Align Inositol 2-dehydrogenase; EC 1.1.1.18; Myo-inositol 2-dehydrogenase; MI 2-dehydrogenase (uncharacterized)
to candidate Pf1N1B4_4526 Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
Query= curated2:A0LVX1 (341 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4526 Length = 371 Score = 80.1 bits (196), Expect = 8e-20 Identities = 84/280 (30%), Positives = 122/280 (43%), Gaps = 29/280 (10%) Query: 5 RSVRIGLIGAGAIGEDHA---RRLSTVIR---GADVVAVHDVDPSRAKTVATRFRDARVI 58 R + IGLIG G +G HA R +S V + A+ D DP RA+ A + Sbjct: 2 RELGIGLIGTGFMGRAHALAFRNVSAVFELPLKLKLAALADADPQRARHCADAWGFDAAH 61 Query: 59 PDGNSLIGDPDVDAVVVASAAPTHEAYVLAAIAARKPVFCEKPLATTAAGCLRIVEAEKA 118 D LI DP V+ + + + H +AA+AA KPV+CEKPLA + A KA Sbjct: 62 SDWQQLINDPKVNLIAITTPNHLHYPMAMAALAAGKPVYCEKPLAVNLEQASAMRLAAKA 121 Query: 119 HGRRFVRVGFMRRFDPAYLGLKAEL-RSGAIGHPL-----LAHLAHRNPAVPSTLR---- 168 G RVG+ + +P +GL +L +SGA+G + + +P P + R Sbjct: 122 AG-VVTRVGYNYQHNP-IIGLARDLIQSGALGQIISFQGEFSEDFMADPVSPWSWRCDAD 179 Query: 169 -TTDAIADSLVHEMDLVRWLF--------DTE-IREVRAVAGRRNAKAGPDLHDPLLVLV 218 A+AD H + + R L DT+ + R V + + D + L+ Sbjct: 180 YAGGALADLGSHLLAMARHLLGDIQAVCADTQTVHAQRPVTLGGQERREVAVDDQVHALL 239 Query: 219 RMATDVVVDVELS-LNIGYGYHIRAEIVGENGTVALASEQ 257 R A S L GY H+ EI G GT+A E+ Sbjct: 240 RFANGARGTFSSSWLKHGYKNHLSFEISGTRGTLAFDQER 279 Lambda K H 0.320 0.134 0.395 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: 312 Number of extensions: 21 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: 341 Length of database: 371 Length adjustment: 29 Effective length of query: 312 Effective length of database: 342 Effective search space: 106704 Effective search space used: 106704 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