GapMind for catabolism of small carbon sources

 

Protein WP_068461491.1 in Hyphomicrobium sulfonivorans WDL6

Annotation: NCBI__GCF_001541235.1:WP_068461491.1

Length: 254 amino acids

Source: GCF_001541235.1 in NCBI

Candidate for 36 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% 85% 159.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 45% 56% 171.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 65% 164.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 65% 164.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 45% 52% 163.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 61% 162.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 61% 162.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 41% 63% 159.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 42% 57% 159.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 43% 59% 157.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 43% 57% 157.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
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) 42% 57% 154.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
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) 42% 57% 154.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
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) 42% 57% 154.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
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) 42% 57% 154.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
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) 42% 57% 154.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
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) 42% 57% 154.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
sucrose 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) 42% 57% 154.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
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) 42% 57% 154.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 43% 54% 152.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 42% 57% 152.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 40% 58% 152.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 54% 152.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 55% 147.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 55% 147.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 55% 147.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 40% 64% 144.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 41% 53% 142.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 57% 141.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 57% 141.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 57% 141.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 57% 141.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 57% 141.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 57% 141.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 61% 110.9 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 31% 50% 99.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 46% 190.7

Sequence Analysis Tools

View WP_068461491.1 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

MLHIGHVSKAFARGGAVLADVDLTVERGESVAIVGASGCGKSTLLRIIAGLEPPSRGTVT
VAGEEIRTPHPAVGMIFQEPRLLPWLTVAENIAFGITSLPASERTARVQEALDLIGLVEH
ASKWPRELSGGQSQRVAIARALVARPSVILLDEPFSALDAVTRVDLQRHMRALGRRMHLT
LVIVTHDLEEALILGDRVAIMQPNPGRIAKIVTVPGDGDTDLALRELASSFAHLNGARNA
AILEGAHIQYAHTS

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