Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate 6937211 Sama_1381 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__SB2B:6937211 Length = 252 Score = 129 bits (325), Expect = 5e-35 Identities = 89/272 (32%), Positives = 138/272 (50%), Gaps = 36/272 (13%) Query: 5 LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHG----------GDKHQSSGNYN 54 + LK+K+I +TGGA G+GLA+ +L A GA + +ID+ GD + G Sbjct: 1 MELKDKVIVITGGAGGLGLAMAKDLAAHGAKLALIDVDQERLERACADIGDATEVQG--- 57 Query: 55 FWPTDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEK 114 + DI+ +V +I++ FG I GLVNNAG+ LL+ K ++ F+ Sbjct: 58 -YALDITDEEDVVAGFRYILEDFGVIHGLVNNAGILRDGLLIKAKDGVVTDRMSLDQFQS 116 Query: 115 MVNINQKGVFLMSQAVARQMVKQ-RSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRS 173 ++N+N G FL + A M++ + GVIVN+SS + G+ GQ+ YAA+KA + + Sbjct: 117 VINVNLTGTFLCGREAAAAMIESGQGGVIVNISSLARA-GNMGQTNYAASKAGVATMAVG 175 Query: 174 WSKELGKHGIRVVGVAPGIL--EKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGR 231 W+KEL + IR VAPG++ E T PE E L + +P+GR Sbjct: 176 WAKELARFNIRAAAVAPGVIATEMTAAMKPEALERL----------------EKMVPVGR 219 Query: 232 SGRLTEVADFVCYLLSERASYMTGVTTNIAGG 263 G+ E+A V +++ Y+ G I GG Sbjct: 220 LGQAEEIASTVRFIMEN--DYVNGRVFEIDGG 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: 178 Number of extensions: 11 Number of successful extensions: 5 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: 252 Length adjustment: 24 Effective length of query: 243 Effective length of database: 228 Effective search space: 55404 Effective search space used: 55404 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