Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF377 Psest_0378 Lactate dehydrogenase and related dehydrogenases
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__psRCH2:GFF377 Length = 309 Score = 162 bits (410), Expect = 1e-44 Identities = 105/255 (41%), Positives = 138/255 (54%), Gaps = 7/255 (2%) Query: 47 GSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSL 106 GS + ++ LKA+ + VG+D DV RGI ++NTP+VL + AD L Sbjct: 49 GSRFGCSAELMARLPALKAIVSFGVGYDPIDVPAAQARGIAISNTPEVLNDCVADLAMGL 108 Query: 107 ILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNM 166 I+ R++ +V+AG W P V G LGI+GLGRIG AVA+RA GF+M Sbjct: 109 IIDGRRQLSRADRFVRAGGWPSGNLP--LARRVTGSRLGILGLGRIGHAVAKRAE-GFSM 165 Query: 167 KVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSA 226 V Y NR Y VELA AD + L P+T+ L+ L ++ Sbjct: 166 PVRYHNRRPLADCPYEYAGSLVELARW---ADVLLLTCVGGPQTRGLVSREVLDALGPDG 222 Query: 227 ILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSAT 286 +L+N +RG+ VDE AL+EALQ G + GA LDVF EP ++ LL + NVV LPHIGSAT Sbjct: 223 LLVNVARGSVVDEPALVEALQAGRLGGAALDVFAEEPQAPEA-LLGMDNVVLLPHIGSAT 281 Query: 287 HETRHAMARNAAENL 301 ETR AM NL Sbjct: 282 RETRGAMEDLVLANL 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: 215 Number of extensions: 17 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 321 Length of database: 309 Length adjustment: 27 Effective length of query: 294 Effective length of database: 282 Effective search space: 82908 Effective search space used: 82908 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