Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate RR42_RS14190 RR42_RS14190 2-hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Cup4G11:RR42_RS14190 Length = 332 Score = 230 bits (586), Expect = 4e-65 Identities = 142/312 (45%), Positives = 190/312 (60%), Gaps = 14/312 (4%) Query: 22 AQVVQVDATQHDAFV--AALKDADGG-----IGSSVKITPAMLEGATRLKALSTISVGFD 74 AQ VD Q D + AALK G ++ +I ++ G L+A+ ++VG++ Sbjct: 21 AQYFDVDDNQPDVALDGAALKARLAGKAGVLANAADRIDAGLVAGLPALRAVCNMAVGYN 80 Query: 75 QFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPAL 134 DV LT GIV NTPDVLTE+TAD ++L++A+ARRV E W++AG W+ Sbjct: 81 NLDVPALTAAGIVATNTPDVLTETTADFGWALLMATARRVTESEHWLRAGKWERWSYDMF 140 Query: 135 FGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ-AEEAYGARRVELAEL 193 G+D+ TLGI+G+GRIG A+ARRAA GF M VLY NRS P+ E AR V AEL Sbjct: 141 LGMDLYRSTLGILGMGRIGQALARRAA-GFGMSVLYHNRSRLPEDTERVLNARYVSKAEL 199 Query: 194 LATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHG 253 LA +D + L +P + ++ H IGAAEL MK SA L+N +RG VD+ AL AL+ G I Sbjct: 200 LAQSDHLLLVLPYSAQSHHSIGAAELAQMKPSATLVNLARGGVVDDAALARALREGRIFA 259 Query: 254 AGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAAL----DGTL 309 AGLDVFE EP LL + NVV PHI SA+ +TR AMA AA+NL+AAL Sbjct: 260 AGLDVFEAEP-QVHPDLLTVPNVVLTPHIASASEKTRRAMADLAADNLIAALGVGPQAGQ 318 Query: 310 TSNIVNREVLSK 321 +++N EV+++ Sbjct: 319 PPSVINPEVMAR 330 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: 252 Number of extensions: 11 Number of successful extensions: 4 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: 332 Length adjustment: 28 Effective length of query: 293 Effective length of database: 304 Effective search space: 89072 Effective search space used: 89072 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