelaDEFEKENPGIEVKVQVLPWGDAH-TKITTAAASGDGPDVVQLGNTWVAEFAAM-GALEDL 78

                          90
                  ....*....|....*....
gi 2157295329 110 RT-LGSDDIESSFLDWRWS 127
Cdd:cd14747    79 TPyLEDLGGDKDLFPGLVD 97
PBP2_XBP1_like cd14749
The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; ...
 45-105 1.68e-06

The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; possesses type 2 periplasmic binding fold; This group represents the periplasmic component of an ABC transport system XBP1 that shows preference for xylo-oligosaccharides in the order of xylotriose > xylobiose > xylotetraose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are 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.


Pssm-ID: 270452 [Multi-domain]  Cd Length: 388  Bit Score: 45.45  E-value: 1.68e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2157295329  45 LDEAFATYQEENPNIILKVTNAGGsDEQAQALTTALAGGKGPDVAAIEVG-----YMSQFKAQPQN 105
Cdd:cd14749    17 MDELIADFEKENPNIKVKVVVFPY-DNYKTKLKTAVAAGEGPDVFNLWPGgwlaeFVKAGLLLPLT 81
SBP_bac_1 pfam01547
Bacterial extracellular solute-binding protein; This family also includes the bacterial ...
 44-102 2.28e-05

Bacterial extracellular solute-binding protein; This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.


Pssm-ID: 460248 [Multi-domain]  Cd Length: 294  Bit Score: 42.02  E-value: 2.28e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2157295329  44 GLDEAFATYQEENPNIilKVT-NAGGSDEQAQALTTALAGGKGP-DVAAIEVGYMSQFKAQ 102
Cdd:pfam01547   9 ALQALVKEFEKEHPGI--KVEvESVGSGSLAQKLTTAIAAGDGPaDVFASDNDWIAELAKA 67
MalE COG2182
Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism];
23-91 3.78e-05

Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism];


Pssm-ID: 441785 [Multi-domain]  Cd Length: 410  Bit Score: 41.47  E-value: 3.78e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2157295329  23 CSGGGDT-------DGKITLDVWTFG--GMGLDEAFATYQEEnPNIILKVTNAGgSDEQAQALTTALAGGKGPDVAAI 91
Cdd:COG2182    22 CGSGSSSsgsssaaGAGGTLTVWVDDdeAEALEEAAAAFEEE-PGIKVKVVEVP-WDDLREKLTTAAPAGKGPDVFVG 97
PBP2_ABC_oligosaccharides cd13522
The periplasmic-binding component of ABC transport systems specific for maltose and related ...
 34-88 1.63e-04

The periplasmic-binding component of ABC transport systems specific for maltose and related oligosaccharides; possess type 2 periplasmic binding fold; This family represents the periplasmic binding component of ABC transport systems involved in uptake of oligosaccharides including maltose, trehalose, maltodextrin, and cyclodextrin. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is 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.


Pssm-ID: 270240 [Multi-domain]  Cd Length: 368  Bit Score: 39.70  E-value: 1.63e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2157295329  34 TLDVWTFGGMG----LDEAFATYQEENPNIILKVTNaGGSDEQAQALTTALAGGKGPDV 88
Cdd:cd13522     1 TITVWHQYDTGenqaVNELIAKFEKAYPGITVEVTY-QDTEARRQFFSTAAAGGKGPDV 58
PBP2_GacH cd14751
The periplasmic-binding component of the putative oligosacchride ABC transporter GacHFG; ...
 52-99 4.46e-04

The periplasmic-binding component of the putative oligosacchride ABC transporter GacHFG; possesses type 2 periplasmic binding fold; This group represents the periplasmic component GacH of an ABC import system. GacH is identified as a maltose/maltodextrin-binding protein with a low affinity for acarbose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are 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.


Pssm-ID: 270454 [Multi-domain]  Cd Length: 376  Bit Score: 38.51  E-value: 4.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2157295329  52 YQEENPNIILKVTNAGgSDEQAQALTTALAGGKGPDVAAIEVGYMSQF 99
Cdd:cd14751    23 FEKEYPKIKVKAVRVP-FDGLHNQIKTAAAGGQAPDVMRADIAWVPEF 69
 
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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