GapMind for catabolism of small carbon sources

 

Protein 6937163 in Shewanella amazonensis SB2B

Annotation: FitnessBrowser__SB2B:6937163

Length: 229 amino acids

Source: SB2B in FitnessBrowser

Candidate for 7 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 ABC transporter for L-Lysine, ATPase component (characterized) 39% 84% 143.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 60% 262.7
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) 39% 84% 140.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 60% 262.7
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 40% 85% 137.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 60% 262.7
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% 73% 103.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 60% 262.7
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 93% 94.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 60% 262.7
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 93% 94.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 60% 262.7
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 88% 92.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 60% 262.7

Sequence Analysis Tools

View 6937163 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

MQDILLKVENVSKTYREGKLETQVLCGVDLSVYRGEQLAIVGGSGSGKSTLLHIMGSLDK
PTSGKVLLEGEDLYSLSAARQAQIRNASLGFIYQFHHLLPEFSALENVAMPARIAGVDKK
TAFGRAEALLERVGLSHRLSHAPSELSGGERQRVAIARALINQPRLVLADEPTGNLDAAS
GEAVYALIRELAAQLGTAFVVVTHDNALAARMDRQLSMKSGKLTTGARQ

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