GapMind for catabolism of small carbon sources

 

Protein 17511 in Escherichia coli BW25113

Annotation: b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)

Length: 356 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
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 52% 97% 359.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 53% 97% 357.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 50% 99% 347.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 50% 99% 347.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 51% 93% 344.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 48% 96% 343.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 51% 99% 342.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 51% 97% 341.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 51% 97% 341.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 51% 97% 341.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 51% 97% 341.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 51% 97% 341.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 51% 97% 341.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 51% 97% 341.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 51% 97% 341.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 50% 98% 335.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 49% 95% 334 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 49% 100% 331.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 50% 96% 330.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 50% 100% 329.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
trehalose catabolism malK 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) 50% 100% 329.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 49% 99% 328.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 49% 95% 328.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 46% 89% 326.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 48% 100% 321.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 47% 96% 314.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 48% 99% 314.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 48% 99% 314.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 48% 99% 314.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 47% 99% 314.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 45% 99% 308.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 48% 93% 307.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 48% 93% 307.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 46% 100% 303.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 96% 290.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 96% 290.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 96% 290.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 96% 290.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 96% 290.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 96% 290.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 44% 96% 284.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 48% 76% 236.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 37% 90% 218.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 78% 207.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 78% 207.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 78% 207.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 78% 207.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 96% 196.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2
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) 35% 95% 187.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 100% 707.2

Sequence Analysis Tools

View 17511 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

MAGLKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGD
IWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAAR
ILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQL
HRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAM
NLLTGRVNNEGTHFELDGGIELPLNGGYRQYAGRKMTLGIRPEHIALSSQAEGGVPMVMD
TLEILGADNLAHGRWGEQKLVVRLAHQERPTAGSTLWLHLAENQLHLFDGETGQRV

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