Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate SMc00572 SMc00572 3-ketoacyl-ACP reductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Smeli:SMc00572 Length = 245 Score = 110 bits (276), Expect = 2e-29 Identities = 80/257 (31%), Positives = 132/257 (51%), Gaps = 33/257 (12%) Query: 14 VTGGASGIGLAIVDELLAQGANVQMIDIHGG--DKHQSSGN-----YNFWPTDISSASEV 66 VTG + GIG I L AQGA ++ +HG +K ++ N +P ++S +EV Sbjct: 11 VTGASGGIGEEIARMLHAQGA---VVGLHGTRVEKLETLANTLGERVQIFPANLSDRAEV 67 Query: 67 HKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKGVFLM 126 + G +D LVNNAG+ L V +++ ++ ++ +N VF + Sbjct: 68 KALGEKAEADLGGVDILVNNAGITKDGLFV---------RMSDEDWDNVIEVNLTAVFRL 118 Query: 127 SQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHGIRVV 186 ++ + M+++R G IVN++S G+ G+ GQ+ Y A+KA + F++S ++E+ + V Sbjct: 119 TRELTHPMMRRRFGRIVNITSVVGVTGNPGQANYCASKAGMIGFSKSLAQEIATRNVTVN 178 Query: 187 GVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFVCYLL 246 VAPG +E A T + +Q +EG ++IP+ R G EVA V YL Sbjct: 179 CVAPGFIES------------AMTGKLNDKQ-KEGI-MSAIPMRRMGSGAEVASAVAYLA 224 Query: 247 SERASYMTGVTTNIAGG 263 S A Y+TG T ++ GG Sbjct: 225 SNEAGYVTGQTIHVNGG 241 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: 159 Number of extensions: 10 Number of successful extensions: 4 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: 245 Length adjustment: 24 Effective length of query: 243 Effective length of database: 221 Effective search space: 53703 Effective search space used: 53703 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