Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate N515DRAFT_3581 N515DRAFT_3581 D-3-phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Dyella79:N515DRAFT_3581 Length = 410 Score = 141 bits (356), Expect = 2e-38 Identities = 101/275 (36%), Positives = 138/275 (50%), Gaps = 10/275 (3%) Query: 45 GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVF 104 GI S +T +LE A RL A+ +G +Q D+ ++G+ + N P T S A+ V Sbjct: 57 GIRSRSHLTADVLEQARRLIAVGCFCIGTNQVDLETARQQGVPVFNAPYSNTRSVAELVI 116 Query: 105 SLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGF 164 + + R + + G W S A +V+ K LGIVG G IG V A Sbjct: 117 AEAIMLLRGIPQKNALCHRGGWTKS---AAGSFEVRDKVLGIVGYGHIGTQVGVLAE-SL 172 Query: 165 NMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKK 224 M+V++ + A A ++ +LL AD V L VP TP TK +IGA EL M+K Sbjct: 173 GMRVIFHDIETKLSLGNARAAGSLD--DLLERADVVTLHVPETPATKLMIGATELAKMRK 230 Query: 225 SAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSD----SPLLKLANVVALP 280 A LINASRG VD AL AL+ G + GA +DVF EP +D SPL+ + NV+ P Sbjct: 231 GAALINASRGTVVDIDALAAALRTGHVAGAAVDVFPLEPKGNDDPFVSPLVGMDNVILTP 290 Query: 281 HIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315 HIG +T E + + A LV D T + VN Sbjct: 291 HIGGSTLEAQDNIGIEVASKLVRYSDNGSTLSAVN 325 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: 281 Number of extensions: 13 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: 410 Length adjustment: 29 Effective length of query: 292 Effective length of database: 381 Effective search space: 111252 Effective search space used: 111252 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