GapMind for catabolism of small carbon sources

 

Protein 642683972 in Chlorobium phaeobacteroides BS1

Annotation: IMG__ChlphaBS1_FD:642683972

Length: 244 amino acids

Source: ChlphaBS1_FD in IMG

Candidate for 39 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 42% 78% 144.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 42% 78% 144.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-asparagine catabolism aapP med 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) 41% 81% 142.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-aspartate catabolism aapP med 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) 41% 81% 142.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-glutamate catabolism aapP med 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) 41% 81% 142.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-histidine catabolism aapP med 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) 41% 81% 142.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-leucine catabolism aapP med 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) 41% 81% 142.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-proline catabolism aapP med 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) 41% 81% 142.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 40% 64% 150.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 144.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 144.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 144.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 144.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 144.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 144.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 144.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 144.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 84% 144.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 84% 144.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 90% 142.9 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 87% 136.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 37% 89% 136.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 38% 92% 136 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 89% 135.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 89% 135.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 60% 132.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 60% 132.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 60% 132.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 60% 132.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-arginine catabolism artP lo L-Arginine ABC transporter, ATPase component (characterized) 37% 92% 129 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 36% 92% 128.6 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
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% 89% 128.6 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 56% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 56% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 56% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 56% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 56% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 56% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 56% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 42% 188.7

Sequence Analysis Tools

View 642683972 at IMG

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

MMDAFMEHETDSPVLRVDRVSKIYTMGEVEVHALKHVSVDFYAGELVVLLGTSGSGKSTL
LNIIGGLDVPSEGKLYFHSQEMTAASEAEMTAYRRESIGFVFQFYNLISSLTALENIQLV
TEISTQPMPAEEALRRVNLGDRMNHFPSQLSGGEQQRVAIARAVSKRPELLLCDEPTGAL
DYETGKLVLDVIRKVNEELGTTTLVITHNVSIAAMADRVIHMRSGEITEIERNERKLSPS
ELSW

This GapMind analysis is from Apr 09 2024. 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