Align myo-inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate CCNA_02094 CCNA_02094 MviM-like NAD-dependent oxidoreductase
Query= metacyc::MONOMER-13035 (337 letters) >FitnessBrowser__Caulo:CCNA_02094 Length = 305 Score = 70.5 bits (171), Expect = 5e-17 Identities = 58/179 (32%), Positives = 85/179 (47%), Gaps = 12/179 (6%) Query: 2 SLKLGVIGAGAIGKEHIRRCTQVLQGATVVAVSDINADNARAAVALPGVQAEVYADGHDV 61 +LK GV+GAG G H ++ + L G T+V V DI+ A+A G Q D D Sbjct: 4 TLKAGVVGAGVFGGYHAKKYVE-LDGVTLVGVFDIDLARAKALAEPLGAQGY---DDMDA 59 Query: 62 IKASDVDAVLVTSWDPTHEEYTLAAIEAGKPVFCEKPLAMSAEGCRRIVDAEMKAGRRLV 121 A+ VD V V + H LAA++AGKPV+ EKPLA+S + ++V A KAG L Sbjct: 60 FLAA-VDVVTVAAPAVHHAAPALAALKAGKPVYSEKPLAVSPDDADKMVAAAAKAGVPLA 118 Query: 122 QVGFMRPYDEGYLALKKVIDDGDIGAPLMLRCAHRNQSVGENYTTDMAITNTLIHELDV 180 G + L + + PL L R N + + + +IH++D+ Sbjct: 119 -CGHQERVVFQAMGLLDIPEQ-----PLRLEAVRRGTPSDRNLDVSV-VLDLMIHDIDL 170 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: 258 Number of extensions: 17 Number of successful extensions: 3 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: 305 Length adjustment: 28 Effective length of query: 309 Effective length of database: 277 Effective search space: 85593 Effective search space used: 85593 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: 48 (23.1 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