GapMind for catabolism of small carbon sources

 

Protein AZOBR_RS28565 in Azospirillum brasilense Sp245

Annotation: AZOBR_RS28565 sugar ABC transporter ATPase

Length: 602 amino acids

Source: azobra in FitnessBrowser

Candidate for 4 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 med ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 50% 97% 229.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 39% 346.3
L-phenylalanine catabolism livG med ABC transporter ATP-binding protein (characterized, see rationale) 48% 98% 222.2 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 39% 346.3
L-serine catabolism Ac3H11_1693 med ABC transporter ATP-binding protein (characterized, see rationale) 48% 98% 222.2 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 39% 346.3
L-tyrosine catabolism Ac3H11_1693 med ABC transporter ATP-binding protein (characterized, see rationale) 48% 98% 222.2 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 39% 346.3

Sequence Analysis Tools

View AZOBR_RS28565 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

MDASVLRPAARRFALLRAAPALGIGAALVALALTLSNDFYLYVAFMAGVYYICASGMNVL
AGYAGQKSLGQAGLFAAGAYTVALLTTRLELPPALALAAAPLVAAAVGVLIALPSLRVKG
PSLALVTLAFGLVVEKLVTEWTDLFGGAQGIYGIAPLTLGDEPFALKHWVVLVIVLGVAV
HLALSHLLNGRFGRALLALQSDEIAAECAGISVYRYKTLAFVLAAALCGLGGALVAQQNQ
YFNSDFVTFHLSVFILLLVLLGGAGNIYGPIAGAAILTMTEVFLAQWPSVQHFIYGAMLL
FALYLMPTGVAGAIARVLPRRMAVLDGVETPPLTAMQRGRAEPSAGPLLEVTDVSKAFGG
VVTADKVGLRLHAHRIHALIGPNGAGKSTLINILTGVISADSGTIRLAGQDITRGTAHAR
AARGIARTFQNLRLFGSMTVLDNVLIGAHARIGVTGREEDAVAKAKAVLDFVGLGEHAGA
LAGSLPYGLQRRVELARALAGDPVLLLLDEPAAGLNPRETAELGQLIKRIGQLGVAVLMV
EHDMGLVMRISDEIVVLDRGVVIAEGAPRDIQTNPRVIEAYLGREDSPAPDGPESDKEER
PC

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 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