GapMind for catabolism of small carbon sources

 

Protein Dsui_0628 in Dechlorosoma suillum PS

Annotation: Dsui_0628 ABC-type branched-chain amino acid transport system, permease component

Length: 358 amino acids

Source: PS 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
L-isoleucine catabolism livM hi ABC transporter ATP-binding protein (characterized, see rationale) 61% 96% 416.4 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 32% 157.5
L-leucine catabolism livM hi ABC transporter ATP-binding protein (characterized, see rationale) 61% 96% 416.4 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 32% 157.5
L-phenylalanine catabolism livM hi ABC transporter ATP-binding protein (characterized, see rationale) 61% 96% 416.4 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 194.9
L-proline catabolism HSERO_RS00890 hi ABC transporter ATP-binding protein (characterized, see rationale) 61% 96% 416.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-serine catabolism Ac3H11_1694 hi ABC transporter ATP-binding protein (characterized, see rationale) 61% 96% 416.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-tyrosine catabolism Ac3H11_1694 hi ABC transporter ATP-binding protein (characterized, see rationale) 61% 96% 416.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-arginine catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 47% 74% 266.2 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-glutamate catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 47% 74% 266.2 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-histidine catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 47% 74% 266.2 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-valine catabolism livM med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 47% 74% 266.2 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 32% 157.5
L-alanine catabolism braE med High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 45% 78% 258.5 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 43% 243.0
L-serine catabolism braE med High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 45% 78% 258.5 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 43% 243.0
L-threonine catabolism braE med High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 45% 78% 258.5 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 43% 243.0
D-alanine catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 47% 64% 265 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-proline catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 47% 64% 265 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-isoleucine catabolism natC lo NatC, 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) 31% 56% 89.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-leucine catabolism natC lo NatC, 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) 31% 56% 89.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-proline catabolism natC lo NatC, 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) 31% 56% 89.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5
L-valine catabolism natC lo NatC, 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) 31% 56% 89.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 45% 258.5

Sequence Analysis Tools

View Dsui_0628 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

MSWNDLKHDRRVLWAGYAAIGIVLAVLPFLVGAGLGNAWLRILNFAMLYIMLALGLNIVV
GFAGLLDLGYIAFYAVGAYLYALLASPHFGLHWPVWAILPLGAVVAGGAGALLGAPTLRL
RGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGISSIDPFHVGGVTLAKPLSVLGVTV
PSLHAYYYLFLLLALVIIFVTIRLEDSRIGRAWVAIREDEIAAKACGINVRNIKLLAFSM
GATFGGVAGGLFASFQGFVSPESFGLMESIMVLCMVVLGGMGHIPGVILGGILLTILPEA
FRHAAVPLQKYAFGKVVVDPESLRMLLFGLALIAVMLYRPAGLWPSATRKRELQGGSK

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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