GapMind for catabolism of small carbon sources


Protein GFF2770 in Phaeobacter inhibens BS107

Annotation: PGA1_c28130 ABC transporter, ATP-binding protein

Length: 505 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2'-deoxyinosine catabolism nupA lo RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) 36% 98% 327.8 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 39% 354.4
L-fucose catabolism HSERO_RS05250 lo Ribose import ATP-binding protein RbsA; EC (characterized, see rationale) 35% 94% 295 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 39% 354.4
D-ribose catabolism rbsA lo ribose transport, ATP-binding protein RbsA; EC (characterized) 37% 95% 287 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 39% 354.4
myo-inositol catabolism iatA lo Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 35% 97% 276.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 39% 354.4
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC (characterized, see rationale) 35% 92% 266.5 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 39% 354.4
D-xylose catabolism xylG lo Xylose import ATP-binding protein XylG, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas (characterized) 32% 98% 262.7 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 39% 354.4
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC (characterized) 33% 95% 258.1 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 39% 354.4
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 33% 94% 248.1 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 39% 354.4

Sequence Analysis Tools

View GFF2770 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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



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 (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 paper from 2022 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