GapMind for catabolism of small carbon sources

 

Protein WP_027698103.1 in Weissella oryzae SG25

Annotation: NCBI__GCF_000691805.2:WP_027698103.1

Length: 347 amino acids

Source: GCF_000691805.2 in NCBI

Candidate for 48 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) 42% 100% 254.2 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 42% 99% 192.2 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 40% 97% 187.6 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-glutamate catabolism gltL med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 40% 97% 187.6 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 42% 90% 171.4 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 42% 90% 171.4 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 44% 85% 170.6 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 44% 85% 170.6 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 40% 83% 164.1 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 40% 83% 164.1 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 42% 59% 182.2 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 40% 98% 178.3 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 40% 98% 178.3 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
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) 34% 71% 174.5 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 90% 168.3 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 90% 168.3 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 38% 96% 167.9 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 39% 91% 166 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 89% 166 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 86% 164.5 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 86% 164.5 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 86% 164.5 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 86% 164.5 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 39% 86% 164.5 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 36% 99% 163.3 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 36% 92% 161.8 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 37% 84% 160.6 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 93% 159.8 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
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) 36% 76% 158.7 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 69% 154.8 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 69% 154.8 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 69% 154.8 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 69% 154.8 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 36% 90% 154.1 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 89% 151 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 30% 72% 150.2 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 78% 148.3 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 84% 145.2 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 77% 141.4 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 85% 136.7 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 91% 132.1 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
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) 30% 88% 109 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
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) 30% 88% 109 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
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) 30% 88% 109 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
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) 30% 88% 109 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
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) 30% 88% 109 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
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) 30% 88% 109 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4
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) 30% 88% 109 AtmD (MetN), component of The methionine porter, AtmBDE 56% 379.4

Sequence Analysis Tools

View WP_027698103.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MPVIELSKVNVTFQQKNQTIVAVKEESLTVERGDIYGIVGYSGAGKSTLVRTINFLQKPS
SGTVLINGTNIANLSSVELREQRKNIGMIFQHFNLMDELTVFGNIALPLKHSNLTKEAKN
QKIKSLLELVGLADRADNYPAQLSGGQKQRVAIARALANDPEILISDEATSALDPRTTNQ
ILDLLKELNEKLNLTIVLITHEMQAIKKIANKVAVMEAGAIIERGSLLEIFTQPKARLTK
DFINTATNRDEALQKVLELLETKPLNADEELVELHYVGSETAQPLLSTIYADFKVMTNIL
YSNMEILRQTPVGTIIAILNGTPEQIRAAKSSIVDHNVQLTVLEEGK

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