GapMind for catabolism of small carbon sources

 

Protein AZOBR_RS08840 in Azospirillum brasilense Sp245

Annotation: AZOBR_RS08840 ABC transporter ATP-binding protein

Length: 387 amino acids

Source: azobra in FitnessBrowser

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 58% 95% 407.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 261.2
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 41% 85% 171.8 PotG aka B0855, component of Putrescine porter 58% 407.1
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 93% 198.7 PotG aka B0855, component of Putrescine porter 58% 407.1
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 93% 198.7 PotG aka B0855, component of Putrescine porter 58% 407.1
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 93% 198.7 PotG aka B0855, component of Putrescine porter 58% 407.1
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 93% 198.7 PotG aka B0855, component of Putrescine porter 58% 407.1
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 40% 65% 181.8 PotG aka B0855, component of Putrescine porter 58% 407.1
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 39% 83% 164.9 PotG aka B0855, component of Putrescine porter 58% 407.1
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 39% 74% 134 PotG aka B0855, component of Putrescine porter 58% 407.1

Sequence Analysis Tools

View AZOBR_RS08840 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

MAVQPIRKPTRLEPWQDPGQKPYVRIEKVTKTFGDFVAVDEVSLSIYRGEFFALLGGSGS
GKTTLLRMLAGFETPTEGKIFIDGVDMAGIPPYERPVNMMFQSYALFPHMSVEQNVAFGL
KQDGVAKAEIKERVGAILDLVQLGQFGKRKPHQLSGGQRQRVALARSLVKRPKLLLLDEP
LGALDKRLRERTQFELVNIQEKLGVTFIVVTHDQEEAMTMSSRIAVMNHGVIAQTGTPTE
IYEYPQSRFVAEFIGSVNMFEGRVVEDQADHVLIRSEDAGCDLYINHAVAVPAGATVGVA
VRPEKIALSKEPPANAATNADGRNVTSGIVREIAYLGDVSIYLVELKTGKTVRVTAPNVV
RRTEMPITWDDEVHLSWRPFAGVVLTQ

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