GapMind for catabolism of small carbon sources

 

Protein 5210884 in Shewanella loihica PV-4

Annotation: Shew_3310 ABC transporter-related protein (RefSeq)

Length: 243 amino acids

Source: PV4 in FitnessBrowser

Candidate for 29 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-alanine catabolism braF 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) 35% 96% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
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) 35% 96% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-leucine 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) 35% 96% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-proline 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) 35% 96% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-serine catabolism braF 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) 35% 96% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-threonine catabolism braF 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) 35% 96% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
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) 35% 96% 150.6 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 97% 149.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 97% 149.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 97% 149.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 97% 149.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 97% 149.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 97% 149.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
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) 33% 99% 141.7 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 94% 138.3 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 100% 137.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 100% 137.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 100% 137.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 100% 137.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 100% 137.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 100% 137.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 32% 100% 132.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 94% 123.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 94% 123.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 94% 123.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 100% 122.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 31% 99% 120.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 98% 119.8 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 98% 119.8 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 75% 356.3

Sequence Analysis Tools

View 5210884 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

MTDLILKAENLAKSYKSRAVVQDVSLTVKTGQIVGLLGPNGAGKTTTFYMVVGLVQSDKG
RIFIDDDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAVLQTRSDLNNDGREEEL
EHLLEEFHITHIRDSHGMALSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKK
IIEQLKNRGLGVLITDHNVRETLDVCEKAYIVSHGNLIAEGTPAEILDNQQVRAVYLGEQ
FKL

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