GapMind for catabolism of small carbon sources

 

Protein AO353_25130 in Pseudomonas fluorescens FW300-N2E3

Annotation: AO353_25130 ABC transporter

Length: 381 amino acids

Source: pseudo3_N2E3 in FitnessBrowser

Candidate for 48 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
sucrose catabolism thuK hi ABC transporter (characterized, see rationale) 91% 100% 681 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 57% 98% 375.6 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 52% 367.9
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 52% 99% 367.9 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 52% 99% 367.9 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 51% 100% 360.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 52% 100% 345.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 52% 100% 345.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 52% 100% 345.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 52% 100% 345.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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% 96% 339.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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% 96% 339.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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% 96% 339.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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% 96% 339.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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% 96% 339.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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% 96% 339.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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% 96% 339.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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% 96% 339.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 95% 324.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 49% 100% 323.2 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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) 47% 100% 322.8 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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) 48% 98% 322.4 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 49% 94% 319.7 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 49% 94% 319.7 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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) 46% 98% 318.2 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 46% 97% 311.6 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 97% 308.5 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 97% 308.5 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 97% 308.5 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 97% 308.5 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 97% 308.5 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 97% 308.5 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 47% 99% 308.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 93% 307.4 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 45% 97% 300.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 47% 90% 299.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 46% 99% 294.7 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 45% 99% 289.3 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
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% 92% 285.8 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 43% 96% 285.4 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 44% 95% 282.7 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 42% 98% 262.7 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 38% 96% 231.5 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 98% 202.2 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 90% 200.7 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 98% 196.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 98% 196.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 98% 196.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 98% 196.1 Maltose-transporting ATPase (EC 3.6.3.19) 57% 375.6

Sequence Analysis Tools

View AO353_25130 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

MIKLKLDNVNKQLGGVRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAGDL
LIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTAQI
LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH
ARLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN
FLAARLHAPGETSLVDTPVLGMTSLPFDSSNLAADTPLSLGVRPEHVSLKAADGTVGVIV
TGVEYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGNLHLFDADGTALRRP
PQAIETLPDGVSLRSVRAGAL

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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