GapMind for catabolism of small carbon sources

 

Protein WP_084150835.1 in Azohydromonas australica DSM 1124

Annotation: NCBI__GCF_000430725.1:WP_084150835.1

Length: 389 amino acids

Source: GCF_000430725.1 in NCBI

Candidate for 44 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) 43% 91% 264.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 41% 91% 242.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-cellobiose catabolism gtsD 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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-glucose catabolism gtsD 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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
lactose catabolism gtsD 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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-maltose catabolism gtsD 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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-maltose 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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
sucrose catabolism gtsD 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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
trehalose catabolism gtsD 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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
trehalose 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) 43% 86% 241.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 87% 237.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-mannitol catabolism mtlK med ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 43% 78% 236.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 41% 83% 233.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
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% 84% 230.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
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) 45% 76% 230.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 42% 79% 229.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 99% 229.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 99% 229.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 40% 90% 225.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 90% 225.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 41% 79% 215.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 41% 79% 215.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 41% 79% 215.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 45% 70% 213.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 41% 82% 211.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 77% 211.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 77% 211.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 77% 211.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 77% 211.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 77% 211.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 77% 211.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 73% 204.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 94% 221.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 91% 221.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 40% 90% 219.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 40% 92% 214.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 87% 214.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 91% 207.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
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) 35% 95% 202.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
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% 90% 200.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
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) 42% 57% 176.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 39% 66% 163.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 301.2

Sequence Analysis Tools

View WP_084150835.1 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

Fitness BLAST: loading...

Sequence

MLAAVQKAQRFSATVLPHPAAAGAPAGAAAPNDVLVRFRGVQKTYDGDALVVRNLDLDIR
RGEFLSLLGPSGSGKTTCLMMLAGFESPTAGEILLDGQPITRTPPHKRNFGMVFQNYALF
PHLTVAQNVAYPLTVRRVPKAEIAARVARALAMVRLDGRDKAYPQQLSGGQQQRVALARA
MVFEPQLVLMDEPLGALDKQLREHMQIELKELHRQLGVTFVYVTHDQGEALTMSDRVAVF
NDGAIQQIDPVERLYETPANRFVAGFVGDSTLLQGVVGAASGESCELVLPGGERLAGINV
NGALPGDAVMASVRPERIEALFTPPANESNTLKAAVNDVIYFGDHLRLRCALPGQAQATV
KLPLSRNEQPVAGQTVWLHFPTPYLRVYA

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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