GapMind for catabolism of small carbon sources

 

Protein WP_017867858.1 in Lactobacillus pobuzihii E100301

Annotation: NCBI__GCF_000349725.1:WP_017867858.1

Length: 368 amino acids

Source: GCF_000349725.1 in NCBI

Candidate for 58 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism malK med 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) 66% 100% 499.2 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism malK_Sm med 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) 64% 100% 477.6 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 60% 96% 436.8 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
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) 57% 99% 413.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
trehalose catabolism thuK 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) 57% 99% 413.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-cellobiose catabolism gtsD med 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) 54% 97% 383.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-glucose catabolism gtsD med 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) 54% 97% 383.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
lactose catabolism gtsD med 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) 54% 97% 383.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism gtsD med 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) 54% 97% 383.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism thuK med 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) 54% 97% 383.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-mannose catabolism TT_C0211 med 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) 54% 97% 383.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
sucrose catabolism gtsD med 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) 54% 97% 383.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
sucrose catabolism thuK med 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) 54% 97% 383.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
trehalose catabolism gtsD med 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) 54% 97% 383.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 50% 99% 332 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 50% 99% 332 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 50% 99% 332 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 50% 96% 330.5 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 46% 99% 322 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 53% 87% 320.5 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 46% 96% 313.5 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 46% 88% 310.8 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 48% 96% 309.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-cellobiose catabolism msiK med 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) 47% 98% 307.8 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 47% 99% 307.4 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 45% 94% 304.7 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 46% 96% 302.8 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 45% 98% 302.4 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 94% 297 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 46% 97% 295.8 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-mannitol catabolism mtlK med ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 43% 96% 295.8 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.9 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.9 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.9 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.9 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.9 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.9 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 58% 71% 283.5 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 44% 99% 283.5 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 58% 71% 283.5 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 52% 81% 281.2 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 42% 79% 230.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 80% 227.6 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
L-proline catabolism opuBA med 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) 44% 73% 199.9 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 97% 207.6 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 94% 207.2 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 94% 207.2 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 94% 207.2 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 94% 207.2 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 195.7 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 195.7 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 195.7 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 195.7 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 195.7 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 195.7 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 195.7 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 195.7 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 91% 175.3 ATP-binding protein MsmK aka ABC transporter nucleotide binding protein, component of The fructooligosaccharide porter, MsmEFGK 70% 522.7

Sequence Analysis Tools

View WP_017867858.1 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

MVELNLEHIYKKYDNADDYSVTDFNLDIKDREFIVFVGPSGCGKSTTLRMIAGLEDITKG
DLKIDGKIVNDEAPKDRDIAMVFQNYALYPHMTVYDNMAFGLKLRKYSKEKIDKQVHHAA
DILGLEEYLDRKPAALSGGQRQRVALGRAIVRDAPIFLMDEPLSNLDAKLRVAMRAQIAK
LHQDLETTTIYVTHDQTEAMTMADRIVVMKDGEVQQIGTPQEVYDSPTNVFVGGFIGAPA
MNFFNVTLDGEYIFDEGKNFRLKVPEGCLKVLRDKRYDKQKLVFGIRPEDMHTEQAFIET
FPESLVKATVSVSELLGAESQLYSKVGETEFVCKVDARDFVKPGSEVTMGVDLNKAHFFD
PESEKAVY

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