GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS22760 in Burkholderia phytofirmans PsJN

Annotation: FitnessBrowser__BFirm:BPHYT_RS22760

Length: 384 amino acids

Source: BFirm in FitnessBrowser

Candidate for 30 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 med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 55% 99% 384.8 ABC transporter for D-Sorbitol, ATPase component 55% 382.9
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 55% 97% 382.9 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
D-mannitol catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 52% 98% 379.8 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 51% 99% 359.8 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 51% 99% 359.8 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 51% 99% 359.8 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 51% 99% 359.8 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 54% 99% 357.5 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 50% 94% 345.1 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
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) 50% 95% 339.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
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) 50% 95% 339.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
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) 50% 95% 339.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
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) 50% 95% 339.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
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) 50% 95% 339.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
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) 50% 95% 339.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
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) 50% 95% 339.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
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) 50% 95% 339.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 96% 336.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 96% 336.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 96% 336.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 96% 336.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 96% 336.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 96% 336.3 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 50% 89% 333.2 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 49% 97% 331.6 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 49% 100% 318.9 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
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) 46% 99% 308.5 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 57% 82% 305.4 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 57% 82% 305.4 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 45% 98% 291.2 Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 55% 384.8

Sequence Analysis Tools

View BPHYT_RS22760 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MASISLRGVQKAYGEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD
LSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAAR
ILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIARL
HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFVA
GFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAGLQTSQAVTLGVRPEHLEF
VDPSSVAPDDAVLTRTVSLVEQLGEHSYVHLDQPGGAALVAKAPGNTRLAPGERASLRVP
RAACHLFTEDGFAAASLESVEHYA

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:

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