GapMind for catabolism of small carbon sources

 

Protein BWI76_RS07290 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS07290

Length: 626 amino acids

Source: Koxy in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism bglG lo PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs (characterized) 34% 98% 396.4 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
D-cellobiose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 36% 99% 382.9 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
D-glucose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 36% 99% 382.9 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
lactose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 36% 99% 382.9 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
D-maltose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 36% 99% 382.9 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
sucrose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 36% 99% 382.9 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
trehalose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 36% 99% 382.9 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
sucrose catabolism ptsS lo protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized) 33% 99% 315.8 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
sucrose catabolism sacP lo protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized) 33% 100% 256.1 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
trehalose catabolism treB lo PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 (characterized) 31% 99% 208.8 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
D-cellobiose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 37% 91% 116.7 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
D-glucose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 37% 91% 116.7 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
lactose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 37% 91% 116.7 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
D-maltose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 37% 91% 116.7 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
sucrose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 37% 91% 116.7 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
trehalose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 37% 91% 116.7 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 38% 98% 94.4 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 38% 98% 94.4 Aryl β-glucoside porter, IIBCA (BglP; SytA) (35% identical to 4.A.1.2.2) 38% 458.0

Sequence Analysis Tools

View BWI76_RS07290 at FitnessBrowser

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

MNYNETADKILHAVGGAENIRMLTHCATRLRMEFNDRAKVNDAQIGTLPGVISVVEKGGQ
FQIVIGNEVQQVYRRLNKALPEKKGPAGGDKNAKPAGIVARIISVISTTFTPVIPAITGA
GMIKALLAILKLTGVISETSSTYQLLNIIADAAFFFLPVLLAYGASLKFECNPILAMTLA
GVLLHPGIGQMLAAGKAVDFVGINVLLSDYAGSVLPIILTVWLMSWVERFAEKVSPSIIK
FFVKPMLILLITAPLALVVVGPAGILLNDLVAAGAGAIDRHASWLIPMLMGTLQPFLIIT
GTAWAMTPIATGQLSKSGYEMINGPGMLASNVAMGAATLCVALKTKNSNLRQLASSSGFT
ALLGITEPALYGVLLKFRRVLIAAMIGGGCAGVYAGVSGLVRYAFVSPGLAALPAFIGEN
PMNIVHALVTCAISIVVTFTLTWFIAFKDVPEEQEEVGEAPQPAVSPKNEGETEVFSPLR
GQVVALSEVNDDVFSGGLLGEGLAIRPEEGVLRAPFSGTVMMFLPSCHAVGLQSDSGLEL
LIHIGIDTVNLNGQHFSSTLKVGDRVEAGQELIRFDIPAIEQAGYDLITPVIVVNGDEQH
SLRLTAAAQVDYGEQLMVQSAKEAQA

This GapMind analysis is from Sep 17 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