Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate 18291 b4266 gluconate 5-dehydrogenase (NCBI)
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Keio:18291 Length = 254 Score = 104 bits (259), Expect = 2e-27 Identities = 80/271 (29%), Positives = 121/271 (44%), Gaps = 30/271 (11%) Query: 1 MNTWLNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDK-------HQSSGNY 53 MN +L K I +TG A GIG + L GA + + DI HQ Sbjct: 1 MNDLFSLAGKNILITGSAQGIGFLLATGLGKYGAQIIINDITAERAELAVEKLHQEGIQA 60 Query: 54 NFWPTDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFE 113 P +++ E+ V+HI + G ID LVNNAG+ E E + Sbjct: 61 VAAPFNVTHKHEIDAAVEHIEKDIGPIDVLVNNAGIQRRHPFT---------EFPEQEWN 111 Query: 114 KMVNINQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRS 173 ++ +NQ VFL+SQAV R MV++++G ++N+ S G + + YAA+K A+ TR Sbjct: 112 DVIAVNQTAVFLVSQAVTRHMVERKAGKVINICSMQSELGRDTITPYAASKGAVKMLTRG 171 Query: 174 WSKELGKHGIRVVGVAPGILEKTGLRTPEYEEAL-AWTRNITVEQLREGYSKNSIPLGRS 232 EL +H I+V G+APG + + +EA AW T P R Sbjct: 172 MCVELARHNIQVNGIAPGYFKTEMTKALVEDEAFTAWLCKRT-------------PAARW 218 Query: 233 GRLTEVADFVCYLLSERASYMTGVTTNIAGG 263 G E+ +L S+ + ++ G + GG Sbjct: 219 GDPQELIGAAVFLSSKASDFVNGHLLFVDGG 249 Lambda K H 0.315 0.132 0.378 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: 146 Number of extensions: 4 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: 267 Length of database: 254 Length adjustment: 24 Effective length of query: 243 Effective length of database: 230 Effective search space: 55890 Effective search space used: 55890 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: 42 (22.0 bits) S2: 47 (22.7 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