Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF3560 PGA1_c36140 D-3-phosphoglycerate dehydrogenase SerA
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Phaeo:GFF3560 Length = 531 Score = 181 bits (459), Expect = 4e-50 Identities = 106/284 (37%), Positives = 158/284 (55%), Gaps = 6/284 (2%) Query: 33 DAFVAALKDADG-GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANT 91 D A + D DG I S+ K+T +L+ AT LK ++ +G D D +++G+++ NT Sbjct: 37 DKLAAIIGDYDGLAIRSATKVTQKILDNATNLKVIARAGIGTDNIDKDAASQKGVIVMNT 96 Query: 92 PDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGR 151 P +TA+ +++ A AR++ E + AG W+ S GV++ KTLG++G G Sbjct: 97 PFGNMITTAEHAIAMMFAVARQIPEASASTHAGKWEKS---KFMGVELTNKTLGVIGAGN 153 Query: 152 IGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETK 211 IGG V RA G MKV+ + + + + G +VEL ELLA ADF+ L VPLT +T+ Sbjct: 154 IGGIVCDRAR-GLKMKVVAYDPFLSQEKADKIGVEKVELDELLARADFITLHVPLTDQTR 212 Query: 212 HLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLL 271 +++ L+ KK +IN +RG VDE AL E L +G + GA DVF EP + +PL Sbjct: 213 NILSKENLEKTKKGVRIINCARGGLVDEAALAELLTSGHVAGAAFDVFSEEPAKT-NPLF 271 Query: 272 KLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315 L NVV PH+G+AT E + +A AE + L N +N Sbjct: 272 GLPNVVCTPHLGAATSEAQENVALQVAEQMSNYLLDGAVENALN 315 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: 330 Number of extensions: 19 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: 531 Length adjustment: 31 Effective length of query: 290 Effective length of database: 500 Effective search space: 145000 Effective search space used: 145000 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