GapMind for catabolism of small carbon sources

 

Protein WP_010960192.1 in Methylococcus capsulatus Bath

Annotation: NCBI__GCF_000008325.1:WP_010960192.1

Length: 385 amino acids

Source: GCF_000008325.1 in NCBI

Candidate for 76 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 55% 96% 375.6 Uncharacterized ABC transporter ATP-binding protein YdcT 45% 265.4
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 84% 243 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 84% 243 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 43% 82% 233 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 44% 84% 232.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 41% 81% 230.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 90% 228.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 43% 82% 228 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 43% 82% 228 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 43% 82% 228 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 44% 78% 225.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 92% 225.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 92% 225.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 48% 70% 224.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 42% 82% 223.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-cellobiose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-glucose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
lactose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-maltose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 41% 78% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
sucrose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
trehalose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 77% 222.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 41% 82% 221.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 42% 72% 218.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 76% 217.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 70% 206.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 45% 83% 167.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
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) 41% 83% 164.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
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) 41% 83% 164.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 49% 70% 231.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
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) 48% 61% 229.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
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) 39% 91% 228.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 61% 219.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
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) 34% 94% 217.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
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) 34% 94% 217.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
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% 80% 216.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 99% 214.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 80% 213.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 96% 213.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 96% 213.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 96% 213.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 96% 213.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 96% 213.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 96% 213.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 96% 213.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 96% 213.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
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) 43% 62% 183 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 41% 64% 179.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 34% 82% 166.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 37% 72% 166 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 39% 93% 159.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 39% 93% 153.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 94% 145.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-asparagine catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 38% 88% 137.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-aspartate catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 38% 88% 137.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-glutamate catabolism gltL lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 38% 88% 136.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 120.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 120.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 120.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 36% 74% 117.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 34% 84% 108.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 30% 87% 104.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 96.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 96.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 96.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 96.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 96.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 96.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 55% 375.6

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Sequence

MRPSRRPRFRNILENRTIAAMTRSTIASFRAVSKHYGSHCALRDFNLELREGELLTLLGP
SGCGKTTVLRLLAGLEIPDSGEIFLDGRTLAGVPPEARNVNTVFQSYALFPHLSVAENVA
FGLRMKKLGSAEIRARTAEALRMVRLDGLGGHRPLQLSGGQQQRVALARALVNRPRVLLL
DECLSALDYQLRREMQLELKGLQRQTGITFVFVTHDREEALSMSDRIAVMRTGRIEQLGP
PRDIYERPANLFVAQFAGESNVLEATVTAITAPDSLIVELAGTPLTVRTDRRFRVGARLV
LVLRPEDLHVHDDAAAEGGLAGHVLERTYRGVTLDTVIALDAGPRIKTSEFFREDTPALD
HPPGQRVRVSWTPGWEIVLPHDPET

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