GapMind for catabolism of small carbon sources

 

Protein WP_028998531.1 in Azohydromonas australica DSM 1124

Annotation: NCBI__GCF_000430725.1:WP_028998531.1

Length: 358 amino acids

Source: GCF_000430725.1 in NCBI

Candidate for 62 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) 41% 95% 266.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 40% 94% 259.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 44% 78% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
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) 42% 91% 252.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
trehalose catabolism thuK 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) 42% 91% 252.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-cellobiose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 80% 249.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-glucose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 80% 249.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
lactose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 80% 249.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 80% 249.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
sucrose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 80% 249.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
trehalose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 80% 249.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 80% 249.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 45% 75% 246.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 40% 95% 245.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 46% 82% 242.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 42% 90% 240.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 41% 90% 240.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 80% 240 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
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) 41% 91% 239.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
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) 41% 91% 239.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 79% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 79% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 79% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 79% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 79% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 79% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 79% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 79% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 79% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 43% 70% 235.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism malK_Sm med 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) 43% 80% 233.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
trehalose catabolism malK med 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) 43% 80% 233.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 43% 77% 231.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 42% 81% 230.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 47% 71% 226.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 47% 71% 226.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 44% 77% 223 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 41% 75% 217.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 40% 92% 249.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 88% 242.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 39% 96% 239.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
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% 95% 238.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 46% 70% 218.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 211.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 211.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 211.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 211.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 211.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 211.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 211.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 88% 211.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 74% 195.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 74% 195.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 74% 195.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 74% 195.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 36% 92% 186.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
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) 38% 74% 176.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 72% 164.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 98% 164.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 98% 164.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 94% 161 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 34% 82% 131.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 44% 288.5

Sequence Analysis Tools

View WP_028998531.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSTIVLFKDVQKTYDGEHLVVKNLNLSIEEGEFLTMLGPSGSGKTTCLMMLAGFETATSG
QILLKGREINRIPPERRNIGMVFQSYALFPNMSVAENLAFPLKVRKVAKSDIEAKVKRAL
AMVNMQKFADRMPAQLSGGQQQRIAVARALVFEPALVLMDEPLGALDKQLREQMQYEIKR
IHEASGLTTVYVTHDQGEAMTMSDRVAVFENGRIQQLASPSDLYERPENAFVAGFIGESN
QLQGAVTRREGALCSVKLKQGVQVTAMAGHDITAGSQVTLSLRPERVLLGSQAAGCENVF
NAKVKDVIYYGDHLRLVCDANLAGDFIVKVSNDGEGRRIQSGDTLNLGWKAEACCALQ

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