GapMind for catabolism of small carbon sources

 

Protein WP_009778714.1 in Leeuwenhoekiella blandensis MED217

Annotation: NCBI__GCF_000152985.1:WP_009778714.1

Length: 234 amino acids

Source: GCF_000152985.1 in NCBI

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 39% 86% 151.8 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 83% 149.8 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 83% 149.8 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-glutamate catabolism gltL lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 83% 149.8 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 38% 97% 148.7 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
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% 84% 147.5 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
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% 84% 147.5 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
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% 84% 147.5 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
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% 84% 147.5 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
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% 84% 147.5 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 140.2 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 140.2 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 38% 83% 139.8 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 35% 91% 138.7 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 35% 88% 137.5 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 78% 136.3 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 36% 69% 131 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 36% 51% 123.6 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 78% 116.7 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 34% 78% 109.4 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 61% 107.1 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 55% 103.2 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 32% 79% 97.1 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 30% 91% 95.9 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 71% 94.7 As-48G, component of The enterocin AS-48 exporter, As-48FGH 45% 209.9

Sequence Analysis Tools

View WP_009778714.1 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

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Sequence

MIKITDLEKYYATEEVRTIALNKLSFQVQEGEFVAVMGPSGCGKSTLLNILGLLDDPDGG
SFIFNGIEVAGFNERKRADLRKHNIGFVFQSFNLIDELTVFENVELPLIYTGVKPAERKK
RVDEVLEKMQIMHRRKHFPQQLSGGQQQRVAVARAVVNNPKLILADEPTGNLDSSNGNEV
MDLLTELNEAGTTIIMVTHSEHDAKYSHRIIRMLDGQKVTENVLTEYKSKTLEV

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