GapMind for catabolism of small carbon sources

 

Protein WP_054254772.1 in Acidovorax caeni R-24608

Annotation: NCBI__GCF_001298675.1:WP_054254772.1

Length: 229 amino acids

Source: GCF_001298675.1 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artQ hi ABC transporter for L-Arginine, permease component 1 (characterized) 54% 100% 255.4
L-citrulline catabolism AO353_03050 hi ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 54% 100% 255.4 ABC transporter for L-Arginine, permease component 2 51% 223.8
L-histidine catabolism hisQ med Histidine transport system permease protein HisQ (characterized) 49% 97% 221.9 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-lysine catabolism hisQ med Histidine transport system permease protein HisQ (characterized) 49% 97% 221.9 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-citrulline catabolism PS417_17595 med ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale) 47% 95% 208.8 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-histidine catabolism BPHYT_RS24005 med Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) 41% 84% 161.4 ABC transporter for L-Arginine, permease component 1 54% 255.4
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-glucosamine, permease component 1 (characterized) 37% 94% 130.2 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-histidine catabolism Ac3H11_2554 lo ABC transporter for L-Histidine, permease component 1 (characterized) 34% 92% 125.6 ABC transporter for L-Arginine, permease component 1 54% 255.4
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 30% 90% 102.4 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-arginine catabolism artM lo L-Arginine ABC transporter, permease component 1 (characterized) 34% 92% 100.9 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-histidine catabolism hisM lo Histidine transport system permease protein HisM (characterized) 31% 94% 100.5 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-lysine catabolism hisM lo Histidine transport system permease protein HisM (characterized) 31% 94% 100.5 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-citrulline catabolism AO353_03045 lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 33% 92% 99.8 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 30% 86% 86.7 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 30% 86% 86.7 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 30% 86% 86.7 ABC transporter for L-Arginine, permease component 1 54% 255.4
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 30% 74% 79.3 ABC transporter for L-Arginine, permease component 1 54% 255.4

Sequence Analysis Tools

View WP_054254772.1 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

MRDYYLAILNGSLLTVAVSLASLAVATLIGLLGAAAKLSGRRPLVWLASSYTTVVRGIPE
LLMMLLIFYGGAIGLNNLLEAFGYEEGVDLDPFIAGVLTIGFIYGAYMTETFRGAILAIP
KGQMEAAWAFGMGRAQTFVRITLPQMVRYALPSFTNNWLVLIKATALVSLIGLHDMTYLA
KQSSAAVREPFAFFLFTAALYLVYTSLSLWALRRLSERYSLGADKVQLL

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