GapMind for catabolism of small carbon sources

 

Protein WP_109939593.1 in Methanospirillum stamsii Pt1

Annotation: NCBI__GCF_003173335.1:WP_109939593.1

Length: 263 amino acids

Source: GCF_003173335.1 in NCBI

Candidate for 19 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 hi ABC transporter for L-Histidine, ATPase component (characterized) 53% 96% 255 CynD, component of Bispecific cyanate/nitrite transporter 49% 229.2
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 98% 166.4 ABC transporter for L-Histidine, ATPase component 53% 255.0
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 42% 65% 163.3 ABC transporter for L-Histidine, ATPase component 53% 255.0
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 39% 91% 162.9 ABC transporter for L-Histidine, ATPase component 53% 255.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 41% 64% 162.9 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 41% 57% 162.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 41% 57% 162.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 41% 57% 162.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 41% 57% 162.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 41% 57% 162.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 41% 57% 162.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 41% 57% 162.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 41% 57% 162.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 41% 57% 162.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 40% 59% 160.2 ABC transporter for L-Histidine, ATPase component 53% 255.0
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 41% 58% 159.5 ABC transporter for L-Histidine, ATPase component 53% 255.0
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 40% 51% 156.4 ABC transporter for L-Histidine, ATPase component 53% 255.0
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 30% 54% 87.8 ABC transporter for L-Histidine, ATPase component 53% 255.0
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) 31% 68% 87 ABC transporter for L-Histidine, ATPase component 53% 255.0

Sequence Analysis Tools

View WP_109939593.1 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

MGRVEITNLFREFTRDDGGRVVALSDVNLTIADDEFVSFVGPSGCGKTTLLRIIAGLDTA
NSGEVRVDGELITGPGQKVGMVFQEYSLFPWQNVLTNVAFGLRMRGIGKEERYSIAKKFI
ALVGLTQFEESYPYELSGGMRQRVAIARALATDPDLLLMDEPFGALDAQTRNHMQCELLD
IWGTKKKTILFVTHSCDEAVFLSDRVVVLSPRPGRIREIINISIPRPRDRTNKEFIDLRR
SLLEMIDEDERKEERIKCKSGNL

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