GapMind for catabolism of small carbon sources

 

Protein AO356_05325 in Pseudomonas fluorescens FW300-N2C3

Annotation: FitnessBrowser__pseudo5_N2C3_1:AO356_05325

Length: 307 amino acids

Source: pseudo5_N2C3_1 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) 99% 100% 586.6 L-proline and D-alanine ABC transporter, permease component 1 57% 350.9
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) 99% 100% 586.6 L-proline and D-alanine ABC transporter, permease component 1 57% 350.9
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) 84% 100% 517.3 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 67% 402.9
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) 84% 100% 517.3 L-proline and D-alanine ABC transporter, permease component 1 57% 350.9
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) 84% 100% 517.3 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 67% 402.9
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) 84% 100% 517.3 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 67% 402.9
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) 84% 100% 517.3 L-proline and D-alanine ABC transporter, permease component 1 57% 350.9
D-alanine catabolism AZOBR_RS08235 med L-proline and D-alanine ABC transporter, permease component 1 (characterized) 57% 99% 350.9 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3
L-proline catabolism AZOBR_RS08235 med L-proline and D-alanine ABC transporter, permease component 1 (characterized) 57% 99% 350.9 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3
L-arginine catabolism braD med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 51% 99% 299.3 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3
L-glutamate catabolism braD med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 51% 99% 299.3 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3
L-histidine catabolism braD med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 51% 99% 299.3 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3
L-proline catabolism HSERO_RS00885 med ABC transporter permease (characterized, see rationale) 45% 99% 253.4 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3
L-serine catabolism Ac3H11_1695 med ABC transporter permease (characterized, see rationale) 45% 99% 253.4 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3
L-tyrosine catabolism Ac3H11_1695 med ABC transporter permease (characterized, see rationale) 45% 99% 253.4 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3

Sequence Analysis Tools

View AO356_05325 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MPDIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL
SMMGLDSVPLLMTAAFLASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT
VLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG
RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK
AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILG
RPEVEKV

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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