GapMind for catabolism of small carbon sources

 

Protein WP_087412571.1 in Bacteroides clarus YIT 12056

Annotation: NCBI__GCF_900129655.1:WP_087412571.1

Length: 250 amino acids

Source: GCF_900129655.1 in NCBI

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 41% 53% 136.3 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 34% 66% 122.1 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 105.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 105.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 105.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 105.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 105.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 105.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 30% 96% 104 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 30% 67% 100.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 95% 98.6 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 62% 325.9

Sequence Analysis Tools

View WP_087412571.1 at NCBI

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

Fitness BLAST: loading...

Sequence

MNKIETRDVNFWYGDFHALKGISMDIAEKSVVAFIGPSGCGKSTFLRLLNRMNDLIPDTR
LTGEILIDGQDIYKKGVQVDELRKNVGMVFQRPNPFPKSIFENVAYGLRVNGVTDNAFIR
RRVEETLKGAALWDEVKDKLKVSAYALSGGQQQRLCIARAMAVSPSVLLMDEPASALDPI
STAKVEELIHELKKQYTIVIVTHNMQQAARVSDSTAFFYMGEMVEFGDTKKIFTNPDKVE
TQNYITGRFG

This GapMind analysis is from Sep 24 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