GapMind for catabolism of small carbon sources

 

Protein WP_040533847.1 in Leeuwenhoekiella blandensis MED217

Annotation: NCBI__GCF_000152985.1:WP_040533847.1

Length: 308 amino acids

Source: GCF_000152985.1 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
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 35% 72% 163.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 163.3
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% 61% 150.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 64% 149.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 64% 149.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 64% 149.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 64% 149.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 64% 149.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 64% 149.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 63% 146 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 33% 70% 144.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
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) 34% 73% 143.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 36% 65% 143.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 32% 85% 143.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 65% 142.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 36% 77% 142.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 65% 142.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 35% 63% 141.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 58% 140.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 68% 139.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 68% 139.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 35% 54% 138.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 84% 137.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 57% 137.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 65% 136 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 65% 136 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 65% 136 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 59% 135.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 34% 65% 132.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 31% 71% 129 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 31% 71% 129 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 62% 119 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 35% 163.7

Sequence Analysis Tools

View WP_040533847.1 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

MLKVDITDFGYTEKTVLKNLDFTVEKGKHISILGESGCGKSTLLKIIYGLLHVENGTVFW
NDNELLGPNFNLVPGEPFIKYLAQDFDLMPYISVADNIGKHLSRRFMQQREERINELLEV
VDMTAFADVHVKLLSGGQKQRVALARAIAKEPELLLLDEPFSHIDNFRRNALRRNLYAYL
KKENITCITATHDSEEALSFSDEIKMMREGQFIQTATPEALFKNPKNAYVASFFGDVNTL
ELDDEKHLIMPHKLQVSQEETQIKASVLKSYFKGSHYLVEAEAQGQKIYFNTAETLEKDT
AVYLKLKL

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