GapMind for catabolism of small carbon sources

 

Protein WP_008411393.1 in Desulfotomaculum hydrothermale Lam5

Annotation: NCBI__GCF_000315365.1:WP_008411393.1

Length: 227 amino acids

Source: GCF_000315365.1 in NCBI

Candidate for 68 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 41% 83% 144.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 47% 58% 196.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 57% 194.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 57% 194.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 47% 55% 188.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 44% 57% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 47% 69% 184.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 48% 59% 183.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 57% 181.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 58% 181 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 44% 59% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 63% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 63% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 63% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 63% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 44% 59% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 63% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
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) 43% 59% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 63% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 63% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 63% 180.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 45% 50% 178.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism malK_Sm lo 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) 45% 54% 178.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
trehalose catabolism malK lo 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) 45% 54% 178.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 45% 62% 177.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 46% 60% 176.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 60% 176 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 60% 176 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 60% 176 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 60% 176 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 60% 176 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 60% 176 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 43% 62% 175.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 40% 60% 174.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
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) 41% 54% 172.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 60% 171.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 60% 171.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 60% 171.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 60% 171.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 41% 54% 171 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 41% 59% 168.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
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) 41% 55% 167.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 62% 167.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 62% 167.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 58% 167.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 55% 167.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 58% 167.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 58% 167.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
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) 41% 56% 166 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 56% 164.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 56% 164.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 56% 164.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 56% 164.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 56% 164.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 56% 164.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 39% 57% 163.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 39% 57% 162.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 52% 152.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 75% 145.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 83% 143.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 86% 141 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 78% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 78% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 78% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 78% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 78% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 74% 136.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 57% 132.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 47% 219.2

Sequence Analysis Tools

View WP_008411393.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MYVEIRDLIFKYKNSQLSTINKVNLSISRGEIIAILGQSGSGKSTILRLLAGLEKPCSGT
IVIDNKVMFDNNTYVNPENRGVGMVFQDYALFPHMTVEKNIIYGLAKLDRKERTKRLKEV
LTLVNLEEFRDRYPYELSGGQQQRVALARALAPKPAVLLLDEPFSNLDADLRCKIRDELK
RIIKDVGITSIFVTHDQEDAISLADRVVYLHKGTVLKVKTKEEYGTG

This GapMind analysis is from Sep 24 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:

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