Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 3609586 Dshi_2970 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Dino:3609586 Length = 328 Score = 180 bits (456), Expect = 5e-50 Identities = 126/318 (39%), Positives = 171/318 (53%), Gaps = 9/318 (2%) Query: 4 IVAWKSLPEDVLAYLQQHAQVVQVDAT---QHDAFVAALKDADGGIGS-SVKITPAMLEG 59 +V + LPE V L++ V ++ DA AA++ AD + + S I AML G Sbjct: 8 VVVTRRLPEAVETRLKELFDVELNESDTPMSRDALQAAMRRADVLVPTVSDHIDGAMLAG 67 Query: 60 A-TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118 RLK ++ G D DVA +RGI ++NTP VLT+ TAD +LILA RR+ E Sbjct: 68 VGDRLKLIANYGAGVDHIDVATARQRGIHVSNTPGVLTDDTADMTLALILAVTRRIPEGL 127 Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178 ++ G W AL G + G+ LGI+G+GRIG AVARRA F M++ Y NR + Sbjct: 128 ALMQTGAWTGWSPTALMGGRIAGRRLGILGMGRIGQAVARRAK-AFGMQIHYHNRRRLHK 186 Query: 179 A--EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGAT 236 EE L ++++ D + + P TP T HL+ A LK MK SA+++N SRG Sbjct: 187 GIEEELEATWWESLDQMVSRMDVISVNCPHTPSTFHLMNARRLKLMKPSAVIVNTSRGEV 246 Query: 237 VDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARN 296 +DE AL L+ G I GAGLDVFE + L +L NVV LPH+GSAT E R M Sbjct: 247 IDENALTRMLRAGDIAGAGLDVFE-HGHEVNPRLRELPNVVLLPHMGSATEEGRAEMGEK 305 Query: 297 AAENLVAALDGTLTSNIV 314 N+ DG ++V Sbjct: 306 VIINIKTFDDGHRPPDLV 323 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: 234 Number of extensions: 11 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: 328 Length adjustment: 28 Effective length of query: 293 Effective length of database: 300 Effective search space: 87900 Effective search space used: 87900 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