GapMind for catabolism of small carbon sources

 

Protein WP_097031115.1 in Rhodobacter ovatus JA234

Annotation: NCBI__GCF_900207575.1:WP_097031115.1

Length: 352 amino acids

Source: GCF_900207575.1 in NCBI

Candidate for 56 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 44% 95% 266.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-cellobiose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 44% 80% 256.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-glucose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 44% 80% 256.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
lactose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 44% 80% 256.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-maltose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 44% 80% 256.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
sucrose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 44% 80% 256.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
trehalose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 44% 80% 256.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 40% 98% 254.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 41% 95% 253.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 44% 83% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 89% 251.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 89% 251.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 43% 86% 251.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 78% 248.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 43% 80% 246.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
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) 42% 91% 245.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 43% 89% 244.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 45% 80% 241.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 42% 95% 241.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
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% 88% 239.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
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) 47% 73% 237.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 41% 84% 237.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 41% 84% 237.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 83% 236.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 83% 236.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 40% 96% 233.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 44% 77% 233.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
trehalose catabolism malK med 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) 44% 73% 219.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 43% 86% 214.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 93% 244.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 40% 95% 231.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 93% 226.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
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) 38% 96% 223.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 85% 203.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 85% 203.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 85% 203.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 85% 203.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 40% 57% 178.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 80% 163.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 91% 162.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 91% 162.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 88% 161.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 36% 98% 160.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 89% 157.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 88% 155.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 76% 134.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 72% 129.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 285.4

Sequence Analysis Tools

View WP_097031115.1 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

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Sequence

MAFLEISRLEKSFGPLHVVRDFNLDIEQGEFVSLLGPSGCGKTTVLRMVAGFETPNHGAI
RIEGRDMVRQRPNQRKIGMVFQAYALFPNLTVAQNVGFGLKVAGVPRREAADRVAEMLAL
IGLPDLGGRYPFQLSGGQQQRVALARALAVRPRVLLLDEPLSALDAKIRVSLRTEIRAIQ
QRLAITTIFVTHDQEEALSISDRIVVMNGGIAEQVGTPFQIYNHPTTKFVANFVGTLNTL
PAEVVDPSAGIVRVGGQTIRLPESLERAAGTRIGLALRPEALHLGTAEGREVVLPATISD
VQFLGSVIRVRAETQGASVALDTFNRADVPPPQVGSPAQISFSARDVIVLEH

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