GapMind for catabolism of small carbon sources

 

Protein 7023042 in Shewanella sp. ANA-3

Annotation: Shewana3_0280 ABC transporter related (RefSeq)

Length: 367 amino acids

Source: ANA3 in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 40% 59% 168.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 30% 88% 156.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 65% 156.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 65% 156.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 38% 57% 152.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 40% 54% 150.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 42% 55% 150.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 39% 65% 149.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 67% 149.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 37% 71% 147.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 42% 56% 145.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-cellobiose catabolism gtsD lo 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) 39% 55% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-glucose catabolism gtsD lo 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) 39% 55% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
lactose catabolism gtsD lo 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) 39% 55% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-maltose catabolism gtsD lo 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) 39% 55% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-maltose catabolism thuK lo 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) 39% 55% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-mannose catabolism TT_C0211 lo 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) 39% 55% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
sucrose catabolism gtsD lo 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) 39% 55% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
trehalose catabolism gtsD lo 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) 39% 55% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
trehalose catabolism thuK lo 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) 39% 55% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 58% 143.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 40% 61% 133.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 34% 67% 84.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 34% 179.9

Sequence Analysis Tools

View 7023042 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

MAQIIADLHCQIQNHKHIKLSAEFSCKAGEVLAVVGPSGGGKTTLLRMIAGLNHPDAGSI
VFGETLWFDHQSRTALTPQQRHIGYMPQHFGLFPNLTALENVVAGLDHIPKSERIARAKD
WLERVNLHGLPDRLPMHLSGGQRQRVALARALAREPSVLLLDEPFSAVDRETRERLYLEL
ARLKEQLLCPVIMVTHDLNEALLLADSMILISQGQMLQQGAPFEVLSRPRNEAVARQMGL
RNIFDGEVVFQDRTKDITWLKFGEQLIASDFGKDRSVGSKVRWVIPNQGIRFNAISNGRL
CRSFNKLDVTIDSLLVMGESVRVVCYATGTELQLNTEVSLHLAQKLGLTKGMQTTVALKS
EQIHILE

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