Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF427 Psest_0431 Lactate dehydrogenase and related dehydrogenases
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__psRCH2:GFF427 Length = 336 Score = 160 bits (404), Expect = 5e-44 Identities = 107/328 (32%), Positives = 167/328 (50%), Gaps = 14/328 (4%) Query: 1 MKKIVAWKSLPEDVLAYLQQHAQVV--QVDAT-QHDAFVAALKDADGGIGSSV-KITPAM 56 + K+V + +++L L H +++ Q D+T + + +DA + ++ Sbjct: 2 LPKLVITHRVHDEILQLLAPHCELMTNQTDSTLPREEILRRCRDAQAMMAFMPDRVDADF 61 Query: 57 LEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVE 116 L+ L+ + GFD FDV T RG+ L PD+LT TA+ L + R + Sbjct: 62 LQACPELRVVGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRA 121 Query: 117 LAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSA- 175 +V++G +Q P +G + T+GI+G+G IG A+A R G+ + Y A Sbjct: 122 ADAFVRSGKFQ-GWQPQFYGTGLDNATVGILGMGAIGLAMADRLQ-GWGATLQYHEAKAL 179 Query: 176 NPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGA 235 + Q E+ G RRV +EL A++DF+ L +PL +T+HL+ A L ++ A+L+N RG+ Sbjct: 180 DTQTEQRLGLRRVACSELFASSDFILLALPLNADTQHLVNAELLALVRPGALLVNPCRGS 239 Query: 236 TVDEKALIEALQNGTIHGAGLDVFETE-------PLPSDSPLLKLANVVALPHIGSATHE 288 VDE A++ AL+ G + G DVFE E P D LL N + PHIGSA Sbjct: 240 VVDEAAVLAALERGQLGGYAADVFEMEDWARADRPRLIDPALLAHPNTLFTPHIGSAVRA 299 Query: 289 TRHAMARNAAENLVAALDGTLTSNIVNR 316 R + R AA+N++ AL G N NR Sbjct: 300 VRLEIERCAAQNIIQALAGARPINAANR 327 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: 226 Number of extensions: 8 Number of successful extensions: 3 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: 336 Length adjustment: 28 Effective length of query: 293 Effective length of database: 308 Effective search space: 90244 Effective search space used: 90244 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