Align myo-inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate SMc04400 SMc04400 oxidoreductase
Query= metacyc::MONOMER-13035 (337 letters) >FitnessBrowser__Smeli:SMc04400 Length = 333 Score = 78.2 bits (191), Expect = 3e-19 Identities = 61/195 (31%), Positives = 97/195 (49%), Gaps = 13/195 (6%) Query: 3 LKLGVIGAGAIGKEHIRRCTQVLQGATVVAVSDINADNARAAVALPGVQAEVYADGHDVI 62 ++ G+IGA I +E + + G VV+V +A+ A A G+ A+ D++ Sbjct: 2 IRWGLIGASTIAREWVIGAIRAA-GGEVVSVMSSSAERGEAYAAENGI-AKAVTSVDDLV 59 Query: 63 KASDVDAVLVTSWDPTHEEYTLAAIEAGKPVFCEKPLAMSA-EGCRRIVDAEMKAGRRLV 121 DVDAV +++ + H LAAI AGK V CEKPLAM+ +GC ++ A +AG L Sbjct: 60 GDPDVDAVYISTTNELHHGQALAAIRAGKHVLCEKPLAMNLNDGCEMVLKA-CEAGVVLG 118 Query: 122 QVGFMRPYDEGYLALKKVIDDGDIGAPLMLRCAH--------RNQSVGENYTTDMAITNT 173 +R + A+++ I G IG P+ R H + + + I + Sbjct: 119 TNHHLR-NAATHRAMREAIAAGRIGRPIAARVFHAVYLPPHLQGWRLDKPEAGGGVILDI 177 Query: 174 LIHELDVLRWLLNDD 188 +H+ D LR++LNDD Sbjct: 178 TVHDADTLRFVLNDD 192 Lambda K H 0.319 0.134 0.399 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: 278 Number of extensions: 14 Number of successful extensions: 2 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: 337 Length of database: 333 Length adjustment: 28 Effective length of query: 309 Effective length of database: 305 Effective search space: 94245 Effective search space used: 94245 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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