GapMind for catabolism of small carbon sources

 

Protein BWI76_RS01840 in Klebsiella michiganensis M5al

Annotation: BWI76_RS01840 ABC transporter ATP-binding protein

Length: 369 amino acids

Source: Koxy in FitnessBrowser

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malK hi Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 95% 100% 700.7 ABC transporter for D-Sorbitol, ATPase component 56% 383.3
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 56% 98% 383.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 54% 98% 377.9 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 56% 94% 369 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 55% 100% 365.5 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 53% 100% 357.1 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 53% 100% 357.1 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 53% 100% 357.1 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 53% 100% 357.1 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
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) 53% 95% 351.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
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) 53% 95% 351.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
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) 53% 95% 351.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
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) 53% 95% 351.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
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) 53% 95% 351.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
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) 53% 95% 351.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
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) 53% 95% 351.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
trehalose 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) 53% 95% 351.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 98% 344.7 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 98% 344.7 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 98% 344.7 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 98% 344.7 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 98% 344.7 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 98% 344.7 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 50% 100% 322.4 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
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) 50% 89% 317 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
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% 89% 317 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 64% 74% 314.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 64% 74% 314.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 46% 96% 300.4 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 45% 98% 296.6 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 46% 100% 296.6 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 45% 98% 285.8 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 46% 78% 234.2 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 95% 700.7

Sequence Analysis Tools

View BWI76_RS01840 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

MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIAGLETVTSGDL
LIGDTRMNDVPPAERGIGMVFQSYALYPHLSVAENMSFGLKLAGAKKELINQRVTQVAEV
LQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLH
KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN
FLPVKVTATAIEQVQVELPNRQQVWLPVDSARVQVGANMSLGIRPEHLLPSDIADVTLEG
EVQVVEQLGHETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGTAC
RRLHKEPGV

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 (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 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