Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 16992 b2913 D-3-phosphoglycerate dehydrogenase (NCBI)
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Keio:16992 Length = 410 Score = 132 bits (333), Expect = 1e-35 Identities = 96/277 (34%), Positives = 138/277 (49%), Gaps = 14/277 (5%) Query: 45 GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVF 104 G+ S +T ++ A +L A+ +G +Q D+ +RGI + N P T S A+ V Sbjct: 58 GLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVI 117 Query: 105 SLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRA-ALG 163 +L R V E G W A + +GK LGI+G G IG + A +LG Sbjct: 118 GELLLLLRGVPEANAKAHRGVWNKL---AAGSFEARGKKLGIIGYGHIGTQLGILAESLG 174 Query: 164 FNMKVLYTNRSANPQAEEAYGARRVE-LAELLATADFVCLQVPLTPETKHLIGAAELKSM 222 + Y + P A +V+ L++LL +D V L VP P TK+++GA E+ M Sbjct: 175 MYV-YFYDIENKLPLGN----ATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLM 229 Query: 223 KKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPL----PSDSPLLKLANVVA 278 K ++LINASRG VD AL +AL + + GA +DVF TEP P SPL + NV+ Sbjct: 230 KPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLL 289 Query: 279 LPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315 PHIG +T E + + A L+ D T + VN Sbjct: 290 TPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVN 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: 251 Number of extensions: 18 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