Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__SynE:Synpcc7942_1501 Length = 546 Score = 172 bits (436), Expect = 2e-47 Identities = 109/317 (34%), Positives = 169/317 (53%), Gaps = 6/317 (1%) Query: 1 MKKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEG 59 M K++ + + L L Q AQV + + D + S ++T ++E Sbjct: 18 MPKVLVSDPIDQVGLDILSQVAQVDVKTGLSPSELAQIIGEYDALMLRSGTRVTAEVIEA 77 Query: 60 ATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE 119 +L+ + VG D DV TRRGIV+ N+P+ T + A+ +++L+ +R + + Sbjct: 78 GQKLRIIGRAGVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDANA 137 Query: 120 WVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQA 179 K+G W + G +V KTLG+VGLG+IG VA A MK+L + + + Sbjct: 138 STKSGGWDRK---SFVGTEVYKKTLGVVGLGKIGSHVAT-VAKAMGMKLLAYDPFISAER 193 Query: 180 EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDE 239 E GAR VEL L AD++ L +P TPET +LI A L MK + +IN +RG ++E Sbjct: 194 AEQIGARLVELDILFQEADYITLHIPKTPETANLINAETLAKMKPTTRIINCARGGVINE 253 Query: 240 KALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLA-NVVALPHIGSATHETRHAMARNAA 298 +AL +A+ G I GA LDV++ EPL +DSPL L N++ PH+G++T E + +A + A Sbjct: 254 QALADAIAAGKIGGAALDVYDQEPLQADSPLRALGKNLILTPHLGASTTEAQVNVAVDVA 313 Query: 299 ENLVAALDGTLTSNIVN 315 E + L G + VN Sbjct: 314 EQIRDVLLGLPARSAVN 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: 338 Number of extensions: 18 Number of successful extensions: 2 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: 546 Length adjustment: 32 Effective length of query: 289 Effective length of database: 514 Effective search space: 148546 Effective search space used: 148546 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: 50 (23.9 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