GapMind for catabolism of small carbon sources

 

Protein 5207560 in Shewanella loihica PV-4

Annotation: Shew_0094 ABC transporter-related protein (RefSeq)

Length: 369 amino acids

Source: PV4 in FitnessBrowser

Candidate for 40 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 68% 175.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 68% 175.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 33% 84% 167.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 68% 160.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 68% 160.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 42% 60% 159.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
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) 39% 56% 159.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 42% 54% 156 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 69% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 69% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 69% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 69% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 69% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 69% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 69% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 69% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 69% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 153.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 37% 66% 152.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-maltose catabolism malK1 lo 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) 36% 68% 152.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-cellobiose catabolism msiK lo 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) 40% 58% 151.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 41% 57% 150.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 39% 68% 149.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 58% 147.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 40% 62% 147.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 37% 59% 147.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 39% 68% 146 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-mannitol catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 39% 64% 145.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
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) 32% 91% 144.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
trehalose catabolism malK lo 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) 31% 94% 144.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 56% 143.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 59% 140.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 71% 136 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 33% 83% 136 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 34% 69% 118.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 33% 176.4

Sequence Analysis Tools

View 5207560 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

MSQDVADLSCKIFQQEGIALDAEFVCKAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGEI
RYGDSVWFSSESGRYLTPQQRHLGYVPQHFGLFPNMTALANVVAALDHIPKAERVARAKD
WLERVNLHGLPDRLPANLSGGQRQRVALARALAREPRVLLLDEPFSAVDRETRERLYLEL
ARLKEQLAIPVIMVTHDLNEALLLADRMILISQGTLLQQGSPREVLSRPRNEAVAKQMGL
RNLFDAHVVAQEAERQITWLRFGEHLIAGNYCEQLAIGAKVRWVIPNQGVRFNSITKGRL
CRSFNKLSITIESCLSMGETMRILASIKGVKHHLNAEVPLHFAQKMGLAPGVETEVALKS
ELIHILEND

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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