GapMind for catabolism of small carbon sources

 

Protein Ga0059261_4235 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_4235 ABC-type multidrug transport system, ATPase component

Length: 310 amino acids

Source: Korea in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 90% 123.2 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 33% 98% 115.5 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 94% 114.4 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 94% 114.4 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 94% 114.4 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 89% 112.8 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 89% 112.8 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 89% 112.8 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 89% 112.8 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 89% 112.8 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 89% 112.8 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 95% 108.6 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 95% 108.6 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 95% 108.6 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 32% 93% 106.3 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 32% 93% 106.3 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 32% 93% 106.3 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 32% 93% 106.3 PltI, component of The pyoluteorin (a chlorinated polyketide) efflux pump, PltHIJKN 49% 213.0

Sequence Analysis Tools

View Ga0059261_4235 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

VTGDAAISVEGLTKRFGNRTVVDTVSLEVGRGRICGFLGPNGSGKTTTLRMICGLLIPDG
GGGEVLGMDLLTQRELIKRRIGYMTQRFGLFEDLTIRENLAFVADAYGLDEKMKRVDAAL
ERLGLETRAGQLAGTLSGGWKQRLALAACVLHDPEILLLDEPTAGVDPLARREFWDQVHM
LSAEGTTVLVSTHYMDEAERCHDIAYIAYGVLLARGTADEIVVQSGLVALAGEGPGADRL
APKLERAPGVAMAAAFGPTVHVCGRDMAALRAAVADIAPGISWRETEPTLEDVFIHLMRG
ATDNSTEPRT

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