Definition of D-ribose catabolism
As rules and steps, or see full text
Rules
Overview: Ribose degradation in GapMind is based on the MetaCyc pathway ribose phosphorylation (link), which yields the central metabolic intermediate D-ribofuranose 5-phosphate, or on uptake by a phosphotransferase system.
- all:
- ribose-transport and rbsK
- or ribose-PTS
- Comment: Besides the kinase rbsK, the MetaCyc pathway includes D-ribose pyranase (rbsD). RbsD appears to be absent or not important for fitness in many bacteria that grow with ribose as the sole carbon source, so rbsD is not included in GapMind. Alternatively, uptake by a phosphotransferase (PTS) system can form D-ribofuranose 5-phosphate.
- ribose-PTS: fru2-IIA, fru2-IIB and fru2-IIC
- Comment: This PTS system probably forms ribose 5-phosphate
- ribose-transport:
- rbsA, rbsB and rbsC
- or frcA, frcB and frcC
- or rbsU
- or BT2809
- or LmGT2
- or PLT5
- Comment: Transporters and PTS systems were identified using: query: transporter:ribose:D-ribose:D-ribofuranose:CPD-10330:CPD0-1108:D-ribopyranose:CPD-15829:CPD0-1110:CPD-15818
Steps
rbsA: D-ribose ABC transporter, ATPase component RbsA
- Curated sequence CH_003578: ribose transport, ATP-binding protein RbsA; EC 3.6.3.17. Ribose import ATP-binding protein RbsA; EC 7.5.2.7. RbsA aka B3749, component of Ribose porter. ribose ABC transporter ATP binding subunit. ribose ABC transporter ATP binding subunit
- Curated sequence Q9X051: Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose
- UniProt sequence D8IUD1: SubName: Full=ABC-type sugar transport system, ATPase component protein {ECO:0000313|EMBL:ADJ63793.1};
- UniProt sequence A0A1N7TZ92: SubName: Full=Ribose ABC transporter ATPase {ECO:0000313|EMBL:ERH60791.1}; SubName: Full=Sugar ABC transporter ATP-binding protein {ECO:0000313|EMBL:PRW85404.1}; SubName: Full=Sugar ABC transporter ATPase {ECO:0000313|EMBL:AIB37520.1};
- UniProt sequence A0A166R419: SubName: Full=Sugar ABC transporter ATP-binding protein {ECO:0000313|EMBL:KZN21271.1};
- Comment: E. coli rbsABC and the related system from T. maritima. The fitness data also identified a related system in Herbaspirillum: rbsBAC = HSERO_RS11480 (D8IUD0), HSERO_RS11485 (D8IUD1), HSERO_RS11490 (D8IUD2); and in various Pseudomonas: rbsBAC = PS417_18405 (A0A1N7UEH6) PS417_18400 (A0A1N7TZ92) PS417_18395 (A0A1N7UNQ5) or Pf1N1B4_6035 (A0A161ZH48), Pf1N1B4_6034 (A0A166R419), Pf1N1B4_6033 (A0A166R405).
- Total: 5 characterized proteins
rbsB: D-ribose ABC transporter, substrate-binding component RbsB
- Curated sequence CH_003593: D-ribose-binding periplasmic protein; EC 3.6.3.17. Ribose import binding protein RbsB. RbsB aka RBSP aka PRLB aka B3751, component of Ribose porter. ribose ABC transporter periplasmic binding protein. ribose ABC transporter periplasmic binding protein
- Curated sequence Q9X053: Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose
- UniProt sequence D8IUD0: SubName: Full=ABC-type sugar transport system, periplasmic component protein {ECO:0000313|EMBL:ADJ63792.1};
- UniProt sequence A0A1N7UEH6: SubName: Full=LacI family transcriptional regulator {ECO:0000313|EMBL:AIB37521.1}; SubName: Full=Ribose transport system substrate-binding protein {ECO:0000313|EMBL:SFA82006.1}; SubName: Full=Sugar ABC transporter substrate-binding protein {ECO:0000313|EMBL:PRW85403.1};
- UniProt sequence A0A161ZH48: SubName: Full=LacI family transcriptional regulator {ECO:0000313|EMBL:KZN21272.1};
- Total: 5 characterized proteins
rbsC: D-ribose ABC transporter, permease component RbsC
- Curated sequence P0AGI1: Ribose import permease protein RbsC. Ribose transport system permease protein RbsC aka B3750, component of Ribose porter. ribose ABC transporter membrane subunit. ribose ABC transporter membrane subunit
- Curated sequence Q9X050: ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose
- UniProt sequence D8IUD2: SubName: Full=ABC-type sugar transport system, permease component protein {ECO:0000313|EMBL:ADJ63794.1};
- UniProt sequence A0A1N7UNQ5: SubName: Full=ABC transporter permease {ECO:0000313|EMBL:AIB37519.1}; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family {ECO:0000313|EMBL:SFA82032.1};
- UniProt sequence A0A166R405: SubName: Full=ABC transporter permease {ECO:0000313|EMBL:KZN21270.1};
- Total: 5 characterized proteins
frcA: D-ribose ABC transporter, ATPase component FrcA
- Curated sequence Q9F9B0: Fructose import ATP-binding protein FrcA; EC 7.5.2.-. FrcA, component of Fructose/mannose/ribose porter
- Comment: FrcABC from S. meliloti
- Total: 1 characterized proteins
frcB: D-ribose ABC transporter, substrate-binding component FrcB
frcC: D-ribose ABC transporter, permease component FrcC
fru2-IIA: D-ribose PTS, IIA component
- Curated sequence Q3JZE3: PTS system, fructose-specific, IIA component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence
- Comment: The fru2 PTS system in Streptococcus agalactiae is thought to transport ribose (TC 4.A.2.1.22); it is not proven that this is coupled to phosphorylation to form ribose 5-phosphate, but it seems likely
- Total: 1 characterized proteins
fru2-IIB: D-ribose PTS, IIB component
- Curated sequence Q3JZE2: PTS system, fructose-specific, IIB component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence
- Total: 1 characterized proteins
fru2-IIC: D-ribose PTS, IIC component
- Curated sequence Q3JZE4: PTS system, fructose-specific, IIC component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence
- Total: 1 characterized proteins
rbsU: probable D-ribose transporter RbsU
BT2809: D-ribose transporter
LmGT2: D-ribose transporter LmGT2
PLT5: D-ribose transporter PLT5
- Curated sequence CH_091483: polyol transporter 5. Polyol transporter 5; Protein POLYOL TRANSPORTER 5; AtPLT5; Sugar-proton symporter PLT5. The broad specificity sugar/sugar alcohol (myo-inositol, glycerol, ribose, sorbitol, mannitol, xylitol, erythritol, etc) H+ symporter, AtPLT5 (transports a wide range of hexoses, pentoses, tetroses, sugar alcohols and a sugar acid, but not disaccharides) (Reinders et al., 2005) (expressed in roots, leaves and floral organs)
- Total: 1 characterized proteins
rbsK: ribokinase
- Curated proteins or TIGRFams with EC 2.7.1.15
- Comment: deoxyribose kinases are sometimes annotated with the same EC number; most of these sequences are thought to be ribokinases as well
- Total: 1 HMMs and 21 characterized proteins
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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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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