Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_085544045.1 B9Y55_RS03840 hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_900177735.1:WP_085544045.1 Length = 316 Score = 137 bits (346), Expect = 3e-37 Identities = 97/274 (35%), Positives = 143/274 (52%), Gaps = 9/274 (3%) Query: 36 VAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVL 95 V L AD I +++ + ++ RLK +S G+D D+ + I ++N Sbjct: 43 VKRLAGADVAIIANMPLGGQVISSCDRLKMISVAFTGYDHVDMESCLSKRITVSNCAGYS 102 Query: 96 TESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGA 155 T+S + L LA R++V V+AG + L G + GKT+GIVG G IG Sbjct: 103 TDSVVELALGLSLAVVRKIVPCDGAVRAGKTKDG----LIGNQLAGKTVGIVGTGAIGVK 158 Query: 156 VARR-AALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLI 214 VA ALG N V+ +RS + + G + L +L+++ D + L +P ET LI Sbjct: 159 VAAVFKALGCN--VVAYSRSQRDEVL-SMGIPYLSLKDLMSSCDLISLHLPCNGETAGLI 215 Query: 215 GAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETE-PLPSDSPLLKL 273 + SMK+S+ LIN +RG VD KAL +AL++G+I GAG+DVF+ E PL PLL Sbjct: 216 DRDMISSMKRSSFLINTARGPIVDNKALADALKSGSIAGAGIDVFDMEPPLLEGYPLLDA 275 Query: 274 ANVVALPHIGSATHETRHAMARNAAENLVAALDG 307 N V PH+ AT E + A A +N+ +DG Sbjct: 276 PNCVLTPHVAFATPEALQSRAVIAIDNVRLWMDG 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: 192 Number of extensions: 9 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: 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