GapMind for catabolism of small carbon sources


Protein HSERO_RS17540 in Herbaspirillum seropedicae SmR1

Annotation: FitnessBrowser__HerbieS:HSERO_RS17540

Length: 240 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 5 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 53% 94% 248.4 glutamine ABC transporter, ATP-binding protein GlnQ 73% 337.4
L-histidine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 49% 96% 240 glutamine ABC transporter, ATP-binding protein GlnQ 73% 337.4
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 51% 94% 235.7 glutamine ABC transporter, ATP-binding protein GlnQ 73% 337.4
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 73% 181 glutamine ABC transporter, ATP-binding protein GlnQ 73% 337.4
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 87% 136 glutamine ABC transporter, ATP-binding protein GlnQ 73% 337.4

Sequence Analysis Tools

View HSERO_RS17540 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.



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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:

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