GapMind for catabolism of small carbon sources

 

Protein AZOBR_RS08250 in Azospirillum brasilense Sp245

Annotation: AZOBR_RS08250 amino acid ABC transporter ATPase

Length: 236 amino acids

Source: azobra in FitnessBrowser

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism AZOBR_RS08250 hi Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 100% 100% 457.2 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-proline catabolism AZOBR_RS08250 hi Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 100% 100% 457.2 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-arginine catabolism braG hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 70% 96% 337.8 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-glutamate catabolism braG hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 70% 96% 337.8 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-histidine catabolism braG hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 70% 96% 337.8 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-isoleucine catabolism livF hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 70% 96% 337.8 Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 48% 208.0
L-leucine catabolism livF hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 70% 96% 337.8 Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 48% 208.0
L-valine catabolism livF hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 70% 96% 337.8 Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 48% 208.0
L-phenylalanine catabolism livF hi high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 62% 98% 270 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 53% 243.4
L-alanine catabolism braG med High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 59% 100% 273.1 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF 62% 270.0
L-serine catabolism braG med High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 59% 100% 273.1 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF 62% 270.0
L-threonine catabolism braG med High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 59% 100% 273.1 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF 62% 270.0
L-proline catabolism HSERO_RS00900 med ABC transporter ATP-binding protein (characterized, see rationale) 51% 96% 233 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-serine catabolism Ac3H11_1692 med ABC transporter ATP-binding protein (characterized, see rationale) 51% 96% 233 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-tyrosine catabolism Ac3H11_1692 med ABC transporter ATP-binding protein (characterized, see rationale) 51% 96% 233 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-isoleucine catabolism natE med NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 46% 95% 205.3 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-leucine catabolism natE med NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 46% 95% 205.3 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-proline catabolism natE med NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 46% 95% 205.3 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1
L-valine catabolism natE med NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 46% 95% 205.3 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 59% 273.1

Sequence Analysis Tools

View AZOBR_RS08250 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF
EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLF
PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDIN
REQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEGGH

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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, the preprint on GapMind for carbon sources, 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