Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate BWI76_RS27925 BWI76_RS27925 D-isomer specific 2-hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Koxy:BWI76_RS27925 Length = 314 Score = 169 bits (429), Expect = 6e-47 Identities = 109/300 (36%), Positives = 167/300 (55%), Gaps = 8/300 (2%) Query: 3 KIVAWKSLPEDVLAYLQQHAQVVQVDA-TQHDAFVAALKDADGGIGSSVKITPAMLEGAT 61 KI+ SLP+ + A L +V + +A T+ + V A + +T ++ Sbjct: 4 KILKQASLPDQLTAELNSLYEVYEYEALTREELAVLAEQFTIMITNGEATVTRQLISSLP 63 Query: 62 RLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWV 121 L+ ++ VG+D DV + +++TP VLT+ AD L+LA++R++V +++ Sbjct: 64 SLELIAVFGVGYDGVDVRAAADHRVAVSHTPGVLTDDVADLAMGLMLATSRQIVSAQKFI 123 Query: 122 KAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEE 181 +AG W+ G + V G +GIVG+GRIG A+ARR GF M++ Y++R A P + Sbjct: 124 EAGGWRQ--GGFQWTRKVSGSRVGIVGMGRIGQAIARRCE-GFAMQIAYSDRKAIPGLDY 180 Query: 182 AYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKA 241 + +++ L + DF+ + P + E + LI L ++ S ILIN SRG+ VDE A Sbjct: 181 PWIE---DISTLASQTDFLVICTPGSAENQALIDERVLSALGASGILINISRGSVVDEFA 237 Query: 242 LIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENL 301 LI+AL+ G I GAGLDVF EP LL+ ANVV PH+ SAT TR AM+R EN+ Sbjct: 238 LIKALEQGIIAGAGLDVFSQEP-EVPQALLRRANVVVTPHMASATWSTREAMSRLVLENV 296 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: 15 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: 314 Length adjustment: 27 Effective length of query: 294 Effective length of database: 287 Effective search space: 84378 Effective search space used: 84378 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