GapMind for catabolism of small carbon sources

 

Protein RR42_RS04400 in Cupriavidus basilensis 4G11

Annotation: RR42_RS04400 ABC transporter permease

Length: 219 amino acids

Source: Cup4G11 in FitnessBrowser

Candidate for 23 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) 41% 95% 163.3 L-cystine transport system permease protein YecS 47% 198.0
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-glucosamine, permease component 1 (characterized) 39% 92% 147.9 L-cystine transport system permease protein YecS 47% 198.0
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 37% 86% 141.7 L-cystine transport system permease protein YecS 47% 198.0
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 36% 97% 140.6 L-cystine transport system permease protein YecS 47% 198.0
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 33% 81% 139 L-cystine transport system permease protein YecS 47% 198.0
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 33% 81% 139 L-cystine transport system permease protein YecS 47% 198.0
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 33% 81% 139 L-cystine transport system permease protein YecS 47% 198.0
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 36% 93% 138.7 L-cystine transport system permease protein YecS 47% 198.0
L-arginine catabolism artM lo L-Arginine ABC transporter, permease component 1 (characterized) 34% 94% 137.9 L-cystine transport system permease protein YecS 47% 198.0
L-arginine catabolism artQ lo Probable permease 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) 38% 91% 135.2 L-cystine transport system permease protein YecS 47% 198.0
L-histidine catabolism hisQ lo Probable permease 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) 38% 91% 135.2 L-cystine transport system permease protein YecS 47% 198.0
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) 34% 92% 127.9 L-cystine transport system permease protein YecS 47% 198.0
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 35% 95% 127.5 L-cystine transport system permease protein YecS 47% 198.0
L-citrulline catabolism AO353_03045 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 31% 94% 126.7 L-cystine transport system permease protein YecS 47% 198.0
L-glutamate catabolism gltK 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) 36% 97% 122.1 L-cystine transport system permease protein YecS 47% 198.0
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 53% 120.9 L-cystine transport system permease protein YecS 47% 198.0
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 53% 120.9 L-cystine transport system permease protein YecS 47% 198.0
L-asparagine catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 33% 97% 120.6 L-cystine transport system permease protein YecS 47% 198.0
L-aspartate catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 33% 97% 120.6 L-cystine transport system permease protein YecS 47% 198.0
L-asparagine catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 31% 53% 104.4 L-cystine transport system permease protein YecS 47% 198.0
L-aspartate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 31% 53% 104.4 L-cystine transport system permease protein YecS 47% 198.0
L-glutamate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 31% 53% 104.4 L-cystine transport system permease protein YecS 47% 198.0
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) 33% 88% 103.2 L-cystine transport system permease protein YecS 47% 198.0

Sequence Analysis Tools

View RR42_RS04400 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSALQLVATSLPVLLQGMLLTIKFALLSMIFGLVLGTVVALMGISHQPVPKAVARAYVSI
MRGTPLLVQIFVVYYGLPGIGIALEPTPAGVLTLSLNVGAYLSESMRGAILGIPRGQWLA
AYSLGLTQGQALRYVIGPQALRLAVPSLSNSLISLIKDTSLVSVITVTELLRTAQEVIAA
TYQPLPLYLAVAAIYWMLSTALAHMQRLLERRLSLPGRH

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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