GapMind for catabolism of small carbon sources

 

Protein 14400 in Escherichia coli BW25113

Annotation: b0262 putative ATP-binding component of a transport system (VIMSS)

Length: 348 amino acids

Source: Keio in FitnessBrowser

Candidate for 49 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 42% 89% 254.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 45% 79% 249.6 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 86% 244.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 86% 244.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 82% 243.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 82% 243.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 46% 79% 243.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-maltose catabolism malK1 med MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 41% 90% 240.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 40% 84% 239.6 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 41% 88% 238 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-cellobiose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 92% 237.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-glucose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 92% 237.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
lactose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 92% 237.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-maltose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 92% 237.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
sucrose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 92% 237.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
trehalose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 92% 237.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 92% 237.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 44% 75% 237.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 97% 237.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 46% 80% 235.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 41% 80% 229.6 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 41% 85% 228.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 41% 85% 228.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 41% 85% 228.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 39% 97% 240 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 40% 92% 237.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 40% 92% 232.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-mannose catabolism TT_C0211 lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 40% 88% 229.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 37% 97% 228.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 39% 89% 228 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 39% 92% 223 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 87% 222.6 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 39% 80% 219.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
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) 39% 88% 219.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 215.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 215.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 215.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 215.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 210.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 210.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 210.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 210.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 210.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 210.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 210.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 210.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 97% 190.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
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% 59% 186 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 94% 172.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 100% 696.0

Sequence Analysis Tools

View 14400 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTQKNFVELRNVTKRFGSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSE
GQIFIDGEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEA
LAMVDLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIR
ELQKQFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGDA
NLFPATFSDGYVDIYGYHLPRPLHFGTQGEGMVGVRPEAITLSDRGEESQRCVIRHVAYM
GPQYEVTVEWHGQEILLQVNATRLQPDVGEQYYLEIHPYGMFVLADAA

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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