Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_007680625.1 BN137_RS02000 glyoxylate/hydroxypyruvate reductase GhrB
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_000319285.1:WP_007680625.1 Length = 325 Score = 336 bits (861), Expect = 5e-97 Identities = 176/321 (54%), Positives = 225/321 (70%), Gaps = 3/321 (0%) Query: 4 IVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVA---ALKDADGGIGSSVKITPAMLEGA 60 ++ +KSLP+D+LA L+ H V +V A A A G +GSS K+ A+LE Sbjct: 5 VILYKSLPDDLLARLESHFSVTRVSDLSPQTVAAHAQAFSQAQGLLGSSEKVDAALLEKM 64 Query: 61 TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEW 120 L+A ST+SVG+D FDV L + I L +TP VLTE+ ADT+ +L+L +ARR +E+A+ Sbjct: 65 PALRATSTVSVGYDNFDVDALNAKQIALMHTPTVLTETVADTLMTLVLTTARRALEVADR 124 Query: 121 VKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAE 180 VKAG W SIGP FG+DV KTLGI+G+GRIG A+A+RA GFNM +LY R + +AE Sbjct: 125 VKAGEWTGSIGPDWFGIDVHHKTLGIIGMGRIGLALAQRAHFGFNMPILYNARRHHSEAE 184 Query: 181 EAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEK 240 E + AR ++ LLA +DFVC+ +PLT ET H+IGA + + MKKSAI INA RG VDE Sbjct: 185 ERFNARYCDIDTLLAESDFVCVILPLTDETHHMIGAEQFRKMKKSAIFINAGRGPVVDEN 244 Query: 241 ALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300 ALI ALQ+G IH AGLDVFE EPLP DSPLL L NVVALPHIGSATHETR+ MA A +N Sbjct: 245 ALISALQSGEIHAAGLDVFEQEPLPKDSPLLSLKNVVALPHIGSATHETRYNMAACAVDN 304 Query: 301 LVAALDGTLTSNIVNREVLSK 321 L+ AL+G ++ N VN +V+ K Sbjct: 305 LINALNGDVSQNCVNPQVVKK 325 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: 244 Number of extensions: 3 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: 325 Length adjustment: 28 Effective length of query: 293 Effective length of database: 297 Effective search space: 87021 Effective search space used: 87021 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