GapMind for catabolism of small carbon sources

 

Protein WP_047213008.1 in Pandoraea thiooxydans ATSB16

Annotation: NCBI__GCF_001931675.1:WP_047213008.1

Length: 219 amino acids

Source: GCF_001931675.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2554 med ABC transporter for L-Histidine, permease component 1 (characterized) 42% 94% 162.9 L-cystine transport system permease protein YecS 47% 197.2
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-glucosamine, permease component 1 (characterized) 38% 96% 144.8 L-cystine transport system permease protein YecS 47% 197.2
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 37% 93% 142.5 L-cystine transport system permease protein YecS 47% 197.2
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 34% 88% 133.7 L-cystine transport system permease protein YecS 47% 197.2
L-arginine catabolism artM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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) 32% 97% 133.3 L-cystine transport system permease protein YecS 47% 197.2
L-arginine catabolism artQ lo arginine/ornithine transport protein (characterized) 34% 93% 133.3 L-cystine transport system permease protein YecS 47% 197.2
L-histidine catabolism hisM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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) 32% 97% 133.3 L-cystine transport system permease protein YecS 47% 197.2
L-lysine catabolism hisM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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) 32% 97% 133.3 L-cystine transport system permease protein YecS 47% 197.2
L-citrulline catabolism PS417_17595 lo ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale) 35% 92% 131.3 L-cystine transport system permease protein YecS 47% 197.2
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 34% 94% 127.9 L-cystine transport system permease protein YecS 47% 197.2
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 32% 90% 126.7 L-cystine transport system permease protein YecS 47% 197.2
L-histidine catabolism hisQ lo Histidine transport system permease protein HisQ (characterized) 32% 96% 120.9 L-cystine transport system permease protein YecS 47% 197.2

Sequence Analysis Tools

View WP_047213008.1 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

MHPYDLIVQSLPVLLLGAAITVKFALWSMLFGLMIGVVAALMGIGRRRWLQHIARAYVSI
MRGTPLLVQIFVVYYGLPSVGLSLDPTPAGILTLSLNVGAYLSESMRGAILGIPQGQWLA
AYSLGLTHRQTLRYVVGAQALRLAVPSLGNSLISLIKDTSLVSVITVTELLRSAQEVIAA
TYQPLPLYLAAAAIYWVLSTGLAWVQRRVEQRLALPGKH

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