GapMind for catabolism of small carbon sources

 

Protein 352022 in Bacteroides thetaiotaomicron VPI-5482

Annotation: FitnessBrowser__Btheta:352022

Length: 238 amino acids

Source: Btheta in FitnessBrowser

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 41% 83% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 40% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 87% 153.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 39% 84% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 84% 151.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 84% 151.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-glutamate catabolism gltL lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 84% 151.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 67% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-arginine catabolism artP lo AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) 39% 89% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 90% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 90% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 90% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 90% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 90% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 37% 89% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 86% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 36% 62% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 37% 83% 139.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-histidine catabolism hisP lo Probable ATP-binding component 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) 36% 88% 138.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7

Sequence Analysis Tools

View 352022 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MIKLTDINKTYNNGAPLHVLKGINLDIQRGEFVSIMGASGSGKSTLLNILGILDNYDTGD
YYLNNVLIKDLSETKAAEYRNRMIGFIFQSFNLISFKDAVENVALPLFYQGVSRKKRNAL
ALEYLDRLGLKEWAHHMPNEMSGGQKQRVAIARALITQPQIILADEPTGALDSKTSVEVM
QILKDLHRMGMTIVVVTHESGVANQTDKIIHIKDGIIERIEENLDHDASPFGQNGIMK

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 (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