GapMind for catabolism of small carbon sources

 

Protein WP_085770045.1 in Methylocystis bryophila S285

Annotation: NCBI__GCF_002117405.1:WP_085770045.1

Length: 352 amino acids

Source: GCF_002117405.1 in NCBI

Candidate for 79 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% 86% 282.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 280.0
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 47% 70% 231.9 PotG aka B0855, component of Putrescine porter 46% 282.7
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 41% 82% 227.6 PotG aka B0855, component of Putrescine porter 46% 282.7
D-cellobiose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 219.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-galactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 219.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-glucose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 219.9 PotG aka B0855, component of Putrescine porter 46% 282.7
lactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 219.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-maltose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 219.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-mannose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 219.9 PotG aka B0855, component of Putrescine porter 46% 282.7
sucrose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 219.9 PotG aka B0855, component of Putrescine porter 46% 282.7
trehalose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 219.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 41% 79% 219.5 PotG aka B0855, component of Putrescine porter 46% 282.7
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 41% 79% 219.5 PotG aka B0855, component of Putrescine porter 46% 282.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 46% 70% 218.8 PotG aka B0855, component of Putrescine porter 46% 282.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 46% 70% 218.8 PotG aka B0855, component of Putrescine porter 46% 282.7
D-cellobiose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 75% 216.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 75% 216.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-glucose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 75% 216.9 PotG aka B0855, component of Putrescine porter 46% 282.7
lactose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 75% 216.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-maltose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 75% 216.9 PotG aka B0855, component of Putrescine porter 46% 282.7
sucrose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 75% 216.9 PotG aka B0855, component of Putrescine porter 46% 282.7
trehalose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 75% 216.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 44% 72% 216.5 PotG aka B0855, component of Putrescine porter 46% 282.7
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 41% 73% 212.6 PotG aka B0855, component of Putrescine porter 46% 282.7
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% 84% 185.7 PotG aka B0855, component of Putrescine porter 46% 282.7
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% 84% 185.7 PotG aka B0855, component of Putrescine porter 46% 282.7
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 44% 84% 165.2 PotG aka B0855, component of Putrescine porter 46% 282.7
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 39% 96% 243 PotG aka B0855, component of Putrescine porter 46% 282.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 39% 95% 238 PotG aka B0855, component of Putrescine porter 46% 282.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 94% 236.9 PotG aka B0855, component of Putrescine porter 46% 282.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 94% 236.9 PotG aka B0855, component of Putrescine porter 46% 282.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 94% 236.9 PotG aka B0855, component of Putrescine porter 46% 282.7
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 39% 89% 233.8 PotG aka B0855, component of Putrescine porter 46% 282.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 88% 233 PotG aka B0855, component of Putrescine porter 46% 282.7
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) 39% 92% 226.1 PotG aka B0855, component of Putrescine porter 46% 282.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 90% 225.7 PotG aka B0855, component of Putrescine porter 46% 282.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 93% 224.2 PotG aka B0855, component of Putrescine porter 46% 282.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 93% 224.2 PotG aka B0855, component of Putrescine porter 46% 282.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 93% 224.2 PotG aka B0855, component of Putrescine porter 46% 282.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 39% 96% 224.2 PotG aka B0855, component of Putrescine porter 46% 282.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 93% 224.2 PotG aka B0855, component of Putrescine porter 46% 282.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 93% 224.2 PotG aka B0855, component of Putrescine porter 46% 282.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 93% 224.2 PotG aka B0855, component of Putrescine porter 46% 282.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 90% 222.2 PotG aka B0855, component of Putrescine porter 46% 282.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 95% 221.5 PotG aka B0855, component of Putrescine porter 46% 282.7
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 36% 96% 220.3 PotG aka B0855, component of Putrescine porter 46% 282.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 85% 219.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 98% 219.5 PotG aka B0855, component of Putrescine porter 46% 282.7
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% 78% 217.2 PotG aka B0855, component of Putrescine porter 46% 282.7
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) 36% 95% 214.9 PotG aka B0855, component of Putrescine porter 46% 282.7
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) 36% 95% 214.9 PotG aka B0855, component of Putrescine porter 46% 282.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 37% 81% 214.5 PotG aka B0855, component of Putrescine porter 46% 282.7
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) 37% 91% 212.2 PotG aka B0855, component of Putrescine porter 46% 282.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 76% 209.1 PotG aka B0855, component of Putrescine porter 46% 282.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 77% 186.4 PotG aka B0855, component of Putrescine porter 46% 282.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 77% 186.4 PotG aka B0855, component of Putrescine porter 46% 282.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 77% 186.4 PotG aka B0855, component of Putrescine porter 46% 282.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 77% 186.4 PotG aka B0855, component of Putrescine porter 46% 282.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 98% 185.7 PotG aka B0855, component of Putrescine porter 46% 282.7
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 36% 78% 174.1 PotG aka B0855, component of Putrescine porter 46% 282.7
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 34% 70% 171 PotG aka B0855, component of Putrescine porter 46% 282.7
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 87% 162.9 PotG aka B0855, component of Putrescine porter 46% 282.7
L-arginine catabolism artP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 96% 144.4 PotG aka B0855, component of Putrescine porter 46% 282.7
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 96% 144.4 PotG aka B0855, component of Putrescine porter 46% 282.7
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 96% 144.4 PotG aka B0855, component of Putrescine porter 46% 282.7
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 35% 72% 131 PotG aka B0855, component of Putrescine porter 46% 282.7
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 36% 86% 122.5 PotG aka B0855, component of Putrescine porter 46% 282.7
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 80% 121.3 PotG aka B0855, component of Putrescine porter 46% 282.7
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 35% 84% 119.4 PotG aka B0855, component of Putrescine porter 46% 282.7
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 91% 117.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 91% 117.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 91% 117.9 PotG aka B0855, component of Putrescine porter 46% 282.7
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 91% 117.9 PotG aka B0855, component of Putrescine porter 46% 282.7
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 106.3 PotG aka B0855, component of Putrescine porter 46% 282.7
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 106.3 PotG aka B0855, component of Putrescine porter 46% 282.7
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 106.3 PotG aka B0855, component of Putrescine porter 46% 282.7
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 106.3 PotG aka B0855, component of Putrescine porter 46% 282.7
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 106.3 PotG aka B0855, component of Putrescine porter 46% 282.7
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 106.3 PotG aka B0855, component of Putrescine porter 46% 282.7

Sequence Analysis Tools

View WP_085770045.1 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

MAAVPLLAIERASKRFGSTVALDDVSVDVAPGEFFALLGPSGCGKTTLMRLIAGFERPDS
GRLTLEGRDLAGLPPHQRPINMMFQSYALFPHLDVFENIAFGLRRKGLAQDDVKKRVQEL
LDVVQLGGFNARRIHQLSGGQKQRVALARALAPGPKLLLLDEPLGALDRKLREETQLQLK
QIQRKLNTAFVIVTHDQDEALALADRIAVMRAGKIEQIGAPPDVYRRPQNRFVADFIGAT
NLIEGHVSRADGVWFVAPFGKIARAVCTLDDGARAALSLRPQDIRLARDGAGLPGRVAQA
SFRGETTLLWVELDTGGTLRVSCPPDAGLAQGDSVRVTIPPEAGALLAEPRP

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