GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_2923 in Pseudomonas fluorescens FW300-N2E2

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

Length: 307 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 15 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 hi 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) 100% 100% 588.6 L-proline and D-alanine ABC transporter, permease component 1 57% 351.7
L-phenylalanine catabolism livH hi 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) 100% 100% 588.6 L-proline and D-alanine ABC transporter, permease component 1 57% 351.7
L-alanine catabolism braD hi High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 85% 100% 518.5 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 67% 403.7
L-leucine catabolism livH hi High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 85% 100% 518.5 L-proline and D-alanine ABC transporter, permease component 1 57% 351.7
L-serine catabolism braD hi High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 85% 100% 518.5 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 67% 403.7
L-threonine catabolism braD hi High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 85% 100% 518.5 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 67% 403.7
L-valine catabolism livH hi High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 85% 100% 518.5 L-proline and D-alanine ABC transporter, permease component 1 57% 351.7
D-alanine catabolism AZOBR_RS08235 med L-proline and D-alanine ABC transporter, permease component 1 (characterized) 57% 99% 351.7 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 85% 518.5
L-proline catabolism AZOBR_RS08235 med L-proline and D-alanine ABC transporter, permease component 1 (characterized) 57% 99% 351.7 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 85% 518.5
L-arginine catabolism braD med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 51% 99% 299.7 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 85% 518.5
L-glutamate catabolism braD med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 51% 99% 299.7 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 85% 518.5
L-histidine catabolism braD med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 51% 99% 299.7 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 85% 518.5
L-proline catabolism HSERO_RS00885 med ABC transporter permease (characterized, see rationale) 45% 99% 255.4 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 85% 518.5
L-serine catabolism Ac3H11_1695 med ABC transporter permease (characterized, see rationale) 45% 99% 255.4 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 85% 518.5
L-tyrosine catabolism Ac3H11_1695 med ABC transporter permease (characterized, see rationale) 45% 99% 255.4 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 85% 518.5

Sequence Analysis Tools

View Pf6N2E2_2923 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

MPDIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL
AMMGLDSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT
VLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG
RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK
AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILG
RPEVEKV

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