GapMind for catabolism of small carbon sources

 

Protein WP_109941010.1 in Methanospirillum stamsii Pt1

Annotation: NCBI__GCF_003173335.1:WP_109941010.1

Length: 209 amino acids

Source: GCF_003173335.1 in NCBI

Candidate for 30 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 46% 52% 171.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
trehalose catabolism thuK 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) 46% 52% 171.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 45% 53% 167.5 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 41% 64% 167.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 42% 57% 164.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 60% 163.7 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 60% 163.7 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 42% 57% 161.4 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 41% 57% 161 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 52% 161 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 40% 59% 160.6 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 42% 52% 157.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 51% 154.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 51% 154.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 51% 154.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 51% 154.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 51% 154.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 51% 154.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 51% 154.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
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) 40% 55% 153.7 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 52% 152.5 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 52% 152.5 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 52% 152.5 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 52% 150.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 52% 150.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 52% 150.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 52% 150.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 52% 150.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 52% 150.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 30% 64% 76.6 ABC-type molybdate transporter (EC 7.3.2.5) 47% 198.0

Sequence Analysis Tools

View WP_109941010.1 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

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Sequence

MIRIRDLLVRVGSFELPVKNLDVSDNDWVVITGRSGSGKTVFLETIAGFFKPESGSIILD
GADITSLPPEKRGISIVFQDYSLFPHMTARENIGYGLKLRNNPEIHSIVSDYARMLGIDS
LLDRSPAQLSGGEKQRVAIARALVVNPKLLLLDEPASALDHETRRSLWNDLCSLHDRGDL
TIIHVTHDRNEAEVLGNRRIIIDGGKFVE

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