Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Pf1N1B4_4763 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43)
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4763 Length = 341 Score = 311 bits (798), Expect = 1e-89 Identities = 167/317 (52%), Positives = 220/317 (69%), Gaps = 3/317 (0%) Query: 2 KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVA---ALKDADGGIGSSVKITPAMLE 58 K++V +K L ++A L + +V +D+ + AL A G +G+S+K+ +L+ Sbjct: 3 KQVVLYKKLSPLLMARLHEQTEVTLIDSLDAEGLAQLRRALPRAQGLLGASLKLDAGLLD 62 Query: 59 GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118 A L+A++++SVG D +D+ LT R I+L+NTPDVLTE+TADT F+LILA+ARRVVELA Sbjct: 63 LAPNLEAIASVSVGVDNYDIDYLTERRILLSNTPDVLTETTADTGFALILATARRVVELA 122 Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178 V+AG W +IGP FG DV GKTLGI+G+GRIG A+A+R GF M V+Y + S P Sbjct: 123 NMVRAGQWNRNIGPTHFGSDVHGKTLGIIGMGRIGEALAQRGHFGFGMPVVYHSHSPKPA 182 Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238 E+ + A+ L++LL ADFVCL +PLT T+ LIGA + M+ I IN SRG VD Sbjct: 183 VEQRFNAQYRSLSDLLQQADFVCLTLPLTAATEGLIGAEQFALMRPETIFINISRGKVVD 242 Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298 E ALIEAL++ I AGLDVFE EPL +DSPLL+L NVVA PHIGSATHETR AMAR A Sbjct: 243 EPALIEALRHKRIRAAGLDVFEREPLGNDSPLLQLNNVVATPHIGSATHETREAMARCAV 302 Query: 299 ENLVAALDGTLTSNIVN 315 +NL+AAL G +N+VN Sbjct: 303 DNLLAALAGERPANLVN 319 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: 252 Number of extensions: 3 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: 321 Length of database: 341 Length adjustment: 28 Effective length of query: 293 Effective length of database: 313 Effective search space: 91709 Effective search space used: 91709 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: 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