Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate RR42_RS33330 RR42_RS33330 hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Cup4G11:RR42_RS33330 Length = 312 Score = 183 bits (465), Expect = 4e-51 Identities = 120/295 (40%), Positives = 165/295 (55%), Gaps = 10/295 (3%) Query: 10 LPEDVLAYLQQHAQVVQVDA-TQHDAFVAALKDADGGIGS--SVKITPAMLEGATRLKAL 66 LP + A L +H V + A T AF+A+ + + ++ + AM+ LK + Sbjct: 11 LPAALEASLAEHYDVHPLWAETDPAAFLASHGGEFAALTTRAAIGVDAAMIAAMPNLKVI 70 Query: 67 STISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHW 126 S+ VG D+ D+ RGI + TPDVL + ADT F L++ AR +V+ G W Sbjct: 71 SSFGVGLDKIDLDAARARGIAVGYTPDVLNDCVADTAFGLLMDVARGFSAADRFVRRGEW 130 Query: 127 QHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGAR 186 + P V GK +GIVG+GRIG +ARR +GF+M+V Y +R A++A Sbjct: 131 PKAQFP--LATRVSGKRMGIVGMGRIGRVIARRG-VGFDMEVRYHSRRP---AQDAPYRH 184 Query: 187 RVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEAL 246 L+EL ADF+ + PET+HL+ A L+++ + LIN +RG VDE AL++AL Sbjct: 185 EPSLSELARWADFLVIATAGGPETRHLVSAEVLEALGPNGFLINIARGTVVDETALVDAL 244 Query: 247 QNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENL 301 G I GAGLDVFE EP + L L NVV LPHI SATHETR+AMA ENL Sbjct: 245 VQGRIAGAGLDVFENEPQVPQA-LFALDNVVLLPHIASATHETRNAMADLVFENL 298 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: 216 Number of extensions: 13 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: 321 Length of database: 312 Length adjustment: 27 Effective length of query: 294 Effective length of database: 285 Effective search space: 83790 Effective search space used: 83790 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