GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_4608 in Pseudomonas fluorescens GW456-L13

Annotation: FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4608

Length: 307 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 21 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) 97% 100% 580.5 L-proline and D-alanine ABC transporter, permease component 1 58% 352.1
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) 97% 100% 580.5 L-proline and D-alanine ABC transporter, permease component 1 58% 352.1
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% 400.2
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 58% 352.1
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% 400.2
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% 400.2
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 58% 352.1
D-alanine catabolism AZOBR_RS08235 med L-proline and D-alanine ABC transporter, permease component 1 (characterized) 58% 99% 352.1 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) 58% 99% 352.1 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% 300.8 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% 300.8 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% 300.8 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% 256.1 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% 256.1 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% 256.1 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 natD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 97% 151.4 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-leucine catabolism natD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 97% 151.4 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-proline catabolism natD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 97% 151.4 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-isoleucine catabolism natD lo NatD, 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) 30% 97% 146 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-valine catabolism natD lo NatD, 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) 30% 97% 146 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3
D-lactate catabolism PGA1_c12660 lo D-lactate transporter, permease component 2 (characterized) 30% 70% 90.9 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 84% 517.3

Sequence Analysis Tools

View PfGW456L13_4608 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

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Sequence

MPDIYHFFQQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL
AMLGLDSVPLLMTAAFLATIVVTSAYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT
VLLAQDSKDKSIPNLIPGNFAFGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG
RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK
AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGLLG
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