GapMind for catabolism of small carbon sources

 

Protein WP_004387893.1 in Cronobacter universalis NCTC 9529

Annotation: NCBI__GCF_001277175.1:WP_004387893.1

Length: 254 amino acids

Source: GCF_001277175.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 34% 99% 129.8 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 34% 99% 129.8 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 34% 99% 129.8 Basic amino acid uptake transporter, BgtAB 36% 152.9
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 32% 89% 125.9 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-arginine catabolism artM lo L-Arginine ABC transporter, permease protein AotM (characterized) 31% 95% 124.8 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 31% 90% 117.9 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-histidine catabolism hisM lo Histidine transport system permease protein HisM (characterized) 32% 95% 117.1 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-lysine catabolism hisM lo Histidine transport system permease protein HisM (characterized) 32% 95% 117.1 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-citrulline catabolism PS417_17600 lo ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale) 32% 95% 112.1 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-glutamate catabolism gltJ lo Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 35% 82% 104.8 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-asparagine catabolism aatQ lo ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 31% 87% 102.1 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-aspartate catabolism aatQ lo ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 31% 87% 102.1 Basic amino acid uptake transporter, BgtAB 36% 152.9
L-histidine catabolism BPHYT_RS24005 lo Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) 31% 55% 84.7 Basic amino acid uptake transporter, BgtAB 36% 152.9

Sequence Analysis Tools

View WP_004387893.1 at NCBI

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

MSGFHWEIIQEYGPLFMQGAWMTIKCTIICVILGTLWGLTLGLGRMAHAEHGPWKYVLRY
LVQFPVRFYVSAFRGTPLFVQIMVVHFALVPLFINPRDGWLVESGLMSSEFARMLRSDYG
AFLSCIVAITLNAGAYVSEIFRAGIQSIDRGQMEASRALGMPWWKTMRKVILPQAFRRIL
PPLGNNAIAIVKDSSLASAIGLADLAYAARTVSGAYATYWEPYLTISLVYWVITFLLSQL
VARLEKRFGKSDSR

This GapMind analysis is from Sep 24 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