GapMind for catabolism of small carbon sources

 

Protein WP_051000578.1 in Actinomyces timonensis 7400942

Annotation: NCBI__GCF_000295095.1:WP_051000578.1

Length: 675 amino acids

Source: GCF_000295095.1 in NCBI

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
sucrose catabolism ptsS hi The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) (characterized) 52% 98% 657.9 PTS beta-glucoside transporter, EIIBCA of 647 aas and 10 predicted TMSs 45% 563.1
sucrose catabolism sacP med protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized) 48% 99% 448.4 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
trehalose catabolism treB med PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 (characterized) 42% 98% 386.7 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
N-acetyl-D-glucosamine catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 42% 92% 133.7 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
D-glucosamine (chitosamine) catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 42% 92% 133.7 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
D-maltose catabolism malEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 42% 92% 133.7 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
trehalose catabolism treEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 42% 92% 133.7 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
D-cellobiose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 34% 100% 352.8 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
D-cellobiose catabolism bglG lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 34% 100% 352.8 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
D-glucose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 34% 100% 352.8 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
lactose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 34% 100% 352.8 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
D-maltose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 34% 100% 352.8 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
sucrose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 34% 100% 352.8 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
trehalose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 34% 100% 352.8 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 39% 97% 97.1 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 39% 97% 97.1 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) 52% 657.9

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Sequence

MAMDHARVATDVLTYVGGAENITAAAHCATRLRLVLADLDKVDQKALDKDPDIKGTFIAG
GMYQIIVGPGDVDQVFDRMIATGGVKEVSKDEAKQVAAQSGNLVSRFIKMIADIFVPILP
ALIAGGLMMAINNVLTAEGLFGDMSLKERWTWLGDYADLINLISSAAFAFLPVLVGFSAA
KRFGGNVYLGGAMGAAMVSSSLLSAYDMSKPEAAAKFWEFTGAASSWHLFGLEVQKIGYQ
AMVIPIICVAYLMSVIEKRLHKRLSGTADFLLTPLITLLGTGFLTFVVIGPITRQLSIWI
TDGLDWTYNTLGPLGGALFGLVYSPIVVTGLHQSFPAVEIPLISDIANTGGSFIFPIASM
ANVAQGAVAIAVFFRARDAKMKGLAGAGGVSALLGITEPAIFGVNLRLRWPFFIGMGSAA
IGAALVAVFNVRSQALGAAGFVGFVSMVPKHIPAYLALEVLVAAIAFSGAYFYSRTAKGA
ASLADGDVEDEAALEAEAEAAHEHTAEDAPHEAVKAELPAEAAEDYSVTSPIEGRVVPLS
EVEDAVFSQGLLGPGLAVVPSTGPVVSPVDGEVIVAFPSGHAYGIRAASGVEILIHVGMD
TVQLDGKHFSPKVHQGDVIRRGTPLVEVDWDAVKKAGYQIVTPIVVSNGDKFSGISEAGT
RDASRGDALFSVNHD

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