GapMind for catabolism of small carbon sources

 

Protein WP_011384838.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS12350 ABC transporter ATP-binding protein

Length: 234 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 94% 219.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
L-glutamate catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 94% 219.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
L-histidine catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 94% 219.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
L-isoleucine catabolism livF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 94% 219.2 Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 49% 212.6
L-leucine catabolism livF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 94% 219.2 Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 49% 212.6
L-valine catabolism livF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 94% 219.2 Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 49% 212.6
D-alanine catabolism AZOBR_RS08250 med Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 47% 98% 214.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
L-proline catabolism AZOBR_RS08250 med Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 47% 98% 214.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
L-phenylalanine catabolism livF med High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 47% 100% 213.8 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
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) 47% 100% 210.3 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
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) 47% 100% 210.3 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
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) 47% 100% 210.3 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
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) 43% 94% 193.7 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
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) 43% 94% 193.7 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
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) 43% 94% 193.7 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7
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) 43% 94% 193.7 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 215.7

Sequence Analysis Tools

View WP_011384838.1 at NCBI

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

MLDVRDLDLFYGDAQALAGVSFTVPDGSITAIVGANGAGKTSLIRAIAGMEPPRAGSIRF
DGHDITGKESFEICDLGLGQVAEGRQVFPTMSVQDNLELGAMVPRARKLATQSLERVWEM
FPRLLERRKQLAGTLSGGEQQMLAIGRCLMGRPKMIMFDEPSLGLSPAMVHEVFAIIRRL
HEDGMTVVLVEQNVAVSLHMADHACVLENGHVVMEGRGADLLGDDRVRAAYLGL

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