GapMind for catabolism of small carbon sources

 

Protein 6937163 in Shewanella amazonensis SB2B

Annotation: Sama_1333 lipoprotein releasing system ATP-binding protein LolD (RefSeq)

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

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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