Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_092482325.1 BM299_RS04760 hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_900115975.1:WP_092482325.1 Length = 330 Score = 167 bits (422), Expect = 4e-46 Identities = 107/325 (32%), Positives = 169/325 (52%), Gaps = 8/325 (2%) Query: 2 KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGAT 61 KK++ +++ E+ + +++ A++ + + A+ DAD I S K+T A++E Sbjct: 3 KKVLLTEAIHEEGMNIIREAAELEIAADPGEETVIKAIADADALIVRSSKVTSAIIEAGK 62 Query: 62 RLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWV 121 +LK + +G D D+ + G+ + NTPD S A+ V + +L +R+ E+ + Sbjct: 63 KLKVIGRHGMGLDNIDLKAADQYGVAVVNTPDANVLSVAEHVLATMLYLCKRLKEVDNAL 122 Query: 122 KAGHWQHSIG-PAL---FGVDVQ---GKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS 174 + G + P L G Q GKTLG+VG+G+I +A GF+M+V + Sbjct: 123 RTGEFDRPGSLPGLVTKLGYTTQELYGKTLGLVGVGKIARRIAEICTKGFDMQVCGYDAY 182 Query: 175 ANPQAEEAYGARRV-ELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASR 233 P + G L E+ ADF+ + VPLTP T+ LIG +L MK +A LIN++R Sbjct: 183 LAPDVIQQAGVEPCGSLEEVFEKADFISVHVPLTPGTRGLIGKKQLDLMKPTAFLINSAR 242 Query: 234 GATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAM 293 G V+E L +AL+ +I GA +DVF EP + PL L NVV PHI + T M Sbjct: 243 GGVVNEDDLYQALKEKSIAGAAVDVFAQEPPGKNHPLFTLDNVVVTPHIAAMTDGALVRM 302 Query: 294 ARNAAENLVAALDGTLTSNIVNREV 318 AR+ AE +V+ L G +VN + Sbjct: 303 ARDVAEGVVSVLRGERPKYLVNPRI 327 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: 234 Number of extensions: 16 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: 330 Length adjustment: 28 Effective length of query: 293 Effective length of database: 302 Effective search space: 88486 Effective search space used: 88486 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 Apr 09 2024. 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