Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate SMc02486 SMc02486 oxidoreductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Smeli:SMc02486 Length = 250 Score = 107 bits (267), Expect = 2e-28 Identities = 87/271 (32%), Positives = 130/271 (47%), Gaps = 43/271 (15%) Query: 11 IITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQ--------SSGNYNFWPTDISS 62 ++ VTGG+ GIG A+ ++G V + D + + G ++ Sbjct: 6 VLLVTGGSRGIGAAVALAAASEGWRVAVNYASNRDAAEDVVRRIAEAGGTAVSVEGNVGR 65 Query: 63 ASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKG 122 V + FGR+DGLVNNAG+ P VDE +P E++ +N G Sbjct: 66 EEGVRAIFAAVDTAFGRLDGLVNNAGIIGPPQRVDEVSPE--------RIEQLFRVNVTG 117 Query: 123 -VFLMSQAVARQMVKQ--RSGVIVNVSSESGLEGSEGQSC-YAATKAALNSFTRSWSKEL 178 + ++AV R + R G IVN+SS + + G+ GQ YAATK A++SFT ++E+ Sbjct: 118 SIRCAAEAVLRMSARHGGRGGSIVNLSSIAAVLGAPGQYVDYAATKGAIDSFTVGLAREV 177 Query: 179 GKHGIRVVGVAPGILEKT-----GLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSG 233 GIRV V PGI++ GL P+ LA T IP+ R G Sbjct: 178 ATEGIRVNAVRPGIIDTEIHASGGL--PDRARDLAPT----------------IPIQRPG 219 Query: 234 RLTEVADFVCYLLSERASYMTGVTTNIAGGK 264 EVAD + YLLS++A+Y+TG ++GG+ Sbjct: 220 TAGEVADAILYLLSDKATYVTGTILTVSGGR 250 Lambda K H 0.315 0.132 0.378 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 173 Number of extensions: 10 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 267 Length of database: 250 Length adjustment: 24 Effective length of query: 243 Effective length of database: 226 Effective search space: 54918 Effective search space used: 54918 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. 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