GapMind for catabolism of small carbon sources

 

Protein AO353_03840 in Pseudomonas fluorescens FW300-N2E3

Annotation: AO353_03840 ABC transporter ATP-binding protein

Length: 351 amino acids

Source: pseudo3_N2E3 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 med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 43% 96% 268.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 265.8
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 47% 89% 260.8 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 47% 89% 260.8 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 47% 89% 260.8 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 47% 89% 260.8 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 50% 73% 258.1 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 46% 88% 254.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 46% 88% 254.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 46% 88% 254.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 46% 88% 254.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 46% 88% 254.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 46% 88% 254.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 46% 88% 254.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 46% 88% 254.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
D-mannitol catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 43% 87% 248.1 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 43% 87% 248.1 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 47% 82% 245.4 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 44% 91% 245 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 44% 91% 245 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 43% 81% 242.7 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 83% 241.5 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 83% 241.5 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 83% 241.5 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 83% 241.5 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 83% 241.5 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 83% 241.5 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 44% 85% 238.8 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
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) 44% 85% 238.8 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 41% 81% 232.6 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 93% 229.9 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 100% 129 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 100% 129 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 100% 129 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 43% 268.1

Sequence Analysis Tools

View AO353_03840 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

MTGLILENVEKRYGTACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGEI
RLDDEDIGNTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKVDQQARVVELLEL
IQLQEMIDRPVAKLSGGQRQRVAIARAIASHPKILLLDEPLSALDAKLRESMQVEIRQLQ
QRLNITTIMVTHDQREAMTMADIVVVLGQNRVQQVGTPIEIYRHPANEFVADFIGSGNIF
PATALGDGKVGLPGGDALQVPICSSIVVGEKVKMLVRPEDLQLSHPQATAGNRLLGRVTF
VRDIGATIETTVECSGVTLTALSTPCQGIGLSIGNPVSVTIPSEACRVLAA

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 paper from 2022 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