GapMind for catabolism of small carbon sources

 

Protein WP_010441963.1 in Ruegeria conchae TW15

Annotation: NCBI__GCF_000192475.1:WP_010441963.1

Length: 349 amino acids

Source: GCF_000192475.1 in NCBI

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-proline catabolism opuBA med 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) 46% 71% 268.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 50% 271.2
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 49% 97% 257.7 OtaA, component of The salt-induced glycine betaine OtaABC transporter 50% 271.2
L-proline catabolism proV med Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 42% 83% 252.3 OtaA, component of The salt-induced glycine betaine OtaABC transporter 50% 271.2
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 48% 95% 246.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 50% 271.2
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 75% 172.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 50% 271.2
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 78% 135.2 OtaA, component of The salt-induced glycine betaine OtaABC transporter 50% 271.2

Sequence Analysis Tools

View WP_010441963.1 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

MTDANTPAIACQNLWQVFGPGAEKALTDALSRSGNDADKAATDLREHGFIPAVQDANFEV
REGELFVIMGLSGSGKSTLIRCISQLLPGTGGEIRVDGENVIGASKKVLTDLRRKKLGMV
FQHFGLFPHMTVAENVAYPLRVQGVSKKERLARAQEVISLVGLEGREDSFPRQLSGGQRQ
RVGIARSLAVNPDIWFLDEPFSALDPLIRRQLQDEFLRIQATLKKSIVFITHDIQEALKL
ADRIAIMRDGKIVQIGTPTDIVLRPVDDYVREFSKDVAKGQHAKVASVMRDDGERGPDDP
GLTTSMTLDAALAHCMELYEPVPVRDADGNIVGTVHPSDLAAALQVDET

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