GapMind for catabolism of small carbon sources

 

Protein WP_013684402.1 in Archaeoglobus veneficus SNP6

Annotation: NCBI__GCF_000194625.1:WP_013684402.1

Length: 247 amino acids

Source: GCF_000194625.1 in NCBI

Candidate for 45 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 47% 63% 180.3 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 42% 63% 178.3 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 42% 63% 178.3 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 41% 60% 177.9 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
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) 42% 64% 177.6 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 61% 174.1 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 61% 174.1 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 61% 174.1 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 61% 174.1 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 61% 174.1 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 61% 174.1 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 61% 174.1 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 41% 61% 173.7 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 58% 172.9 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 39% 60% 172.9 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 40% 61% 171.4 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-mannitol catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 40% 62% 169.5 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-sorbitol (glucitol) catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 40% 62% 169.5 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 72% 168.7 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 72% 168.7 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
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) 42% 60% 168.7 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
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) 42% 60% 168.7 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 40% 66% 165.6 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 41% 64% 164.9 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 41% 59% 164.1 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
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) 40% 60% 163.7 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
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) 39% 55% 162.9 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 66% 158.3 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 38% 62% 157.5 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 57% 157.1 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 42% 59% 156.4 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 37% 60% 155.6 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 64% 155.2 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 62% 151.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 62% 151.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 62% 151.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 62% 151.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 62% 151.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 62% 151.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 62% 151.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 62% 151.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 62% 151.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 36% 64% 149.8 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 37% 65% 140.6 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 71% 115.2 Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 66% 319.7

Sequence Analysis Tools

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

Fitness BLAST: loading...

Sequence

MGLGQTFLEVNAEKDFGNFKLDAEFSMDRGYCVVLGPTGAGKSLLLEIIAGILMPDRGKV
IIDCEDVTGLPPERRGIGFVPQDYALFPHMSVYGNIAYGLKARGADKSDIRSAVEEIAEN
LGISHLLDRKPATLSGGEKQRVALARALVIQPKLILLDEPLAAVDLRTKEKLMNELKFVH
REFGIPVIHVTHSLIEAATLADEIAVMMNGRIVEKGDAKKVLSSPSKEVADFLAVKGLFK
KLLDILD

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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