Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_094478843.1 B9Z44_RS12305 hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_003063475.1:WP_094478843.1 Length = 337 Score = 149 bits (376), Expect = 9e-41 Identities = 107/320 (33%), Positives = 164/320 (51%), Gaps = 22/320 (6%) Query: 1 MKKIVAWKSLPEDVLAYLQQHAQVVQVDATQ---HDAFVAALKDADGGIGSSV-KITPAM 56 M KIV + + E VLA L+ VV + + LKDAD + ++ Sbjct: 2 MPKIVVTQPIHEAVLARLRSAGDVVMNQGPEPWSEEELYLHLKDADAMMAFMPDRVDMRT 61 Query: 57 LEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVE 116 L A RLK ++ G+D FD+ + G+ ++ PD+LTE TA+ L +A+AR V+ Sbjct: 62 LLNAPRLKTIACALKGYDNFDLMACEKAGVSVSFVPDLLTEPTAELAIGLAIAAARHVLA 121 Query: 117 LAEWVKAGH--WQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS 174 V+ G+ W+ P L+G+ + G + +VGLG +G A+ R GF L Sbjct: 122 GDTRVRRGYAGWR----PQLYGIGLHGSVVSVVGLGAVGRAIVDRLC-GFGCAQLL---G 173 Query: 175 ANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRG 234 +P ++ V L E L+ +D+V L VPL T+HL+ L+ +++ IL+N RG Sbjct: 174 VDPHGDDER-LTMVSLGEALSQSDYVILAVPLLDVTRHLVNDTMLEGVRRGQILVNIGRG 232 Query: 235 ATVDEKALIEALQNGTIHGAGLDVFETEP-LPSDSP------LLKLANVVALPHIGSATH 287 + VDE A+ AL++ + DV+E E L +D P LL+ + V PHIGSA Sbjct: 233 SVVDEAAVARALKDERLGAYAADVYEMEDWLLADRPRQIHPELLQHPSTVFTPHIGSAVK 292 Query: 288 ETRHAMARNAAENLVAALDG 307 + R A+ AAENL+ AL+G Sbjct: 293 KVRRAIELQAAENLLVALNG 312 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: 233 Number of extensions: 14 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: 337 Length adjustment: 28 Effective length of query: 293 Effective length of database: 309 Effective search space: 90537 Effective search space used: 90537 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 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