GapMind for catabolism of small carbon sources

 

Protein WP_036139233.1 in Lysobacter daejeonensis GH1-9

Annotation: NCBI__GCF_000768355.1:WP_036139233.1

Length: 235 amino acids

Source: GCF_000768355.1 in NCBI

Candidate for 53 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 43% 83% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-arginine catabolism artP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 41% 77% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 41% 77% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 41% 77% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 40% 80% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 41% 67% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 84% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 84% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 42% 52% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 39% 89% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 37% 87% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 60% 141.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 61% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 61% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 36% 90% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 61% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 61% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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) 39% 51% 139 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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) 36% 87% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 36% 58% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 87% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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) 37% 86% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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) 37% 86% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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) 37% 86% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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) 37% 86% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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) 37% 86% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 40% 75% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 89% 128.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 89% 128.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 57% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 36% 59% 125.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 33% 55% 119.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 31% 61% 118.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 65% 118.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 36% 75% 116.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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) 35% 76% 115.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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% 112.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0
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% 72% 91.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 52% 233.0

Sequence Analysis Tools

View WP_036139233.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MPSVAPADDVVIRTHNLRKVYAPGTEAEVVALSDADMAVRRGEFVAIIGPSGSGKSTLMN
LIGCLDKPSAGTYLCDGVDVATLDAEERAILRRDKIGFVFQGFNLLPRLSALENVAMPMG
YANVPRAERLRRAQAALEAVGLGGRTGHRPSELSGGQQQRVAIARALINRPPILLADEPT
GALDTHTGDEILRLFKQLQRDGHTVVLITHDPDVAAAANRTFVIRDGVLSEGGSL

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