Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate H281DRAFT_06500 H281DRAFT_06500 Lactate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Burk376:H281DRAFT_06500 Length = 308 Score = 174 bits (441), Expect = 2e-48 Identities = 105/261 (40%), Positives = 146/261 (55%), Gaps = 8/261 (3%) Query: 48 SSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLI 107 SS ++ ++L LK ++T VGFD + RG+++ NTP VL + + L+ Sbjct: 49 SSYQVPASLLASLPNLKIIATSGVGFDGIPLDAARSRGVIVTNTPGVLDAAVCELAIGLL 108 Query: 108 LASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMK 167 L+ RR+ +V+ W H + P + GK +GIVGLGRIG +ARR A GF+++ Sbjct: 109 LSLLRRIPSADRFVRDEAWAHELFPLTSSL--AGKRIGIVGLGRIGQGIARRLA-GFDVE 165 Query: 168 VLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAI 227 + Y + E A ++ EL + AD + + P T+HLI A L ++ S Sbjct: 166 IAY----CGSKVEGLPYAMISDVRELASFADILIVCCPGGDRTRHLIDGAVLSALGSSGF 221 Query: 228 LINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATH 287 L+N SRG VDE ALI+AL+ G I GA LDVFE EPL S L L+NVV PH GSAT Sbjct: 222 LVNVSRGTVVDEAALIDALEKGLIRGAALDVFEKEPL-IGSRLATLSNVVLTPHAGSATE 280 Query: 288 ETRHAMARNAAENLVAALDGT 308 ETRH M R A +N+ LDG+ Sbjct: 281 ETRHTMLRLALDNIHRVLDGS 301 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: 224 Number of extensions: 12 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: 308 Length adjustment: 27 Effective length of query: 294 Effective length of database: 281 Effective search space: 82614 Effective search space used: 82614 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