Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_011021352.1 MA_RS06920 NAD(P)-dependent oxidoreductase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_000007345.1:WP_011021352.1 Length = 319 Score = 195 bits (496), Expect = 1e-54 Identities = 120/289 (41%), Positives = 164/289 (56%), Gaps = 9/289 (3%) Query: 33 DAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTP 92 D F+ +KDAD + ++ L A RLK +S GFD D+ + T G++++N P Sbjct: 36 DEFIDRIKDADIVVVGRYGVSAEALRSAPRLKMISLWQTGFDNVDLEEATDHGVIVSNVP 95 Query: 93 DVLTESTADTVFSLILASARRVVELAEWVKAG--HWQHSIGPALFGVDVQGKTLGIVGLG 150 ES A+ VF+L L RRV ++ G W++ +G L KT+G++G G Sbjct: 96 SYAFESVAEFVFALTLNLLRRVHLADMNLREGLFDWKYYVGNQLMS-----KTIGVLGTG 150 Query: 151 RIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPET 210 IG V + A GFNM VL +P+ +A G + V+L LL+ +D V L VPLTPET Sbjct: 151 EIGKRVIQ-IAHGFNMNVLSVTAHPSPERAKALGVKFVDLDTLLSESDIVTLHVPLTPET 209 Query: 211 KHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPL 270 +H+IGA EL MK +AILIN +RG V+E AL+EAL+ I GAGLDVFE EPL DSPL Sbjct: 210 EHMIGARELAKMKPTAILINTARGKVVEEAALMEALKEKKIAGAGLDVFEREPLSMDSPL 269 Query: 271 LKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVNREVL 319 L++ NVV PHI + E+ + EN+ G N+VN VL Sbjct: 270 LEMHNVVLTPHIAFLSEESLDECTYISIENVEMFAKGK-PQNVVNPSVL 317 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: 218 Number of extensions: 9 Number of successful extensions: 2 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: 319 Length adjustment: 28 Effective length of query: 293 Effective length of database: 291 Effective search space: 85263 Effective search space used: 85263 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 Apr 09 2024. 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