Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 17613 b3553 putative dehydrogenase (VIMSS)
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Keio:17613 Length = 324 Score = 327 bits (837), Expect = 3e-94 Identities = 177/320 (55%), Positives = 223/320 (69%), Gaps = 7/320 (2%) Query: 4 IVAWKSLPEDVLAYLQQHAQVVQV-----DATQHDAFVAALKDADGGIGSSVKITPAMLE 58 ++ +K+LP+D+L LQ+H V QV + +A + A +A+G +GS+ + A+LE Sbjct: 5 VILYKALPDDLLQRLQEHFTVHQVANLSPQTVEQNAAIFA--EAEGLLGSNENVNAALLE 62 Query: 59 GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118 +L+A STISVG+D FDV LT R I+L +TP VLTE+ ADT+ +L+L++ARRVVE+A Sbjct: 63 KMPKLRATSTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARRVVEVA 122 Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178 E VKAG W SIGP +G DV KTLGIVG+GRIG A+A+RA GFNM +LY R + + Sbjct: 123 ERVKAGEWTASIGPDWYGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNARRHHKE 182 Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238 AEE + AR +L LL +DFVCL +PLT ET HL GA + MK SAI INA RG VD Sbjct: 183 AEERFNARYCDLDTLLQESDFVCLILPLTDETHHLFGAEQFAKMKSSAIFINAGRGPVVD 242 Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298 E ALI ALQ G IH AGLDVFE EPL DSPLL +ANVVA+PHIGSATHETR+ MA A Sbjct: 243 ENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSMANVVAVPHIGSATHETRYGMAACAV 302 Query: 299 ENLVAALDGTLTSNIVNREV 318 +NL+ AL G + N VN V Sbjct: 303 DNLIDALQGKVEKNCVNPHV 322 Lambda K H 0.317 0.131 0.366 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: 238 Number of extensions: 4 Number of successful extensions: 2 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: 321 Length of database: 324 Length adjustment: 28 Effective length of query: 293 Effective length of database: 296 Effective search space: 86728 Effective search space used: 86728 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: 41 (21.7 bits) S2: 48 (23.1 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