Align Inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate Pf1N1B4_4280 Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
Query= reanno::pseudo3_N2E3:AO353_21365 (336 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4280 Length = 341 Score = 653 bits (1685), Expect = 0.0 Identities = 324/335 (96%), Positives = 330/335 (98%) Query: 2 SLKLGVIGTGAIGQDHIRRCSQTLLNSQVVAVTDINLQQAAKVVADLKLTAEVYPDGHAL 61 SL++GVIGTGAIGQDHIRRCSQTLLNSQVVAVTDINLQQAAKVV+DLKLTAEVYPDGHAL Sbjct: 7 SLRIGVIGTGAIGQDHIRRCSQTLLNSQVVAVTDINLQQAAKVVSDLKLTAEVYPDGHAL 66 Query: 62 IKAPDVEAILVTSWGPSHEEFVLAAIAAGKPVFCEKPLAVTAEGCRKIVEAEVAHGKRLV 121 IKAP+V+AILVTSWGPSHEEFVLAAIAAGKPVFCEKPLAVTAEGCRKIVEAEVAHGKRLV Sbjct: 67 IKAPEVDAILVTSWGPSHEEFVLAAIAAGKPVFCEKPLAVTAEGCRKIVEAEVAHGKRLV 126 Query: 122 QVGFMRPYDEGYRALKAVIDSGQIGEPLMLHCAHRNPTVGENYKTDMAITDTLIHELDVL 181 QVGFMRPYDEGYRALKAVIDSGQIGEPLMLHCAHRNPTVGENYKTDMAITDTLIHELDVL Sbjct: 127 QVGFMRPYDEGYRALKAVIDSGQIGEPLMLHCAHRNPTVGENYKTDMAITDTLIHELDVL 186 Query: 182 RWLLDDDYVSVQVVFPRKTSKAHAHLKDPQIVLLETAKGTRIDVEVFVNCQYGYDIQCEV 241 RWLLDDDYVSVQVVFPRKTSKAHAHLKDPQIVLLETAKGTRIDVEVFVNCQYGYDIQCEV Sbjct: 187 RWLLDDDYVSVQVVFPRKTSKAHAHLKDPQIVLLETAKGTRIDVEVFVNCQYGYDIQCEV 246 Query: 242 VGETGIAKLPEPSQVQMRSGAKLSNAILMDWKDRFIAAYDVELQAFIDGVRAGQVGGPSA 301 VGETGIAKLPEPSQVQ+RSGAKLSNAILMDWKDRFIAAYDVELQAFIDGVRAGQVGGPSA Sbjct: 247 VGETGIAKLPEPSQVQLRSGAKLSNAILMDWKDRFIAAYDVELQAFIDGVRAGQVGGPSA 306 Query: 302 WDGFAAAVAADACIEAQQSGAIVNVALPDRPRFYG 336 WDGFAAAVAADACIEAQ SG IV V LPDRP FYG Sbjct: 307 WDGFAAAVAADACIEAQSSGQIVKVGLPDRPHFYG 341 Lambda K H 0.320 0.136 0.405 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: 518 Number of extensions: 10 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: 336 Length of database: 341 Length adjustment: 28 Effective length of query: 308 Effective length of database: 313 Effective search space: 96404 Effective search space used: 96404 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