GapMind for catabolism of small carbon sources

 

Protein WP_017598606.1 in Nocardiopsis lucentensis DSM 44048

Annotation: NCBI__GCF_000341125.1:WP_017598606.1

Length: 386 amino acids

Source: GCF_000341125.1 in NCBI

Candidate for 66 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 46% 97% 294.7 Uncharacterized ABC transporter ATP-binding protein YdcT 45% 293.9
D-cellobiose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 273.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-glucose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 273.1 PotG aka B0855, component of Putrescine porter 46% 294.7
lactose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 273.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 273.1 PotG aka B0855, component of Putrescine porter 46% 294.7
sucrose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 273.1 PotG aka B0855, component of Putrescine porter 46% 294.7
trehalose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 273.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-mannitol catabolism mtlK med ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 42% 94% 260.8 PotG aka B0855, component of Putrescine porter 46% 294.7
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 43% 93% 260.4 PotG aka B0855, component of Putrescine porter 46% 294.7
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 41% 94% 257.3 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 92% 255.8 PotG aka B0855, component of Putrescine porter 46% 294.7
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 92% 255.8 PotG aka B0855, component of Putrescine porter 46% 294.7
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 43% 86% 255.4 PotG aka B0855, component of Putrescine porter 46% 294.7
D-cellobiose catabolism msiK med 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) 42% 86% 248.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 42% 84% 243.8 PotG aka B0855, component of Putrescine porter 46% 294.7
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 42% 95% 243 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism malK1 med 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% 88% 242.7 PotG aka B0855, component of Putrescine porter 46% 294.7
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) 40% 96% 241.1 PotG aka B0855, component of Putrescine porter 46% 294.7
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) 40% 96% 241.1 PotG aka B0855, component of Putrescine porter 46% 294.7
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 45% 76% 241.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 80% 234.6 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 43% 86% 234.2 PotG aka B0855, component of Putrescine porter 46% 294.7
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 43% 86% 234.2 PotG aka B0855, component of Putrescine porter 46% 294.7
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 43% 86% 234.2 PotG aka B0855, component of Putrescine porter 46% 294.7
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 80% 231.5 PotG aka B0855, component of Putrescine porter 46% 294.7
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 40% 91% 230.7 PotG aka B0855, component of Putrescine porter 46% 294.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 86% 229.2 PotG aka B0855, component of Putrescine porter 46% 294.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 86% 229.2 PotG aka B0855, component of Putrescine porter 46% 294.7
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 86% 229.2 PotG aka B0855, component of Putrescine porter 46% 294.7
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 44% 76% 226.9 PotG aka B0855, component of Putrescine porter 46% 294.7
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 41% 82% 209.1 PotG aka B0855, component of Putrescine porter 46% 294.7
L-histidine catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 42% 87% 169.5 PotG aka B0855, component of Putrescine porter 46% 294.7
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 42% 87% 169.5 PotG aka B0855, component of Putrescine porter 46% 294.7
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 44% 83% 168.7 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 38% 96% 237.3 PotG aka B0855, component of Putrescine porter 46% 294.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 40% 92% 235 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 86% 234.2 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 88% 231.5 PotG aka B0855, component of Putrescine porter 46% 294.7
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) 38% 95% 225.3 PotG aka B0855, component of Putrescine porter 46% 294.7
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) 37% 95% 219.2 PotG aka B0855, component of Putrescine porter 46% 294.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 88% 217.6 PotG aka B0855, component of Putrescine porter 46% 294.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 88% 217.6 PotG aka B0855, component of Putrescine porter 46% 294.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 88% 217.6 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 88% 217.6 PotG aka B0855, component of Putrescine porter 46% 294.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 88% 217.6 PotG aka B0855, component of Putrescine porter 46% 294.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 88% 217.6 PotG aka B0855, component of Putrescine porter 46% 294.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 97% 206.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 97% 206.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 97% 206.1 PotG aka B0855, component of Putrescine porter 46% 294.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 97% 206.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 97% 206.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 97% 206.1 PotG aka B0855, component of Putrescine porter 46% 294.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 97% 206.1 PotG aka B0855, component of Putrescine porter 46% 294.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 97% 206.1 PotG aka B0855, component of Putrescine porter 46% 294.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 36% 85% 203 PotG aka B0855, component of Putrescine porter 46% 294.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 69% 195.7 PotG aka B0855, component of Putrescine porter 46% 294.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 69% 195.7 PotG aka B0855, component of Putrescine porter 46% 294.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 69% 195.7 PotG aka B0855, component of Putrescine porter 46% 294.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 69% 195.7 PotG aka B0855, component of Putrescine porter 46% 294.7
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 87% 173.7 PotG aka B0855, component of Putrescine porter 46% 294.7
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 41% 60% 172.9 PotG aka B0855, component of Putrescine porter 46% 294.7
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) 40% 59% 169.1 PotG aka B0855, component of Putrescine porter 46% 294.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 36% 95% 149.1 PotG aka B0855, component of Putrescine porter 46% 294.7
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 96% 142.5 PotG aka B0855, component of Putrescine porter 46% 294.7
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 38% 100% 137.9 PotG aka B0855, component of Putrescine porter 46% 294.7
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 31% 100% 122.5 PotG aka B0855, component of Putrescine porter 46% 294.7

Sequence Analysis Tools

View WP_017598606.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MATSTTTSAPEAAVEPPAQTGEPAISLEDVTKSFRSGSETVTAVTGVDLTIGTGEFFSLL
GPSGCGKTTTMRMIAGFEEPTSGTVRLDGRDVTGVPANHRDVNMVFQSYALFPHMNIADN
VAFGLRRRGVAKAEIRTRVADMLDLVELGHRAKHRPSQLSGGQQQRVALARALVNQPGAL
LLDEPLGALDLKLRQSMQVELKRIQREVGITFVYVTHDQGEALTMSDRIAVMNHGRVEQL
GTPAEIYERPATRFVADFIGTSNLLTGVVWDRSGGEPWRVEVGDGATALAAELPDTAEAG
GEVHLTVRPEKVHIGVAEPEGAVSRVPGTVTETVYLGSATHYQVDIGSDQQVTVFQQNAS
GSGLVAERGERVWLSWLPEHSYALSD

This GapMind analysis is from Apr 09 2024. 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