Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 5209856 Shew_2309 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__PV4:5209856 Length = 376 Score = 102 bits (254), Expect = 1e-26 Identities = 92/292 (31%), Positives = 136/292 (46%), Gaps = 37/292 (12%) Query: 3 KIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSV-KITPAMLEGAT 61 KIVA +++P V A +VV VD A +KDAD + SV K+ ++L+G Sbjct: 2 KIVADENMPY-VEALFADLGEVVMVDG--RTLTQAQVKDADVLLVRSVTKVNKSLLDGCD 58 Query: 62 RLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWV 121 RL + + ++G D D+ L +RGI N P + + F+ +L ARR Sbjct: 59 RLSFVGSATIGMDHLDLDYLKQRGIFCTNAPGCNAVAVGEYAFNAMLELARR-------- 110 Query: 122 KAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEE 181 F ++GKT+GIVG G G A+ ++ + +K L +P E+ Sbjct: 111 -------------FHNPLKGKTVGIVGAGNTGTAL-QKCLEAYGVKTLLN----DPLLEQ 152 Query: 182 AYGARR-VELAELLATADFVCLQVPLTPETKH----LIGAAELKSMKKSAILINASRGAT 236 + R V L EL+ D + L VPLT + +H L L ++ + L+N RG Sbjct: 153 SGDEREFVSLDELIERCDVISLHVPLTRDGEHPTHYLFDKRRLNALAEDTWLLNCCRGEV 212 Query: 237 VDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHE 288 +D +ALIE Q + LDV+E EPLP P L VA PHI + E Sbjct: 213 IDNRALIEVKQQRSDLKLVLDVWEGEPLP--MPELVPLVEVATPHIAGYSLE 262 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: 232 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: 376 Length adjustment: 29 Effective length of query: 292 Effective length of database: 347 Effective search space: 101324 Effective search space used: 101324 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