GapMind for catabolism of small carbon sources

 

Protein WP_041277555.1 in Desulfotalea psychrophila LSv54

Annotation: NCBI__GCF_000025945.1:WP_041277555.1

Length: 344 amino acids

Source: GCF_000025945.1 in NCBI

Candidate for 50 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 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 38% 87% 190.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 88% 189.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-mannitol catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 35% 95% 189.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-sorbitol (glucitol) catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 35% 95% 189.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 182.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 182.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 182.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 182.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 182.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 182.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 182.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 182.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 35% 97% 181.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 90% 180.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 90% 180.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 90% 180.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 90% 180.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 90% 180.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 90% 180.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
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) 33% 89% 178.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
trehalose catabolism thuK 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) 33% 89% 178.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 39% 67% 178.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 81% 177.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 81% 177.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 81% 177.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 81% 177.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 72% 176.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 39% 80% 175.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 87% 174.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 97% 170.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 97% 170.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 74% 170.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 37% 79% 170.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 34% 92% 169.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
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) 34% 81% 168.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 34% 92% 168.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
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% 97% 167.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 33% 85% 164.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 96% 163.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 74% 163.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 96% 163.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 96% 163.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 96% 163.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 96% 163.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 31% 96% 163.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
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) 33% 84% 163.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
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) 30% 97% 160.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 38% 83% 151 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 38% 83% 151 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 32% 75% 148.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 38% 228.8

Sequence Analysis Tools

View WP_041277555.1 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

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Sequence

MIKISQLTNNFPDFSVGPVDLTVDTGEFFVLLGPSGSGKTVLLESIVGVRRPDEGKIILN
GVDVTKLAPENRKVGIVYQDQALFPHLSVRENIYFGLRYQRQIEKKTFSLDMVIDTLGLR
VHLDKSPQALSGGERQRVALARALAIQPRVILLDEPLSALDPCFRGEIQRLLKELHSSLG
TTFLMVTHDFNEAFYLADRVGVISKGTVKQVGTINDVFLQPQNVEVGKFVGMKNIFCRRD
GETSVHVGNLSLTLNAQASQSAYGLRPEDIEVAAKDSFPADFHVGQGTIQSVVRQGFGCE
VTIASGRDLLLIHLDQKSLRAQELAMDSPIHFGFSPASLHHFPR

This GapMind analysis is from Sep 24 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:

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