Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_040685231.1 C892_RS0101795 D-2-hydroxyacid dehydrogenase family protein
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_000341205.1:WP_040685231.1 Length = 315 Score = 157 bits (396), Expect = 4e-43 Identities = 98/255 (38%), Positives = 139/255 (54%), Gaps = 9/255 (3%) Query: 55 AMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRV 114 A+L RL+ L T D+ G+ + T ++ TA+ ++LIL AR + Sbjct: 59 ALLGRLPRLRLLVTTGRRNASIDLEAAEAAGVTVCGTSSTISP-TAELTWALILGLARHL 117 Query: 115 -VELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNR 173 E + + G WQ ++G D+ G+TLG++GLGRIGG VAR A F M VL + Sbjct: 118 PAENRAFRQGGPWQSTVG-----ADLHGRTLGVLGLGRIGGRVAR-VATAFGMPVLAWSE 171 Query: 174 SANPQAEEAYGARRVE-LAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINAS 232 + + GAR ELLA +D V + + L+ T+ L+G AEL++M+ A L+N S Sbjct: 172 NLTEERAAEAGARLARGKEELLAGSDVVSVHLQLSERTRGLLGEAELRAMRPHAYLVNTS 231 Query: 233 RGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHA 292 R VD AL+ AL+ G I GAGLDVF+TEP+P D P+ L NV+A PH+G T Sbjct: 232 RSGIVDRSALLRALRGGWIAGAGLDVFDTEPVPEDDPMRTLPNVLATPHLGYVTERNYRT 291 Query: 293 MARNAAENLVAALDG 307 A E++ A LDG Sbjct: 292 FYTEAVEDIAAFLDG 306 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: 220 Number of extensions: 10 Number of successful extensions: 1 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: 315 Length adjustment: 27 Effective length of query: 294 Effective length of database: 288 Effective search space: 84672 Effective search space used: 84672 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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