GapMind for catabolism of small carbon sources

 

Protein Ga0059261_3653 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)

Length: 276 amino acids

Source: Korea in FitnessBrowser

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 37% 95% 150.6 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 98% 149.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 98% 149.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 36% 92% 149.1 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 36% 94% 147.1 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 35% 93% 145.6 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 35% 93% 145.6 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 91% 143.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 91% 143.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 35% 99% 138.3 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 33% 98% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 33% 98% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 33% 98% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-histidine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 33% 98% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 33% 98% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 33% 98% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 93% 131.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 32% 96% 131 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 98% 129.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 35% 78% 125.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 89% 124.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 89% 124.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 34% 69% 124.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 31% 61% 117.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 32% 68% 114 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 312.8

Sequence Analysis Tools

View Ga0059261_3653 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTSVMTQTDLADSADTSAAPARPAEHAKMAARGVNVFYGEKQAIRDVSIDVDMENVTAFI
GPSGCGKSTFLRTLNRMNDTVASARVEGEITLDGENIYDKSMDVVQLRARVGMVFQKPNP
FPKSIYENVAYGPRIHGLARAKGDMDQIVERSLKRAGLWEEVKDRLNDSGTALSGGQQQR
LCIARAIAVDPEVILMDEPCSALDPIATAKIEELIHELRGRYAIVIVTHNMQQAARVSQR
TAFFHLGTLVEYGETDQIFTAPRQERTKDYITGRYG

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory