GapMind for catabolism of small carbon sources

 

Protein RR42_RS34795 in Cupriavidus basilensis 4G11

Annotation: RR42_RS34795 leucine/isoleucine/valine transporter ATP-binding subunit

Length: 254 amino acids

Source: Cup4G11 in FitnessBrowser

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism HSERO_RS00895 hi ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 46% 98% 233 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
L-isoleucine catabolism livG hi ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 220.3 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 42% 189.1
L-leucine catabolism livG hi ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 220.3 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 42% 189.1
L-phenylalanine catabolism livG hi ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 220.3 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 40% 190.3
L-serine catabolism Ac3H11_1693 hi ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 220.3 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
L-tyrosine catabolism Ac3H11_1693 hi ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 220.3 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
L-alanine catabolism braF med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 42% 93% 189.1 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
L-histidine catabolism natA med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 42% 93% 189.1 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
L-leucine catabolism natA med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 42% 93% 189.1 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
L-proline catabolism natA med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 42% 93% 189.1 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
L-serine catabolism braF med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 42% 93% 189.1 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
L-threonine catabolism braF med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 42% 93% 189.1 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
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) 39% 96% 178.3 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
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) 39% 96% 178.3 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2

Sequence Analysis Tools

View RR42_RS34795 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

MLEIRNLTRKFGGLSAVHDVSITFETGHINAIIGPNGAGKTTFFNLIAGTHAPTSGQILL
KGRNVAGLRADQIARLGVARTFQATHLFDRATVLDNLIVGHRLRTQAGLADVIFNTRRLR
EEERLCRAKAEEALDFVGLAHLAHEVAADITQEERKRVAFALALATDAELLLLDEPAGGV
NPEETVGLAELIRKMVRHGKTVCLIEHKMDMIMRLADKIMVLNHGEKIAEGSPAQIQQDP
QVIEAYLGADHVAA

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, 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