Align Probable glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (uncharacterized)
to candidate AO353_23515 AO353_23515 muconate cycloisomerase
Query= curated2:Q9RDE9 (431 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23515 Length = 382 Score = 107 bits (266), Expect = 8e-28 Identities = 104/379 (27%), Positives = 161/379 (42%), Gaps = 57/379 (15%) Query: 36 LIVEVETADGVTGVGET-------YG----DAKYLELARPFAAKLVGRQVSDLNGLFTLA 84 +I+ V ADG+ G+GE+ YG D+ + + FA L+G+ ++N Sbjct: 35 VIIRVRCADGIEGIGESTTIGGLAYGNESPDSIKTNIDKHFAPLLLGQDACNINAAMLRL 94 Query: 85 DEVAVDSSRVFGQVDVGGLRGVQTADKLRLSVVSGFEVACLDALGKALGLPVHALLGGKV 144 + +RG A SG E A LDA GK LGLPV LLGG+V Sbjct: 95 ER---------------SIRGNTFAK-------SGIETALLDAHGKRLGLPVSELLGGRV 132 Query: 145 RDAVEYSAYLFYKWADHPEGVASEKDDWGAAVDPAGVVAQARAFTERYGFTSFKLKGGVF 204 RD++ + L A+ D A +A+A + FKLK G Sbjct: 133 RDSLPVAWTL-------------------ASGDTAKDIAEAEQMLDLRRHRIFKLKIGAG 173 Query: 205 PPEEEIAAVKALAEAFPGH-PLRLDPNGAWSVETSLKVAAEL-GDVLEYLEDPAL--GTP 260 + ++A V A+ +A +R+D N AW +L+ L G+ ++ +E P Sbjct: 174 EVDRDLAHVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGGNGIDLIEQPISRNNRA 233 Query: 261 AMAEVAAKTGVPLATNMCVTTFAEIQEAFTKGAVQVVLSDHHYWGGLRNTQQLAAVCRTF 320 M + A + P+ + + + +GA V GG R + AA+ Sbjct: 234 GMVRLNAMSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTAAIAEAA 293 Query: 321 GVGVSMHSNTHLGISLAAMTHVAATVPDLHHACDSHYP-WQSEDVLTERLAFDGGKVAVS 379 G+G+ + GI A H T+ +L + P +ED+L+E + + VS Sbjct: 294 GIGLYGGTMLEGGIGTLASAHAFLTLNELSWDTELFGPLLLTEDILSEPPVYCDFHLHVS 353 Query: 380 DAPGLGVALDRERLAFLHR 398 APGLG++LD ERLAF R Sbjct: 354 QAPGLGLSLDEERLAFFRR 372 Lambda K H 0.319 0.135 0.410 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: 335 Number of extensions: 15 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: 431 Length of database: 382 Length adjustment: 31 Effective length of query: 400 Effective length of database: 351 Effective search space: 140400 Effective search space used: 140400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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