GapMind for catabolism of small carbon sources

 

Protein WP_067908855.1 in Novosphingobium fuchskuhlense FNE08-7

Annotation: NCBI__GCF_001519075.1:WP_067908855.1

Length: 275 amino acids

Source: GCF_001519075.1 in NCBI

Candidate for 40 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 lo GluA aka CGL1950, component of Glutamate porter (characterized) 38% 97% 152.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 38% 98% 148.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 37% 98% 146.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-asparagine catabolism glnQ lo 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) 36% 96% 146 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 39% 91% 144.8 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
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% 99% 140.6 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 36% 98% 140.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 36% 98% 140.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 34% 98% 139.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
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) 36% 56% 135.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 34% 96% 134.8 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 34% 96% 134.8 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 33% 91% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 91% 132.1 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 91% 132.1 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
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) 32% 95% 131 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
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) 32% 95% 131 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
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) 32% 95% 131 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 35% 82% 131 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
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) 32% 95% 131 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
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) 32% 95% 131 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
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) 33% 91% 127.1 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 33% 80% 123.6 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
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% 68% 119.8 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 63% 115.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 63% 115.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 63% 115.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 63% 115.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 63% 115.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 63% 115.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 63% 115.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 63% 115.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 63% 115.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 59% 109 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 59% 109 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 59% 109 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 59% 109 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 59% 109 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 59% 109 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 59% 109 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 59% 314.7

Sequence Analysis Tools

View WP_067908855.1 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

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Sequence

MNAPVPAAEAANQSAATVFPDPVGASKISARGVSVFYGQKRAIDDVSIEIPQNYVTAFIG
PSGCGKSTFLRSLNRMNDTISGARVDGEILLDGVDIYRSGMDVVQLRARVGMVFQKPNPF
PKSIYENIAYGPRIHGITASKGELDGIVEQSLQRAGLWDEVKDRLSDSGTALSGGQQQRL
CIARAIAVDPEVILMDEPCSALDPIATARVEELIDELRGRYAIVIVTHSMQQAARVSQRT
AFFHLGKIVEYGTTSDIFTNPKEEKTKDYITGRYG

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