GapMind for catabolism of small carbon sources

 

Protein Ac3H11_1002 in Acidovorax sp. GW101-3H11

Annotation: FitnessBrowser__acidovorax_3H11:Ac3H11_1002

Length: 356 amino acids

Source: acidovorax_3H11 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 96% 236.9 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 96% 236.9 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 96% 236.9 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 96% 236.9 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 96% 236.9 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 96% 236.9 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 39% 85% 222.6 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 39% 85% 222.6 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 40% 81% 220.7 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 37% 81% 158.3 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 37% 81% 158.3 Uncharacterized ABC transporter ATP-binding protein YdcT 42% 248.8

Sequence Analysis Tools

View Ac3H11_1002 at FitnessBrowser

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

Find homologs in fast.genomics

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Sequence

MHATTSAQAPAAIEIVALTKRYASGKPAVDAINLRIASGSYCCLLGPSGCGKSTTLRMIA
GHESVTSGDILLENRNITDLPAAARGTAMMFQSFALFPHLSALDNVAFSLKMKGVPKAER
QAKARDLLERVALGHLAERKPAELSGGQQQRVALARALITQPRVLLLDEPLSALDPFLRI
QMRAELRRWQKELGLTFIHVTHSQEEAMALADTMVVMNHGVIEQVGSPHEVYNRPASEFV
ARFMGGHNVIDTPEGKVGVRTDHLQIAPASAELPWGAQRMLAVVTDVEYQGTYVLLGLQK
QGVALSANATAAYSVMVSEAAFAAQPYRVGQGVQLHWTPDQAHPLSVPAPAMAAAV

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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