Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Ga0059261_1479 Ga0059261_1479 Lactate dehydrogenase and related dehydrogenases
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Korea:Ga0059261_1479 Length = 332 Score = 176 bits (447), Expect = 5e-49 Identities = 113/284 (39%), Positives = 155/284 (54%), Gaps = 6/284 (2%) Query: 28 DATQHDAFVAALKDADGGIGSSVKITPAMLEGAT--RLKALSTISVGFDQFDVADLTRRG 85 +A A +AA+ D D + + A L A RLK ++ G + D+ RG Sbjct: 39 EAMDRAALLAAVADCDVLVPTVTDTIDADLIAAAGERLKLIANFGSGVNHIDLKAARARG 98 Query: 86 IVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLG 145 IV+ NTP VLTE TAD +LI++ RR+ E + V++G W+ + G + GK LG Sbjct: 99 IVVTNTPGVLTEDTADMTMALIVSVPRRLAEGEKLVRSGQWKGWSPGGMLGHRIGGKKLG 158 Query: 146 IVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAY--GARRVELAELLATADFVCLQ 203 IVG+GRIG AVARRA F + + Y NR P+ EA A +L +L D + + Sbjct: 159 IVGMGRIGQAVARRAR-AFGLSIHYHNRHRLPEVVEAELGAAWHGDLDAMLREIDILTIH 217 Query: 204 VPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEP 263 PL E++ LI A + + LINASRG VDE+A+++AL+ G + GAGLDV+ EP Sbjct: 218 TPLNEESRDLIDARRIGLLGPQVYLINASRGGIVDEEAMVDALEAGRLAGAGLDVWRFEP 277 Query: 264 LPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307 D LL L NVV PH+GSAT+E RHA N+ DG Sbjct: 278 -QIDPRLLALPNVVMTPHMGSATYEGRHATGEKVIANIRFWADG 320 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: 241 Number of extensions: 10 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: 332 Length adjustment: 28 Effective length of query: 293 Effective length of database: 304 Effective search space: 89072 Effective search space used: 89072 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