Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF2783 PGA1_c28260 glyoxylate reductase GyaR
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Phaeo:GFF2783 Length = 328 Score = 177 bits (450), Expect = 2e-49 Identities = 124/311 (39%), Positives = 168/311 (54%), Gaps = 9/311 (2%) Query: 4 IVAWKSLPEDVLAYLQQHAQV-VQVDAT--QHDAFVAALKDADGGIGSSVKITPAMLEGA 60 +V + LPE V L + V ++ D T ALKDAD + + A L G Sbjct: 8 VVVTRRLPEPVETRLSELFDVRLREDDTPMSRAELATALKDADVLVPTVTDEIDAGLLGQ 67 Query: 61 T--RLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118 RLK ++ G D DVA +RGI+++NTP VLT+ TAD +LI+A RR+ E Sbjct: 68 AGDRLKLIANYGAGVDHIDVATARQRGILVSNTPGVLTDDTADMAMALIMAVVRRIPEGL 127 Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTN-RSANP 177 ++ G WQ AL G + G+ LGI+G+G IG AVA+RAA F M+V Y N R P Sbjct: 128 AVMQKGDWQGWSPTALLGGRLAGRRLGILGMGSIGQAVAKRAA-AFGMQVHYHNRRRLRP 186 Query: 178 QAEEAYGARRVE-LAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGAT 236 + E+ + A E L +++A D + + P TP T HL+ A LK MK A+++N SRG Sbjct: 187 EIEQRFEATYWESLDQMVARMDVLSINCPSTPSTFHLMNARRLKLMKPDAVIVNTSRGEV 246 Query: 237 VDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARN 296 +DE AL L+ I GAGLDV+E + L +L NVV LPH+GSAT E R M Sbjct: 247 IDEHALTRMLRASEIAGAGLDVYE-HGTDINPRLRELENVVLLPHMGSATLEGRLEMGEK 305 Query: 297 AAENLVAALDG 307 N+ DG Sbjct: 306 VLLNIKTFEDG 316 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: 241 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: 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