GapMind for catabolism of small carbon sources

 

Protein WP_015448118.1 in Rhodanobacter denitrificans 2APBS1

Annotation: NCBI__GCF_000230695.2:WP_015448118.1

Length: 255 amino acids

Source: GCF_000230695.2 in NCBI

Candidate for 63 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 41% 62% 170.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 40% 62% 164.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 65% 156 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 35% 72% 155.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 64% 154.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 64% 154.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 83% 153.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 38% 63% 153.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 38% 60% 152.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 37% 73% 152.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 68% 152.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 65% 151.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 71% 150.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 71% 150.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 37% 92% 150.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 58% 149.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 36% 67% 149.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 63% 148.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 63% 148.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 63% 148.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 66% 146.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 66% 146.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 66% 146.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 66% 146.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 66% 146.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 66% 146.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 66% 146.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 66% 146.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 35% 60% 144.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 36% 61% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 36% 61% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 36% 95% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 36% 61% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 36% 61% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 36% 61% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 36% 61% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 36% 61% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 36% 60% 143.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 58% 143.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 61% 142.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 60% 141.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 63% 141.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 37% 87% 141.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 63% 141.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 63% 141.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 63% 141.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 63% 141.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 63% 141.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 36% 63% 141 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 39% 57% 141 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 36% 96% 137.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 36% 56% 137.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 90% 137.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 90% 135.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 90% 135.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 90% 135.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 90% 135.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 36% 90% 135.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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) 35% 63% 134.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 53% 132.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
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% 78% 130.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 63% 125.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 62% 123.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 42% 203.8

Sequence Analysis Tools

View WP_015448118.1 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

MSTAESAGGIAFALVQAGKRYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGL
EWPDHGHVEVDGRPLQRSDVLPLRRRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERI
RQRAEQLAALTHLPTGVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVR
HELQDELKQIFDQLGKTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAF
VNRFVAAQRRLPEAP

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