Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate SMa2137 SMa2137 dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Smeli:SMa2137 Length = 324 Score = 194 bits (493), Expect = 2e-54 Identities = 124/272 (45%), Positives = 157/272 (57%), Gaps = 3/272 (1%) Query: 37 AALKDADGGIGSSV-KITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVL 95 AAL++AD + + KI+ MLEG R K L VGF+ D A T+ G+V+ NTP VL Sbjct: 47 AALEEADAVLPTVTDKISADMLEGGIRAKILGNFGVGFNHIDTAAATKVGLVVTNTPGVL 106 Query: 96 TESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGA 155 T++TAD +L+L ARR E ++AG W L G V GKT+GI+G+GRIG A Sbjct: 107 TDATADLAMTLLLMCARRAGEGERELRAGKWTGWRPTHLCGSHVTGKTVGIIGMGRIGQA 166 Query: 156 VARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIG 215 VARR GF M V++ + S + + + + ++LATADFV L P E HLI Sbjct: 167 VARRCHFGFGMDVVFFD-SHSIAGLDVPARQLPSVDDVLATADFVSLHCPGGGENYHLID 225 Query: 216 AAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLAN 275 L MK SA LIN +RG VDE AL+ AL+ I GAGLDVFE EP L + + Sbjct: 226 DDRLACMKWSAFLINTARGDVVDEHALVRALETRRIAGAGLDVFEGEP-RVPGRLAERQD 284 Query: 276 VVALPHIGSATHETRHAMARNAAENLVAALDG 307 VV LPH+GSAT ETR AM ENL A G Sbjct: 285 VVLLPHLGSATKETRVAMGMRVIENLKAFFSG 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: 215 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: 324 Length adjustment: 28 Effective length of query: 293 Effective length of database: 296 Effective search space: 86728 Effective search space used: 86728 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