GapMind for catabolism of small carbon sources

 

Protein RR42_RS34310 in Cupriavidus basilensis 4G11

Annotation: RR42_RS34310 amino acid ABC transporter permease

Length: 222 amino acids

Source: Cup4G11 in FitnessBrowser

Candidate for 8 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% 93% 166.4 L-cystine transport system permease protein YecS 42% 166.0
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 37% 94% 136.7 ABC transporter for L-Histidine, permease component 1 42% 166.4
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) 34% 93% 127.5 ABC transporter for L-Histidine, permease component 1 42% 166.4
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) 34% 93% 127.5 ABC transporter for L-Histidine, permease component 1 42% 166.4
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) 36% 98% 120.6 ABC transporter for L-Histidine, permease component 1 42% 166.4
L-histidine catabolism BPHYT_RS24005 lo Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) 34% 91% 118.6 ABC transporter for L-Histidine, permease component 1 42% 166.4
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 31% 83% 104.8 ABC transporter for L-Histidine, permease component 1 42% 166.4
L-histidine catabolism aapQ lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized) 34% 50% 95.9 ABC transporter for L-Histidine, permease component 1 42% 166.4

Sequence Analysis Tools

View RR42_RS34310 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

MDANFFQHAREFLPILLQGAVVTVEVTVLAFVLSSLLGLALALMKLSPARTLSWGASGAI
NVIRGLPIIVQLFYIYFVLPDAGIHLTAFQAGVIGLGIAYSAYQAENFRAGIEAVDPGQR
EAAQAMGMRPALVMRRVILPQALRISLPPYGNTLVMMLKDSSLVSTITVAEMTRAGQLIA
SSTFQNMTVYTLVALLYLLMSLPLVFGLRRLERRLGVGRKKP

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