GapMind for catabolism of small carbon sources

 

Protein 349829 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT0301 ATP-binding transport protein natA (Na+ ABC transporter) (NCBI ptt file)

Length: 503 amino acids

Source: Btheta 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-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 64% 75.9 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 64% 75.9 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 64% 75.9 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 64% 75.9 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 34% 62% 73.6 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 34% 62% 73.6 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 34% 62% 73.6 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 34% 62% 73.6 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 62% 71.2 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 62% 71.2 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 62% 71.2 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 62% 71.2 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 62% 71.2 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 62% 71.2 ABC transporter ATP binding domain, component of ABC lantibiotic NAI-107 immunity exporter, MlbYZ 39% 195.7

Sequence Analysis Tools

View 349829 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

MLWQSIYLVALIAGIPGMTYFAQTSLRRAKAEVINPDEEIRISVRNLVKIYDWPGHISRQ
WNSGLQLRKRLGLSNEYHSLKDFINVLWQFGILLFAIYFTYFFIHNRLWIFLFSFAIYAA
VLYLWRKVRSYLYYRYGDNRVTKIVNRVIFWSLPPLILFQLFRKLDNNGLVIMIGLLWLV
GIAIYVTSQYLYDHDVNIERVTGRFAGLRRSYFRMVKSVPMIGKRRKPFKALRGVSFEIQ
TGMFGLLGPNGAGKSTLMRVICGIFEQSYGSIWINGLDTRIYREELQSLIGFLPQEFGTY
ENMTSWEFLDYQAILKGIVDGDLRRERLDYVLKAVHMYERKDEKIGSFSGGMKQRIGIAL
ILLHLPRILVVDEPTAGLDPRERIRFRNLLVELSKDRIVIFSTHIIEDISSSCNQVVVIN
KGELKYFGDPSDMVEMANGKVWQFNIDKTEFEKVLDKSLVIHHIQEGDTIRVRYLSVGQP
YEGAVEVEANLEDAYLCLLKNMN

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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