Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 5210768 Shew_3196 D-3-phosphoglycerate dehydrogenase (RefSeq)
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__PV4:5210768 Length = 409 Score = 146 bits (369), Expect = 7e-40 Identities = 100/288 (34%), Positives = 150/288 (52%), Gaps = 11/288 (3%) Query: 33 DAFVAALKDADG-GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANT 91 + +A++KDA GI S ++T A+L+ A +L ++ +G +Q D+A + GI + N Sbjct: 45 EELLASIKDAHFVGIRSRTQLTKAVLDKAEKLVSIGCFCIGTNQVDLAAAEKLGIPVFNA 104 Query: 92 PDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGR 151 P T S A+ V I+ R + + G W S + + +GKTLG++G G Sbjct: 105 PFSNTRSVAELVLGEIIMLLRGIPQRNALAHRGGWLKSANGSF---EARGKTLGVIGYGH 161 Query: 152 IGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETK 211 IG + A M+V++ + A +E +LL+ AD V L VP TP+TK Sbjct: 162 IGTQLGILAET-LGMRVIFFDIEDKLPLGNAQQIHSLE--QLLSLADVVSLHVPETPQTK 218 Query: 212 HLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSD---- 267 ++IG+ EL +M++ +ILINASRG VD AL EA++ I GA +DVF EP +D Sbjct: 219 NMIGSKELAAMRQGSILINASRGTVVDIDALAEAIRGDHIVGAAIDVFPVEPKSNDDEFV 278 Query: 268 SPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315 SPL L NV+ PH+G +T E + + A L D T VN Sbjct: 279 SPLRGLDNVLLTPHVGGSTQEAQENIGIEVAGKLAKYSDNGSTMTAVN 326 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: 260 Number of extensions: 14 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: 409 Length adjustment: 29 Effective length of query: 292 Effective length of database: 380 Effective search space: 110960 Effective search space used: 110960 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: 49 (23.5 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