GapMind for catabolism of small carbon sources

 

Protein WP_024852149.1 in Hydrogenovibrio kuenenii DSM 12350

Annotation: NCBI__GCF_000526715.1:WP_024852149.1

Length: 263 amino acids

Source: GCF_000526715.1 in NCBI

Candidate for 53 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 41% 65% 168.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 98% 161.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 36% 70% 155.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 66% 152.9 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 66% 152.9 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 40% 72% 151 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 39% 63% 150.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 41% 57% 150.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 40% 64% 150.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 149.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 149.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 149.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 149.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 149.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 67% 149.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 59% 147.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 58% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 58% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 58% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 58% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 58% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 41% 65% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 58% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 58% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 58% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 58% 146 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 37% 60% 145.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 37% 60% 145.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 61% 145.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
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) 36% 71% 143.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 41% 54% 142.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
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% 58% 141.7 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 60% 141.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
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) 39% 61% 141.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 60% 139.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 60% 139.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 60% 139.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 60% 139.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 60% 139.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 60% 139.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 60% 139.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 60% 139.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 39% 60% 137.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 64% 127.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 64% 127.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 64% 127.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 64% 127.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 83% 125.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 83% 125.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
L-glutamate catabolism gltL lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 83% 125.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 33% 65% 121.7 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 35% 91% 117.9 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 30% 84% 97.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 43% 196.8

Sequence Analysis Tools

View WP_024852149.1 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

MTAHASNVWIAELSHSYKKQLPPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLL
PSDGVVRINGKTVVKPSAKWNMMFQKPSLYPWMSVRENAALGLVFAGTYKQKQDRVEELL
DMVGLSEHKDKNVQELSGGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQ
ICHEQGITMIMVTHDIEEAIAMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFIELKE
TLFNQFEQIDLAKQKEMAEVANQ

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