extracellular solute-binding protein [Ectopseudomonas mendocina]
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
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| Periplasmic_Binding_Protein_Type_2 super family | cl21456 | Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ... |
23-345 | 1.66e-145 | ||||||
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. The actual alignment was detected with superfamily member cd13659: Pssm-ID: 473866 [Multi-domain] Cd Length: 331 Bit Score: 414.04 E-value: 1.66e-145
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| Name | Accession | Description | Interval | E-value | ||||||
| PBP2_PotF | cd13659 | The periplasmic substrate-binding component of an ABC putrescine transport system and related ... |
23-345 | 1.66e-145 | ||||||
The periplasmic substrate-binding component of an ABC putrescine transport system and related proteins; contains the type 2 periplasmic-binding fold; This group represents the periplasmic substrate-binding domain that serves as the primary polyamine receptor of ABC-type putrescine-preferential transporter from gram-negative bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270377 [Multi-domain] Cd Length: 331 Bit Score: 414.04 E-value: 1.66e-145
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| PotD | COG0687 | Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; |
4-349 | 2.69e-101 | ||||||
Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Pssm-ID: 440451 [Multi-domain] Cd Length: 348 Bit Score: 302.60 E-value: 2.69e-101
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| PRK10682 | PRK10682 | putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional |
4-351 | 3.76e-91 | ||||||
putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional Pssm-ID: 182645 [Multi-domain] Cd Length: 370 Bit Score: 277.50 E-value: 3.76e-91
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| SBP_bac_6 | pfam13343 | Bacterial extracellular solute-binding protein; This family includes bacterial extracellular ... |
67-322 | 1.12e-16 | ||||||
Bacterial extracellular solute-binding protein; This family includes bacterial extracellular solute-binding proteins. Pssm-ID: 463852 [Multi-domain] Cd Length: 247 Bit Score: 78.56 E-value: 1.12e-16
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| Name | Accession | Description | Interval | E-value | ||||||
| PBP2_PotF | cd13659 | The periplasmic substrate-binding component of an ABC putrescine transport system and related ... |
23-345 | 1.66e-145 | ||||||
The periplasmic substrate-binding component of an ABC putrescine transport system and related proteins; contains the type 2 periplasmic-binding fold; This group represents the periplasmic substrate-binding domain that serves as the primary polyamine receptor of ABC-type putrescine-preferential transporter from gram-negative bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270377 [Multi-domain] Cd Length: 331 Bit Score: 414.04 E-value: 1.66e-145
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| PotD | COG0687 | Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; |
4-349 | 2.69e-101 | ||||||
Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Pssm-ID: 440451 [Multi-domain] Cd Length: 348 Bit Score: 302.60 E-value: 2.69e-101
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| PRK10682 | PRK10682 | putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional |
4-351 | 3.76e-91 | ||||||
putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional Pssm-ID: 182645 [Multi-domain] Cd Length: 370 Bit Score: 277.50 E-value: 3.76e-91
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| PBP2_PotD_PotF_like | cd13590 | The periplasmic-binding component of ABC transporters involved in uptake of polyamines; ... |
23-345 | 2.76e-86 | ||||||
The periplasmic-binding component of ABC transporters involved in uptake of polyamines; possess the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain that functions as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270308 [Multi-domain] Cd Length: 315 Bit Score: 262.94 E-value: 2.76e-86
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| PBP2_PotD_PotF_like_3 | cd13664 | TThe periplasmic substrate-binding component of an uncharacterized active transport system ... |
22-345 | 3.80e-60 | ||||||
TThe periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding domain that functions as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270382 [Multi-domain] Cd Length: 315 Bit Score: 196.04 E-value: 3.80e-60
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| PBP2_PotD | cd13660 | The periplasmic substrate-binding component of an active spermidine-preferential transport ... |
23-326 | 2.44e-54 | ||||||
The periplasmic substrate-binding component of an active spermidine-preferential transport system; contains the type 2 periplasmic binding fold; This group represents the periplasmic binding domain that serves as the primary polyamine receptor of ABC-type spermindine-preferential transport system from gram-negative bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270378 [Multi-domain] Cd Length: 315 Bit Score: 180.86 E-value: 2.44e-54
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| PBP2_polyamines | cd13523 | The periplasmic-binding component of ABC transporters involved in uptake of polyamines; ... |
22-292 | 3.90e-53 | ||||||
The periplasmic-binding component of ABC transporters involved in uptake of polyamines; possess the type 2 periplasmic binding fold; This family represents the periplasmic substrate-binding proteins that function as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270241 [Multi-domain] Cd Length: 268 Bit Score: 176.09 E-value: 3.90e-53
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| PBP2_PotD_PotF_like_2 | cd13663 | The periplasmic substrate-binding component of an uncharacterized active transport system ... |
22-349 | 2.95e-51 | ||||||
The periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold; This group represents the periplasmic substrate-binding domain that serves as a primary polyamine receptor of an uncharacterized ABC-type transport system from gram-negative bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270381 [Multi-domain] Cd Length: 323 Bit Score: 173.25 E-value: 2.95e-51
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| potD | PRK09501 | spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed |
5-323 | 4.82e-50 | ||||||
spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed Pssm-ID: 181913 [Multi-domain] Cd Length: 348 Bit Score: 170.87 E-value: 4.82e-50
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| PBP2_polyamine_1 | cd13588 | The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of ... |
