Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_104487446.1 UN63_RS13580 D-2-hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_002936955.1:WP_104487446.1 Length = 316 Score = 143 bits (360), Expect = 6e-39 Identities = 99/276 (35%), Positives = 137/276 (49%), Gaps = 14/276 (5%) Query: 39 LKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTES 98 L+D D I + V++ +L RLK + + G D D+ + GI + N D S Sbjct: 41 LQDTDIAIVNKVRLGADILSRLPRLKLVVIAATGSDNVDLEACRQAGIAVCNIRDYSKNS 100 Query: 99 TADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGV---DVQGKTLGIVGLGRIGGA 155 + +LILA R + + AG WQ S F D+ G+TLG++G G I Sbjct: 101 VPEHALALILALNRSLNAYRASIVAGRWQQSGQFCYFDYPVRDLAGQTLGLIGYGTIARE 160 Query: 156 VARRA-ALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLI 214 + + A ALG MKV+ R +P +E RV +LL AD + L PL ET+HLI Sbjct: 161 LEKLATALG--MKVIVAARKGHPVSEG-----RVGFEQLLNDADVISLHCPLNAETRHLI 213 Query: 215 GAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPL---L 271 G ELK MK A+L+N RG VDE AL+ AL+ I GAG DV EP D+PL L Sbjct: 214 GERELKLMKSDALLVNVGRGGLVDEAALLAALEQNRIGGAGFDVVTQEPPAPDNPLMQAL 273 Query: 272 KLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307 + N + PHI A+ +A +N+ A + G Sbjct: 274 QYPNFILTPHIAWASRNAMQRLADQLIDNIEAFVAG 309 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: 214 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: 316 Length adjustment: 27 Effective length of query: 294 Effective length of database: 289 Effective search space: 84966 Effective search space used: 84966 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