GapMind for catabolism of small carbon sources

 

Protein GFF3203 in Phaeobacter inhibens BS107

Annotation: PGA1_c32560 high-affinity branched-chain amino acid transport ATP-binding protein

Length: 278 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism HSERO_RS00900 hi ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 47% 98% 218.4 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
L-isoleucine catabolism livF hi ABC transporter ATP-binding protein (characterized, see rationale) 47% 97% 214.2 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) 43% 188.3
L-leucine catabolism livF hi ABC transporter ATP-binding protein (characterized, see rationale) 47% 97% 214.2 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) 43% 188.3
L-valine catabolism livF hi ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 46% 99% 206.5 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) 43% 188.3
L-phenylalanine catabolism livF med ABC transporter ATP-binding protein (characterized, see rationale) 47% 97% 214.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
L-serine catabolism Ac3H11_1692 med ABC transporter ATP-binding protein (characterized, see rationale) 47% 97% 214.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
L-tyrosine catabolism Ac3H11_1692 med ABC transporter ATP-binding protein (characterized, see rationale) 47% 97% 214.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
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) 44% 100% 194.1 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
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) 44% 100% 194.1 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
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) 44% 100% 194.1 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
L-arginine catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 98% 193 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
L-glutamate catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 98% 193 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
L-histidine catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 98% 193 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
D-alanine catabolism AZOBR_RS08250 med Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 45% 98% 192.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
L-proline catabolism AZOBR_RS08250 med Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 45% 98% 192.2 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
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% 188.3 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
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% 188.3 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
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% 188.3 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
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% 188.3 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 37% 98% 162.5 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 46% 206.5

Sequence Analysis Tools

View GFF3203 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

MLDTAKTTDVQAETLLEVNNIEVIYNHVILVLKGVSLKVPKGGITALLGGNGAGKTTTLK
AVSNLLHSERGEVTKGSISYRGERIQDRDPAELVKKGVIQVMEGRHCFEHLTVEENLLTG
AYTRSDGNANIQRDLEMVYSYFPRLKERRRSQAGYTSGGEQQMVAMGRALMSRPETILLD
EPSMGLAPQLVEQIFEIVKSINENEGVTFLLAEQNTNVALRYSHYGYILESGRVVMDGPA
AELRENPDVKEFYLGMSDDGRKSFRDVRSYRRRKRWLS

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