22-305 | 3.69e-36 | ||||||
The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of polyamines; contains the type 2 periplasmic binding fold; This group represents the periplasmic binding domain that functions as the primary high-affinity receptor of an uncharactertized ABC-type polyamine transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270306 [Multi-domain] Cd Length: 279 Bit Score: 132.03 E-value: 3.69e-36
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| PBP2_TpPotD_like | cd13662 | The periplasmic substrate-binding component of an ABC-type polyamine transport system from ... |
25-332 | 3.72e-36 | ||||||
The periplasmic substrate-binding component of an ABC-type polyamine transport system from Treponema pallidum and related proteins; contains the type 2 periplasmic binding fold; This group includes the polyamine-binding component of an ABC-type polyamine transport system from Treponema pallidum and closely related proteins, which is homologous to the spermidine-preferring periplasmic substrate-binding protein component (PotD)of ABC transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270380 Cd Length: 312 Bit Score: 133.03 E-value: 3.72e-36
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| PBP2_polyamine_RpCGA009 | cd13589 | The periplasmic-binding component of an uncharacterized ABC transport system from ... |
36-297 | 3.59e-25 | ||||||
The periplasmic-binding component of an uncharacterized ABC transport system from Rhodopseudomonas palustris CGA009 and related proteins; contains the type 2 periplasmic-binding fold; This group represents the periplasmic binding domain that serves as the primary high-affinity receptor of an uncharacterized ABC-type polyamine transporter from Rhodopseudomonas palustris Cga009 and related proteins from other bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270307 [Multi-domain] Cd Length: 268 Bit Score: 102.30 E-value: 3.59e-25
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| PBP2_polyamine_2 | cd13587 | The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of ... |
23-307 | 1.03e-24 | ||||||
The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of polyamines; contains the type 2 periplasmic binding fold; This family represents the periplasmic binding domain that functions as the primary polyamine receptor of an uncharacterized ABC-type transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270305 [Multi-domain] Cd Length: 292 Bit Score: 101.74 E-value: 1.03e-24
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| SBP_bac_6 | pfam13343 | Bacterial extracellular solute-binding protein; This family includes bacterial extracellular ... |
67-322 | 1.12e-16 | ||||||
Bacterial extracellular solute-binding protein; This family includes bacterial extracellular solute-binding proteins. Pssm-ID: 463852 [Multi-domain] Cd Length: 247 Bit Score: 78.56 E-value: 1.12e-16
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| PBP2_PotD_PotF_like_1 | cd13661 | The periplasmic substrate-binding component of an uncharacterized active transport system ... |
120-347 | 1.66e-13 | ||||||
The periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold; This group represents the periplasmic binding domain that serves as a primary polyamine receptor of an uncharacterized ABC-type transport system from plants and plant-symbiotic cyanobacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. 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. Pssm-ID: 270379 [Multi-domain] Cd Length: 319 Bit Score: 70.14 E-value: 1.66e-13
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| SBP_bac_8 | pfam13416 | Bacterial extracellular solute-binding protein; This family includes bacterial extracellular ... |
35-303 | 2.57e-12 | ||||||
Bacterial extracellular solute-binding protein; This family includes bacterial extracellular solute-binding proteins. Pssm-ID: 433189 [Multi-domain] Cd Length: 281 Bit Score: 66.28 E-value: 2.57e-12
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| UgpB | COG1653 | ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport ... |
1-310 | 3.53e-12 | ||||||
ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism]; Pssm-ID: 441259 [Multi-domain] Cd Length: 363 Bit Score: 66.61 E-value: 3.53e-12
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| AfuA | COG1840 | ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; ... |
36-297 | 5.06e-11 | ||||||
ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Pssm-ID: 441445 [Multi-domain] Cd Length: 286 Bit Score: 62.65 E-value: 5.06e-11
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| SBP_bac_1 | pfam01547 | Bacterial extracellular solute-binding protein; This family also includes the bacterial ... |
29-286 | 9.69e-07 | ||||||
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: 49.72 E-value: 9.69e-07
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| PBP2_Fe3_thiamine_like | cd13518 | Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 ... |
122-286 | 5.48e-06 | ||||||
Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 periplasmic binding fold superfamily; The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. On the other hand, thiamin is an essential cofactor in all living systems. Thiamin diphosphate (ThDP)-dependent enzymes play an important role in carbohydrate and branched-chain amino acid metabolism. Most prokaryotes, plants, and fungi can synthesize thiamin, but it is not synthesized in vertebrates. These periplasmic domains have high affinities for their respective substrates and serve as the primary receptor for transport. After binding iron and thiamine with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The iron- and thiamine-binding proteins belong to the PBPI2 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: 270236 [Multi-domain] Cd Length: 260 Bit Score: 47.30 E-value: 5.48e-06
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| PBP2_TMBP_like | cd13585 | The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and ... |
64-332 | 4.78e-04 | ||||||
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: 41.62 E-value: 4.78e-04
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| PBP2_Fbp_like_2 | cd13547 | Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 ... |
236-297 | 3.34e-03 | ||||||
Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily; The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-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: 270265 [Multi-domain] Cd Length: 259 Bit Score: 38.74 E-value: 3.34e-03
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| Blast search parameters | ||||
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