GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_2924 in Pseudomonas fluorescens FW300-N2E2

Annotation: Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Length: 418 amino acids

Source: pseudo6_N2E2 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 High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale) 100% 100% 815.1 BraE aka Bra2E, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC 32% 163.3
L-phenylalanine catabolism livM hi High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale) 100% 100% 815.1 BraE aka Bra2E, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC 32% 163.3
L-alanine catabolism braE hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 76% 100% 615.9 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 61% 489.6
L-leucine catabolism livM hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 76% 100% 615.9 BraE aka Bra2E, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC 32% 163.3
L-serine catabolism braE hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 76% 100% 615.9 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 61% 489.6
L-threonine catabolism braE hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 76% 100% 615.9 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 61% 489.6
L-valine catabolism livM hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 76% 100% 615.9 BraE aka Bra2E, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC 32% 163.3
L-arginine catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 94% 360.5 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
L-glutamate catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 94% 360.5 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
L-histidine catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 94% 360.5 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
L-proline catabolism HSERO_RS00890 med ABC transporter ATP-binding protein (characterized, see rationale) 46% 96% 275.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
L-serine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 46% 96% 275.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
L-tyrosine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 46% 96% 275.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
D-alanine catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 63% 66% 415.6 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
L-proline catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 63% 66% 415.6 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
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% 51% 87.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
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% 51% 87.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
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% 51% 87.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9
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% 51% 87.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 76% 615.9

Sequence Analysis Tools

View Pf6N2E2_2924 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

MTRHLKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLF
STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLI
LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATF
GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERK
AAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI
ACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM
GSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK

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, 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