GapMind for catabolism of small carbon sources

 

Protein WP_024851414.1 in Hydrogenovibrio kuenenii DSM 12350

Annotation: NCBI__GCF_000526715.1:WP_024851414.1

Length: 264 amino acids

Source: GCF_000526715.1 in NCBI

Candidate for 50 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 41% 95% 183.7 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 65% 160.2 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 35% 62% 156 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 33% 69% 154.5 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 36% 57% 154.5 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
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) 37% 54% 152.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
trehalose catabolism thuK 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) 37% 54% 152.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 36% 63% 151.8 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 69% 151.4 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 69% 151.4 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-cellobiose catabolism gtsD 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) 34% 65% 151 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-glucose catabolism gtsD 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) 34% 65% 151 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
lactose catabolism gtsD 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) 34% 65% 151 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-maltose catabolism gtsD 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) 34% 65% 151 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-maltose catabolism thuK 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) 34% 65% 151 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
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) 34% 65% 151 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 54% 151 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
sucrose catabolism gtsD 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) 34% 65% 151 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
trehalose catabolism gtsD 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) 34% 65% 151 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 36% 59% 150.6 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 56% 146.7 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 56% 146.4 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 32% 74% 145.2 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
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) 32% 70% 145.2 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
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) 32% 70% 145.2 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 35% 56% 144.8 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 63% 144.8 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 58% 144.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 58% 144.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 58% 144.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 57% 143.7 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 32% 68% 142.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
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) 37% 73% 141 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 58% 138.3 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 59% 137.9 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 59% 137.9 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 59% 137.9 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 59% 137.9 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 59% 137.9 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 59% 137.9 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 82% 137.5 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
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) 30% 76% 122.5 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 96% 117.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 96% 117.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 96% 117.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 96% 117.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 96% 117.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 96% 117.1 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 31% 86% 116.7 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 31% 77% 114.4 Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 54% 298.9

Sequence Analysis Tools

View WP_024851414.1 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

MSEVHLELTNVGIEFPTPKGAFRALQGVNLKIEQGEFISLIGHSGCGKSTVMNIVAGLYE
ATEGGVLLDGKEVNSPGPERAVVFQNHSLLPWLTAYENVELAVDQVFKRSKSSAEKKEWI
EHNLKLVHMDHAMHKRPDEISGGMKQRVGIARALAMQPKIMLMDEPFGALDALTRAHLQD
SLMEIQKDLNNTVIMITHDVDEAVLLSDRIIMMTNGPAATIGEILKVELDHPRDRLALAD
DPQYNHYRSEVLRFLYEKQRKVEH

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