Finding step fbp for chorismate biosynthesis in Maridesulfovibrio zosterae DSM 11974
3 candidates for fbp: 6-deoxy-5-ketofructose 1-phosphate synthase
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | H589_RS0115820 | class II fructose-1,6-bisphosphate aldolase | Fructose-bisphosphate aldolase; Glfba; glFBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized) | 52% | 95% | 290.8 | | | |
| hi | H589_RS0115820 | class II fructose-1,6-bisphosphate aldolase | fba: fructose-1,6-bisphosphate aldolase, class II (EC 4.1.2.13) (TIGR01859) | | 100% | 361 | | | |
| lo | H589_RS0105345 | 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase | fructose-1,6-bisphosphate aldolase subunit (EC 4.1.2.13) (characterized) | 36% | 98% | 171.8 | 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase; ADH synthase; ADHS; ADTH synthase; EC 2.2.1.10 | 58% | 322.4 |
| lo | H589_RS0118440 | 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase | Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized) | 30% | 93% | 126.3 | 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase; ADH synthase; ADHS; ADTH synthase; EC 2.2.1.10 | 35% | 167.9 |
Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Definition of step fbp
- Curated proteins or TIGRFams with EC 2.2.1.11 (search)
- Curated proteins or TIGRFams with EC 4.1.2.13 (search)
- Ignore hits to MONOMER-14592 when looking for 'other' hits (2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10). 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase; ADH synthase; ADHS; ADTH synthase; Transaldolase-like ADHS; EC 2.2.1.10. 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase monomer (EC 4.1.2.13; EC 2.2.1.10))
- Ignore hits to items matching fructose%bisphosphate aldolase when looking for 'other' hits
- Ignore hits to P84722 when looking for 'other' hits (Putative fructose-bisphosphate aldolase, chloroplastic; PS6; EC 4.1.2.13)
- Ignore hits to P86979 when looking for 'other' hits (Fructose-bisphosphate aldolase A; Muscle-type aldolase; Allergen Thu a 3.0101; EC 4.1.2.13)
- Ignore hits to P86980 when looking for 'other' hits (Fructose-bisphosphate aldolase A; Muscle-type aldolase; Allergen Gad m 3.0101; EC 4.1.2.13)
- Ignore hits to Q980K6 when looking for 'other' hits (fructose-bisphosphate aldolase (EC 4.1.2.13))
- Ignore hits to A3MSD2 when looking for 'other' hits (fructose-bisphosphatase (EC 3.1.3.11); fructose-bisphosphate aldolase (EC 4.1.2.13))
- Ignore hits to Q8NKR9 when looking for 'other' hits (fructose-bisphosphatase (EC 3.1.3.11). Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; Fructose-1,6-bisphosphatase; FBPase; EC 3.1.3.11; EC 4.1.2.13)
- Ignore hits to A0RV30 when looking for 'other' hits (Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13)
- Ignore hits to A4YIZ5 when looking for 'other' hits (Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13)
- Ignore hits to A8A9E4 when looking for 'other' hits (Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13. fructose-1,6-bisphosphate aldolase/phosphatase (EC 4.1.2.13; EC 3.1.3.11))
- Ignore hits to B1YAL1 when looking for 'other' hits (Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13. fructose-bisphosphatase (EC 3.1.3.11); fructose-bisphosphate aldolase (EC 4.1.2.13))
- Ignore hits to B6YTP6 when looking for 'other' hits (Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13)
- Ignore hits to D9PUH5 when looking for 'other' hits (Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13)
- Ignore hits to F9VMT6 when looking for 'other' hits (Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; Fructose-1,6-bisphosphatase; FBPase; EC 3.1.3.11; EC 4.1.2.13. fructose-bisphosphatase (EC 3.1.3.11); fructose-bisphosphate aldolase (EC 4.1.2.13))
- Ignore hits to Q2RG86 when looking for 'other' hits (Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13)
- Ignore hits to Q72K02 when looking for 'other' hits (Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13)
- Comment: 6-deoxy-5-ketofructose-1-phosphate synthase is an activity of some fructose-bisphosphate aldolases (which are usually annotated as 4.1.2.13). To find the fbp in Desulfovibrio vulgaris Hildenborough and Miyazaki F, it is necessary to match more broadly. MetaCyc reports that AroA' from Methanococcus jannaschii (link) also has activity as a fructose-bisphosphate aldolase, but it's not clear that it carries out this reaction. The bifunctional fructose-1,6-bisphosphate aldolase/phosphatases are ignored because it is not obvious that they would carry out this reaction; this includes Q980K6, A3MSD2, Q8NKR9, A0RV30, A4YIZ5, A8A9E4, B1YAL1, B6YTP6, D9PUH5, F9VMT6, Q2RG86, Q72K02. And ignore CharProtDB items with incorrect EC and very short SwissProt entries.
Or cluster all characterized fbp proteins
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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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