GapMind for catabolism of small carbon sources

 

Protein WP_007705431.1 in Cronobacter universalis NCTC 9529

Annotation: NCBI__GCF_001277175.1:WP_007705431.1

Length: 369 amino acids

Source: GCF_001277175.1 in NCBI

Candidate for 37 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 57% 96% 398.7 LacK, component of Lactose porter 56% 391.7
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 56% 100% 391.7 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 51% 98% 371.7 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 54% 97% 367.9 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 52% 95% 346.7 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-cellobiose catabolism gtsD med 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) 53% 91% 339 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-glucose catabolism gtsD med 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) 53% 91% 339 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
lactose catabolism gtsD med 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) 53% 91% 339 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-maltose catabolism gtsD med 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) 53% 91% 339 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-maltose catabolism thuK med 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) 53% 91% 339 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-mannose catabolism TT_C0211 med 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) 53% 91% 339 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
sucrose catabolism gtsD med 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) 53% 91% 339 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
trehalose catabolism gtsD med 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) 53% 91% 339 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
trehalose catabolism thuK med 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) 53% 91% 339 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 50% 99% 335.1 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 50% 99% 335.1 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 50% 99% 335.1 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 48% 98% 334 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 51% 95% 327 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 51% 95% 327 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 50% 100% 327 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 48% 100% 326.6 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 48% 97% 324.3 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-maltose catabolism malK_Sm med 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) 48% 98% 320.5 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
trehalose catabolism malK med 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) 48% 98% 320.5 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 47% 97% 312.4 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 46% 88% 310.8 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 47% 99% 310.5 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 55% 85% 309.3 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 55% 85% 309.3 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 55% 85% 309.3 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 55% 85% 309.3 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 55% 85% 309.3 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 55% 85% 309.3 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 50% 87% 308.9 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 49% 97% 306.6 ABC transporter for D-Sorbitol, ATPase component 57% 398.7
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 48% 76% 238.4 ABC transporter for D-Sorbitol, ATPase component 57% 398.7

Sequence Analysis Tools

View WP_007705431.1 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

Fitness BLAST: loading...

Sequence

MSSIRLRNVTKRFGKTETLHNINLDIADGEFAVFVGPSGCGKSTLLRMIAGLEEVSDGEV
LIGDEVMNDVAPAHRGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDQIRHQVEMVAKT
LQLSHLLDRKPKQLSGGQRQRVAIGRAIVRNPQVFMFDEPLSNLDAELRVEMRLHIARLH
QELKTTMVYVTHDQIEAMTLADKIVVMNYGKVEQMGSPMALYYNPVNKFVAGFIGSPKMN
FLPATVARWEEGALDVTLSQGKTLRLAIHTAPLKQGDAVTLGIRPEHLSTGAQTGVSLTF
NCEVVERLGNNTYLFGQCYGHDNMKILLPGDVHFSPWQAVEVGFNPRDCMVFDADGLRIS
AETDVPHAH

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