Align inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate H281DRAFT_04465 H281DRAFT_04465 myo-inositol 2-dehydrogenase / D-chiro-inositol 1-dehydrogenase
Query= BRENDA::E1U888 (350 letters) >FitnessBrowser__Burk376:H281DRAFT_04465 Length = 348 Score = 238 bits (606), Expect = 2e-67 Identities = 133/341 (39%), Positives = 194/341 (56%), Gaps = 7/341 (2%) Query: 4 KTIKIGIVGLGRLGKIHATNIATKIQHAKLQAATSVVPAELDWAKKELGVEEVFEDFDDM 63 + ++ G+VGLGRLGK HA N+A ++ A+L AA S + E WA+ L +++D+ + Sbjct: 8 RRLRFGVVGLGRLGKRHAENLAYRVPGAELVAACSPLEEERAWARDALPSPRLYDDYARL 67 Query: 64 VQHADIDAVFIVSPSGFHLQQIESALNAGKHVFSEKPIGLDIEAIEHTQQVIAQHANLKF 123 + D+DAV++V+PS H QQI AL AGKHVF EKP+ LD+ E AQ+ +L+ Sbjct: 68 LDDKDVDAVWLVTPSSLHAQQIVDALRAGKHVFCEKPLSLDLAECERVLHEAAQYPHLQA 127 Query: 124 QLGFMRRFDDSYRYAKQLVDQGKIGDITLIRSYSIDPAAGMASFVKFATSANSGGLFLDM 183 +GFMRRFD SY+ A ++ G IG L+RS + D FV+FA A SGG+FLD Sbjct: 128 TIGFMRRFDPSYKDAFDKIEAGAIGRPFLVRSQTTDKNDTDGFFVRFA--ATSGGIFLDC 185 Query: 184 SIHDIDVIHWFTGK-EIDKVWAIGLNRAYPVLDKAGELETGAALMQLEDKTMAILVAGRN 242 ++HDIDV W GK +V+A G + L + G+++ G A+ + ED +A+ A R Sbjct: 186 TVHDIDVARWLLGKPRAKRVFAAGAVALHEGLREFGDVDNGVAICEFEDGKLAMFYASRT 245 Query: 243 AAHGYHVETEIIGTKGMLRIAQVPEKNLVTVMNEEGIIRPTSQNFPERFAQAFLSEEQAF 302 AHG +E+IGT G L I P N V + + GI + F +RF +AFL E +AF Sbjct: 246 QAHGNDTHSEVIGTAGGLTIGHNPRANRVEIYDATGIRNECTPGFFDRFEEAFLHEARAF 305 Query: 303 VNSILNNQ----DVGITAEDGLQGTKAALALQEAFEKNDIV 339 V S+ G T D L+ T+ AL+++ + V Sbjct: 306 VASVQGGAGSAVQAGATLADALEATRIGNALRQSLQSGQAV 346 Lambda K H 0.318 0.134 0.377 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: 313 Number of extensions: 14 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: 350 Length of database: 348 Length adjustment: 29 Effective length of query: 321 Effective length of database: 319 Effective search space: 102399 Effective search space used: 102399 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: 41 (21.7 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