Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_007674746.1 BN137_RS08125 2-hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_000319285.1:WP_007674746.1 Length = 310 Score = 165 bits (417), Expect = 2e-45 Identities = 102/252 (40%), Positives = 142/252 (56%), Gaps = 7/252 (2%) Query: 52 ITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASA 111 +T + L+ ++ VG+D DVA RGI + +TP VLT+ AD L+LA++ Sbjct: 54 VTREFIATLPALRLIAVFGVGYDGVDVAAARDRGIAVTHTPGVLTDDVADLAIGLMLATS 113 Query: 112 RRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYT 171 RR+V +++ G W H P + V G LGI G+GRIG A+ARRA F+M + YT Sbjct: 114 RRIVSAQRFIEQGGWVHGSFP--WTRKVSGARLGIFGMGRIGQAIARRAQ-AFDMTIRYT 170 Query: 172 NRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINA 231 +R A P + +L EL +DF+ L P T+ ++ AA L ++ +LIN Sbjct: 171 SRHAQPALPYPFVP---DLRELAQESDFLMLCAPGGDATRGVVNAAVLAALGPQGMLINV 227 Query: 232 SRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRH 291 RG+ VDE AL+ AL +GTI GAGLDVF EP + L + NVV PH+ SAT ETR Sbjct: 228 GRGSVVDETALMAALDSGTIAGAGLDVFTDEP-NVPAALQQRDNVVITPHMASATWETRR 286 Query: 292 AMARNAAENLVA 303 M+R EN+ A Sbjct: 287 EMSRLVLENVNA 298 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: 230 Number of extensions: 12 Number of successful extensions: 4 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: 310 Length adjustment: 27 Effective length of query: 294 Effective length of database: 283 Effective search space: 83202 Effective search space used: 83202 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