GapMind for catabolism of small carbon sources

 

Protein WP_091519694.1 in Flavobacterium ummariense DS-12

Annotation: NCBI__GCF_900115115.1:WP_091519694.1

Length: 248 amino acids

Source: GCF_900115115.1 in NCBI

Candidate for 52 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 38% 98% 159.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
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% 97% 153.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-glutamate catabolism gltL 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% 97% 153.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 34% 91% 142.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 34% 95% 140.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 34% 95% 140.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 33% 93% 137.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 91% 137.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 91% 137.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 35% 95% 136.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 98% 134 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 98% 134 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 61% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 61% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 61% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 61% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 61% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 61% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 61% 133.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
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% 93% 132.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
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% 93% 132.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
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% 93% 132.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
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% 93% 132.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 33% 68% 132.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
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% 93% 132.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 37% 69% 132.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 36% 94% 130.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 33% 61% 129.8 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 71% 129.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 71% 129.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 31% 64% 129 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 61% 128.3 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
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) 34% 90% 124.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 33% 98% 124.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 32% 81% 124.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-mannitol catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 30% 64% 122.1 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 32% 61% 121.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 55% 121.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 32% 65% 120.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 31% 61% 118.6 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 31% 65% 116.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 31% 65% 116.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 31% 65% 116.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 31% 65% 116.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 63% 112.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 63% 112.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 63% 112.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 63% 112.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 63% 112.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 63% 112.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 70% 112.1 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 30% 61% 108.6 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 56% 283.5

Sequence Analysis Tools

View WP_091519694.1 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

MKTKLSAENLNISFGEKHVLKNISVSFAEHEITALIGPSGCGKSTLLRSFNRMHDLFPDA
KINGSLHLEELDLYDRHVPVTEIRKRIGMVFQKANPFPKSIYENIAYGLKINNLPCNKEV
VQKALEEAYLWDEVKNDLKMPATRLSGGQQQRLCIARAVALRPEVILMDEPCSALDPVST
LKIEELIKHLKKKYTIVIVTHNMQQAQRIADKTVFMYLGEVKEEGTTDEIFNHPKNEMTA
NYISGYFG

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