GapMind for catabolism of small carbon sources

 

Protein Ac3H11_1432 in Acidovorax sp. GW101-3H11

Annotation: High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Length: 294 amino acids

Source: acidovorax_3H11 in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism livH med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 97% 169.1 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 33% 163.7
L-leucine catabolism livH med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 97% 169.1 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 33% 163.7
L-valine catabolism livH med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 97% 169.1 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 33% 163.7
L-proline catabolism HSERO_RS00885 lo ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale) 30% 98% 152.9 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 33% 169.1
L-alanine catabolism braD lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 142.9 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 33% 169.1
L-phenylalanine catabolism livH lo Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale) 30% 97% 142.9 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 33% 169.1
L-serine catabolism braD lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 142.9 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 33% 169.1
L-threonine catabolism braD lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 142.9 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 33% 169.1

Sequence Analysis Tools

View Ac3H11_1432 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

MEIFGVSLPGLLSQLLLGLVNGSFYAILSLGLAVIFGLLNVINFAHGALFMTGALITWMA
MNYLGINYWLMLVLAPLVVGLFGVLIERLLLRWIYKLDHLYGLLLTLGLTLLIEGVFRSI
YGVSGLGYDTPELLEGATNLGFMIMPNYRAWVVVASIVVCVATWYVIEKTKLGAYLRAGT
ENPRLVEAFGINVPVMVTLTYAFGAALAAFAGVLAAPVYQVTPLMGQNLIIVVFAVVVIG
GMGSIMGSILTGLGLGVIEGFTKVFYPEASSTVVFVIMVIVLLIRPAGLFGKEK

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