Align inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate SMc04129 SMc04129 oxidoreductase
Query= BRENDA::O68965 (330 letters) >FitnessBrowser__Smeli:SMc04129 Length = 433 Score = 85.5 bits (210), Expect = 2e-21 Identities = 62/208 (29%), Positives = 90/208 (43%), Gaps = 21/208 (10%) Query: 4 RFGLLGAGRIGKV---HAKAVSGNADARLVAVADAFPAAAEAI-------AGAYGCEVRT 53 RF L+G G G LVA+AD AE A YG Sbjct: 7 RFALVGTGNRGTTMWGRDLLAGWRGLVDLVAIADTNALRAERARTMIATNAPVYG----N 62 Query: 54 IDAIEAAADIDAVVICTPTDTHADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTK 113 +DA+ A D V++CTP DTH D++ R +G + EKP+ E++R L T Sbjct: 63 VDAMLAETRPDLVIVCTPDDTHDDIVVRALESGADVITEKPMSTTVEKIRRILDAEKRTG 122 Query: 114 AKLMVGFNRRFDPHFMAVRKAIDDGRIGEVEMVTITSRDPSAPPVDYIKR-------SGG 166 ++ V FN RF P +++ ++ G IG V V + DY +R SG Sbjct: 123 RRVDVSFNYRFAPTAARIKELLNAGEIGRVTSVDFHWYLDTRHGADYFRRWHAYAEHSGS 182 Query: 167 IFRDMTIHDFDMARFLLGEEPVSVTATA 194 +F H FD+ + L +P +V+A A Sbjct: 183 LFVHKATHHFDLLNWYLDSDPEAVSAFA 210 Lambda K H 0.320 0.134 0.379 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: 281 Number of extensions: 11 Number of successful extensions: 1 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: 330 Length of database: 433 Length adjustment: 30 Effective length of query: 300 Effective length of database: 403 Effective search space: 120900 Effective search space used: 120900 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: 50 (23.9 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