GapMind for catabolism of small carbon sources

 

Protein WP_008538970.1 in Megamonas funiformis YIT 11815

Annotation: NCBI__GCF_000245775.1:WP_008538970.1

Length: 461 amino acids

Source: GCF_000245775.1 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
N-acetyl-D-glucosamine catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 55% 79% 521.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 54% 500.4
D-glucosamine (chitosamine) catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 55% 79% 521.9 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 54% 500.4
N-acetyl-D-glucosamine catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 54% 71% 500.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-glucosamine (chitosamine) catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 54% 71% 500.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
N-acetyl-D-glucosamine catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 55% 100% 498.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-glucosamine (chitosamine) catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 55% 100% 498.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-glucosamine (chitosamine) catabolism gamP med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 53% 71% 492.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
N-acetyl-D-glucosamine catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 48% 74% 440.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-glucosamine (chitosamine) catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 48% 74% 440.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-maltose catabolism malEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 48% 74% 440.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
trehalose catabolism treEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 48% 74% 440.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-cellobiose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 388.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-glucose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 388.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
lactose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 388.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-maltose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 388.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
sucrose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 388.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
trehalose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 388.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
N-acetyl-D-glucosamine catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 49% 98% 386.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-glucosamine (chitosamine) catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 49% 98% 386.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
N-acetyl-D-glucosamine catabolism ptsB med IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 44% 81% 73.9 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-glucosamine (chitosamine) catabolism ptsB med IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 44% 81% 73.9 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-cellobiose catabolism ptsG-crr lo PTS system glucoside-specific EIICBA component; EIICBA-Glc 2; EC 2.7.1.- (characterized) 41% 53% 314.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-glucose catabolism ptsG-crr lo PTS system glucoside-specific EIICBA component; EIICBA-Glc 2; EC 2.7.1.- (characterized) 41% 53% 314.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
lactose catabolism ptsG-crr lo PTS system glucoside-specific EIICBA component; EIICBA-Glc 2; EC 2.7.1.- (characterized) 41% 53% 314.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-maltose catabolism ptsG-crr lo PTS system glucoside-specific EIICBA component; EIICBA-Glc 2; EC 2.7.1.- (characterized) 41% 53% 314.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
sucrose catabolism ptsG-crr lo PTS system glucoside-specific EIICBA component; EIICBA-Glc 2; EC 2.7.1.- (characterized) 41% 53% 314.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
trehalose catabolism ptsG-crr lo PTS system glucoside-specific EIICBA component; EIICBA-Glc 2; EC 2.7.1.- (characterized) 41% 53% 314.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-maltose catabolism malEIICB lo The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized) 35% 90% 248.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9
D-maltose catabolism malEIICBA lo PTS system, IIABC components (characterized, see rationale) 32% 75% 231.9 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 55% 521.9

Sequence Analysis Tools

View WP_008538970.1 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

MSSWFSKLQAVGKALMLPVAVLPAAALLLRLGAPDVFDIPFITQAGGAVFNNLALIFAVG
IAVGLAKDNNGAAGLAGVIGYLVLTEALKAIDKDLNMGVLAGVIVGIISGILYNKFYNIK
LPEFLGFFSGRRFVPIVTAATFVVLALIFGIIWGPIQNFIHSIGEWIVGAGAAGAFVYGV
LNRLLIPVGLHHILNSLVWFVFGSYTNPETGVTATGDLNRFFAGDPTAGVFMAGFYFIFM
FGVPAIALAMYSAAKPENKSKVAGMMFSIAFTAFLTGITEPVEFTFMFLAPVLYAFHAVM
TGIALAVANMFGILHGFGFSAGLIDYVLNYGLATKAILIIPIGLVFGIIYFIVFRWAIIH
FDLPTPGRFENESDNEAIENANPDELAQSFINKLGGADNLTTISSCITRLRLNVKDIDKI
DEAGLKALGAAGVIKKGNSIQVIVGTKAEAVADDMKKIAKK

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