GapMind for catabolism of small carbon sources

 

Protein WP_017733558.1 in Nafulsella turpanensis ZLM-10

Annotation: NCBI__GCF_000346615.1:WP_017733558.1

Length: 229 amino acids

Source: GCF_000346615.1 in NCBI

Candidate for 29 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 64% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 64% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 64% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 64% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 64% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 64% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 64% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 64% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 37% 86% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 37% 86% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 61% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 36% 52% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 37% 55% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 57% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 59% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 59% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 55% 125.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
D-maltose 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) 35% 53% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
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) 35% 53% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
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) 35% 53% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
trehalose 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) 35% 53% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
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) 34% 57% 124.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
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) 32% 53% 117.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 54% 98.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 223.4

Sequence Analysis Tools

View WP_017733558.1 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

MIQAKNLSKLYTTDEVETTALNNINLHIREGEFVAIMGPSGCGKSTLLNIMGLLDNPSAG
SYQFMGQEVSHYTERQRAGMRKGSIGFIFQSFNLIDELNVFENVELPLLYLKVPASDRKR
KVEQVLEQMNIMHRRKHFPQQLSGGQQQRVAIARAVVARPPLILADEPTGNLDSKNGEEV
MNLLSVLNAKGTTIIMVTHSPHDANYAHRIINLFDGRIVTENVKEQFHV

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