putative selenate ABC transporter periplasmic binding protein; Members of this family ABC ...
24-286
1.39e-147
putative selenate ABC transporter periplasmic binding protein; Members of this family ABC transporter periplasmic binding proteins and represent one clade within a larger family that includes phosphate, phosphite, and phosphonate transporters. All members of the seed alignment occur near a gene for SelD, the selenium-activating protein needed to make selenocysteine or selenouridine. Context therefore suggests members should be able to transport selenate, although transporting other substrates as well (e.g. phosphonates) is possible. This model has no overlap with TIGR03431, whose members are found regularly with phosphonate catabolism operons.
The actual alignment was detected with superfamily member TIGR04553:
Pssm-ID: 275346 [Multi-domain] Cd Length: 266 Bit Score: 414.17 E-value: 1.39e-147
putative selenate ABC transporter periplasmic binding protein; Members of this family ABC ...
24-286
1.39e-147
putative selenate ABC transporter periplasmic binding protein; Members of this family ABC transporter periplasmic binding proteins and represent one clade within a larger family that includes phosphate, phosphite, and phosphonate transporters. All members of the seed alignment occur near a gene for SelD, the selenium-activating protein needed to make selenocysteine or selenouridine. Context therefore suggests members should be able to transport selenate, although transporting other substrates as well (e.g. phosphonates) is possible. This model has no overlap with TIGR03431, whose members are found regularly with phosphonate catabolism operons.
Pssm-ID: 275346 [Multi-domain] Cd Length: 266 Bit Score: 414.17 E-value: 1.39e-147
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
22-276
4.28e-111
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They 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: 270290 [Multi-domain] Cd Length: 249 Bit Score: 321.18 E-value: 4.28e-111
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ...
27-272
2.59e-72
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.
Pssm-ID: 432911 [Multi-domain] Cd Length: 243 Bit Score: 222.52 E-value: 2.59e-72
putative selenate ABC transporter periplasmic binding protein; Members of this family ABC ...
24-286
1.39e-147
putative selenate ABC transporter periplasmic binding protein; Members of this family ABC transporter periplasmic binding proteins and represent one clade within a larger family that includes phosphate, phosphite, and phosphonate transporters. All members of the seed alignment occur near a gene for SelD, the selenium-activating protein needed to make selenocysteine or selenouridine. Context therefore suggests members should be able to transport selenate, although transporting other substrates as well (e.g. phosphonates) is possible. This model has no overlap with TIGR03431, whose members are found regularly with phosphonate catabolism operons.
Pssm-ID: 275346 [Multi-domain] Cd Length: 266 Bit Score: 414.17 E-value: 1.39e-147
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
22-276
4.28e-111
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They 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: 270290 [Multi-domain] Cd Length: 249 Bit Score: 321.18 E-value: 4.28e-111
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ...
27-272
2.59e-72
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.
Pssm-ID: 432911 [Multi-domain] Cd Length: 243 Bit Score: 222.52 E-value: 2.59e-72
Substrate binding domain of phosphonate uptake system-like, a member of the type 2 ...
22-276
2.34e-67
Substrate binding domain of phosphonate uptake system-like, a member of the type 2 periplasmic-binding fold superfamily; This family includes alkylphosphonate binding domain PhnD. These domains are found in PhnD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate. PhnD belongs 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. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
Pssm-ID: 270232 [Multi-domain] Cd Length: 253 Bit Score: 210.20 E-value: 2.34e-67
phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are ...
23-250
3.49e-53
phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a three gene ABC transporter. This family includes the periplasmic binding protein component of ABC transporters for phosphonates as well as other, related binding components for closely related substances such as phosphate and phosphite. A number of members of this family are found in genomic contexts with components of selenium metabolic processes suggestive of a role in selenate or other selenium-compound transport. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system (GenProp0232) has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates. [Transport and binding proteins, Anions]
Pssm-ID: 273442 [Multi-domain] Cd Length: 254 Bit Score: 173.69 E-value: 3.49e-53
phosphonate ABC transporter, periplasmic phosphonate binding protein; This model is a subset ...
19-283
1.87e-44
phosphonate ABC transporter, periplasmic phosphonate binding protein; This model is a subset of the broader subfamily of phosphate/phosphonate binding protein ABC transporter components, TIGR01098. In this model all members of the seed have support from genomic context for association with pathways for the metabolims of phosphonates, particularly the C-P lyase system, GenProp0232. This model includes the characterized phnD gene from E. coli. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Pssm-ID: 132472 [Multi-domain] Cd Length: 288 Bit Score: 152.12 E-value: 1.87e-44
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
30-275
4.85e-39
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding components of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They 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: 270289 [Multi-domain] Cd Length: 253 Bit Score: 137.00 E-value: 4.85e-39
Substrate binding domain of ABC-type phosphonate uptake system; contains the type 2 ...
27-275
6.57e-28
Substrate binding domain of ABC-type phosphonate uptake system; contains the type 2 periplasmic binding fold; This subfamily includes the Escherichia coli PhnD (EcPhnD) which exhibits high affinity for the environmentally abundant 2-aminoethylphosphonate (2-AEP), a precursor in the biosynthesis of phosphonolipids, phosphonoproteins, and phosphonoglycans. The Escherichia coli phn operon encodes 14 genes involved in binding, uptake and metabolism of phosphonate, and is activated under phophophate-limiting conditions. PhnD belongs 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. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate.
Pssm-ID: 270293 [Multi-domain] Cd Length: 259 Bit Score: 107.94 E-value: 6.57e-28
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
23-275
5.06e-26
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They 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: 270291 [Multi-domain] Cd Length: 253 Bit Score: 102.94 E-value: 5.06e-26
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
26-275
2.76e-24
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They 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: 270292 [Multi-domain] Cd Length: 250 Bit Score: 98.15 E-value: 2.76e-24
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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