GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_1583 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1583

Length: 276 amino acids

Source: pseudo1_N1B4 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-histidine catabolism hutV hi ABC transporter for L-Histidine, ATPase component (characterized) 96% 100% 521.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 322.0
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 67% 97% 362.8 ABC transporter for L-Histidine, ATPase component 96% 521.5
L-proline catabolism opuBA med BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 42% 73% 186.4 ABC transporter for L-Histidine, ATPase component 96% 521.5
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 60% 66% 312 ABC transporter for L-Histidine, ATPase component 96% 521.5

Sequence Analysis Tools

View Pf1N1B4_1583 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

Fitness BLAST: loading...

Sequence

MSNEAISKIEVKNVFKIFGNRSKDALEMIRQKKTKDQVLAETGCVVGVNDLSLSIGTGEI
FVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGVDILQYDMEALREFRRHKISMVFQSFG
LLPHKTVLDNVAYGLKVRGESKQMCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLA
RALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIA
ILKDGRLIQVGTPREILHSPADEYVDRFVQRRAAVV

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