GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_5013 in Pseudomonas fluorescens GW456-L13

Annotation: FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5013

Length: 241 amino acids

Source: pseudo13_GW456_L13 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 livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 100% 150.6 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 100% 150.6 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 100% 150.6 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 34% 97% 142.1 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 96% 140.6 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 96% 140.6 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 96% 140.6 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 93% 137.9 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 93% 137.9 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 93% 137.9 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 93% 137.9 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 93% 137.9 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 93% 137.9 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-isoleucine catabolism natA lo NatA, 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) 34% 97% 137.5 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-valine catabolism natA lo NatA, 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) 34% 97% 137.5 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 32% 99% 126.3 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 32% 99% 126.3 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 100% 117.9 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 100% 117.9 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 90% 430.6

Sequence Analysis Tools

View PfGW456L13_5013 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MATLKAQHLAKSYKSRQVVRDVSLSIDSGQIVGLLGPNGAGKTTCFYMIVGLVQADQGRV
LIDDLDVSHQPMHGRAKAGIGYLPQEASIFRKLSVADNIMAILETRKELDKAGRRKELES
LLQEFHISHIRDNLGMSLSGGERRRVEIARALATNPKFILLDEPFAGVDPISVGDIKQII
HHLKAKGIGVLITDHNVRETLDICETAYIVNDGQLIAEGDAETILANDLVKEVYLGHEFR
L

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