Annotation: FitnessBrowser__Btheta:351600
Length: 747 amino acids
Source: Btheta in FitnessBrowser
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| citrate catabolism | acn | hi | aconitate hydratase (EC 4.2.1.3) (characterized) | 85% | 100% | 1314.7 | |||
| citrate catabolism | acn | hi | aconitate hydratase, mitochondrial (EC 4.2.1.3) (TIGR01340) | 100% | 1094.4 | ||||
| L-isoleucine catabolism | acnD | lo | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) | 33% | 57% | 193.7 | aconitate hydratase (EC 4.2.1.3) | 85% | 1314.7 |
| propionate catabolism | acnD | lo | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) | 33% | 57% | 193.7 | aconitate hydratase (EC 4.2.1.3) | 85% | 1314.7 |
| L-threonine catabolism | acnD | lo | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) | 33% | 57% | 193.7 | aconitate hydratase (EC 4.2.1.3) | 85% | 1314.7 |
| L-valine catabolism | acnD | lo | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) | 33% | 57% | 193.7 | aconitate hydratase (EC 4.2.1.3) | 85% | 1314.7 |
View 351600 at FitnessBrowser
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Fitness BLAST: loading...
MVYDLTMLEAFYSAYKGKVEHVRAVLKRPLTLAEKILYAHLFNEGDLKNYKRGEDYVNFR PDRVAMQDATAQMALLQFMNAGKEKVAVPSTVHCDHLIQAYKGAKEDIATATKTNEEVYD FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD AVDVMTGMEWELKMPRIIGVRLTGKLSGWTSPKDVILKLAGILTVKGGTNSIIEYFGPGT ASLSATGKATICNMGAEVGATTSLFPFDGRMATYLRATGRDRIVELAEAVDCELRADQQV TDEPEKYYDRVIDIDLSTLEPYINGPFTPDAATPISEFAEKVLLNGYPRKMEVGLIGSCT NSSYQDLSRAASLARQVKEKNLSVASPLIINPGSEQIRATAERDGMMDDFMQIGAVIMAN ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTYAFVASPELTMALTIAGDLC FNPLKDRLMNHDGEKVKLAEPVGDELPLRGFTSGNEGYITPGGTKTAINVNPASQRLQLL TPFPAWDGQDILNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFNGE TNNVWNRSTNTYGTVSGTAKMYKSEGIPSIVVAEENYGEGSSREHAAMEPRFLNVRVILA KSFARIHETNLKKQGMLALTFADKADYDKIQEHDLLSVIGLPDFAPGRNLTVVLHHEDGT KESFEAQHTYNEQQIAWFRAGSALNAR
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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:
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