GapMind for catabolism of small carbon sources

 

Protein WP_077276703.1 in Vagococcus penaei CD276

Annotation: NCBI__GCF_001998885.1:WP_077276703.1

Length: 345 amino acids

Source: GCF_001998885.1 in NCBI

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 47% 100% 293.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 43% 88% 189.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
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) 40% 82% 175.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 77% 191.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
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) 38% 78% 183.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
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) 40% 75% 171 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 88% 167.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 88% 167.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 88% 167.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 88% 167.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 98% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 98% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 98% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-alanine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-isoleucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-leucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-proline catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-serine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-threonine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
L-valine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 87% 99.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 87% 99.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 87% 99.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 87% 99.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 57% 388.3

Sequence Analysis Tools

View WP_077276703.1 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

MNIIQLKQATKTFKTKDTIVNAVDKIDLAIDKGEIFGIIGYSGAGKSTLIRLLNNLETPT
SGEVIINGEQVSQLKGKALREFRKKVGMIFQHFNLLWSRTVKENIMLPLELSNVPKAERE
KRALELIALVGLEGRENAYPSELSGGQKQRVGIARALANEPEILLCDEATSALDPQTTDE
VLELLLAINKKLNLTIVLITHEMQVIRKICHQVAVMEAGKIIEMGKVLDVFKNPKSAVTA
NFVKQDAVTDEEESADTLRYLTQAYPDGMLVRLIFEGEKAAEAVISKVVREYPIDINILQ
ASIRQTNQSSFGTMLVQVTGESKLLSETLVFFENNGVGVEVIQYG

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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