GapMind for catabolism of small carbon sources

 

Protein 5208211 in Shewanella loihica PV-4

Annotation: FitnessBrowser__PV4:5208211

Length: 240 amino acids

Source: PV4 in FitnessBrowser

Candidate for 6 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 lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 38% 83% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 215.7
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 38% 90% 151 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 215.7
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 39% 89% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 215.7
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 39% 89% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 215.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 38% 83% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 215.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 85% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 215.7

Sequence Analysis Tools

View 5208211 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

MLTMKNINKVFKTDLVETHALRDFNLEVKEGEFVAVTGPSGSGKTTFLNIAGLLEGFTNG
EYHLDDVNISNLSDNKAAAIRNEKIGFIFQGFNLIPDLNLAENVEVPLRYRGFNAKERQR
RVKAALEQVGLGARMKHLPSQLSGGQQQRVAIARALAGEPRFLLADEPTGNLDSLMARQV
MELLEEINKAGTTIIMVTHDPELARRAQRNIQIVDGQVCDFTLYQGGQSHLVDTAEKVAS

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