Align inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate BPHYT_RS13880 BPHYT_RS13880 oxidoreductase
Query= BRENDA::E1U888 (350 letters) >FitnessBrowser__BFirm:BPHYT_RS13880 Length = 349 Score = 240 bits (613), Expect = 3e-68 Identities = 133/342 (38%), Positives = 199/342 (58%), Gaps = 10/342 (2%) Query: 6 IKIGIVGLGRLGKIHATNIATKIQHAKLQAATSVVPAELDWAKKELGVEEVFEDFDDMVQ 65 +++G+VGLGRLGK HA N+A ++ A L AA S V E WA++ L ++ED+ +++ Sbjct: 8 VRVGVVGLGRLGKRHAENLAYRVPGASLVAACSPVEEERAWAREALPAPRLYEDYAELLG 67 Query: 66 HADIDAVFIVSPSGFHLQQIESALNAGKHVFSEKPIGLDIEAIEHTQQVIAQHANLKFQL 125 ++DAV++V+PS H QQI AL AGKHVF EKP+ LD+ E A++ +L+ + Sbjct: 68 DREVDAVWLVTPSSLHAQQIVDALRAGKHVFCEKPLSLDLAECERVLAESARYPHLQATI 127 Query: 126 GFMRRFDDSYRYAKQLVDQGKIGDITLIRSYSIDPAAGMASFVKFATSANSGGLFLDMSI 185 GFMRRFD SYR A + ++ GKIG L+RS + D FV+FA A SGG+FLD ++ Sbjct: 128 GFMRRFDPSYRDAFEKIEAGKIGRPFLVRSQTADQNDSDGFFVRFA--ATSGGIFLDCTV 185 Query: 186 HDIDVIHWFTGK-EIDKVWAIGLNRAYPVLDKAGELETGAALMQLEDKTMAILVAGRNAA 244 HDIDV W GK +V+A G + L + G+++ G A+ + E +A+ A R A Sbjct: 186 HDIDVARWLLGKPRAKRVFAAGAAVMHEGLREFGDVDNGVAICEFEGGKLAMFYASRTQA 245 Query: 245 HGYHVETEIIGTKGMLRIAQVPEKNLVTVMNEEGIIRPTSQNFPERFAQAFLSEEQAFVN 304 HG +E+IGT G L I + P N V + + GI + NF +RF AFL E +AFV Sbjct: 246 HGNDTHSEVIGTAGALAIGRNPRANRVEIYDATGIRNECTPNFFDRFEDAFLFEARAFVA 305 Query: 305 SILN-------NQDVGITAEDGLQGTKAALALQEAFEKNDIV 339 ++ G + D ++ T+ +AL+E+ + + V Sbjct: 306 AVRGGVGASAAQAGAGASLADAVEATRIGVALRESLLRGEAV 347 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: 305 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: 349 Length adjustment: 29 Effective length of query: 321 Effective length of database: 320 Effective search space: 102720 Effective search space used: 102720 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