Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 5209582 Shew_2046 phosphogluconate dehydratase (RefSeq)
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__PV4:5209582 Length = 608 Score = 241 bits (615), Expect = 6e-68 Identities = 167/509 (32%), Positives = 264/509 (51%), Gaps = 35/509 (6%) Query: 34 IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTP-LEFGTIAVCDGIAMGHEGMRYSLP 92 IG+ ++N+++ H + + +K G + G A+CDG+ G GM SL Sbjct: 68 IGIVTAFNDMLSAHQPYEHYPQLLKDACHEVGSVAQVAAGVPAMCDGVTQGQPGMELSLL 127 Query: 93 SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151 SREVIA + + + + D +++ CDKI PG L+ A +P++ + GPM G+ Sbjct: 128 SREVIAMSTAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGPMKSGIPN 187 Query: 152 KERIDFKDLMERMNVLIKEGRTEE--LRKLEESALPGPGSCAGLFTANTMNMLSEAMGLM 209 KE+ R+ +G+ + L + E + G+C TAN+ ++ E MGL Sbjct: 188 KEKA-------RVRQKFAQGQVDRAALLEAESKSYHSAGTCTFYGTANSNQLMLEVMGLQ 240 Query: 210 LPGASTVPAVEARRLWYAKLTGMRIVKMVEEGL--TP-DKILTRKALENAIAVDMALGGS 266 LPG+S V + R K+ ++ ++ E G TP +++ K++ N I +A GGS Sbjct: 241 LPGSSFVNPDDPLREALNKMAAKQVCRLTEMGTQYTPIGEVVNEKSVVNGIVALLATGGS 300 Query: 267 TNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKEL 326 TN +H+ A A GI + + F E+S VP +A + P+G + AGG+ ++KEL Sbjct: 301 TNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKEL 360 Query: 327 GEAGLIHKDALTVTG---------------KTVWENVKDAAVLDREVIRPLDNPYSPFGG 371 +AGL+H+D LTV G + VW + + LD+EV+ + +P+ GG Sbjct: 361 LDAGLLHEDVLTVAGPGLRRYTQEPRLIDNELVWVEGPNES-LDKEVLTAVASPFQANGG 419 Query: 372 LAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYE 431 L +LKG+L AV+K SAV + A V D + + GE++ V+V++ + Sbjct: 420 LKLLKGNL--GRAVIKVSAVAESHRFVEAPAVVIDDQNKLEGLFKAGELDRDCVVVVKGQ 477 Query: 432 GPRGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIA 489 GP+ GM E+ T + +L G KVAL+TDGR SGA+ + PA H++PEA GG IA Sbjct: 478 GPKAN-GMPELHKLTPILGSLQDKGFKVALLTDGRMSGASGKVPAAIHLTPEALDGGLIA 536 Query: 490 LVQDGDEIVIDIEKRRLDLLVDEKELEER 518 V++GD I +D + LLVDE L R Sbjct: 537 KVENGDLIRVDANTGEVSLLVDEAVLASR 565 Lambda K H 0.319 0.138 0.401 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: 811 Number of extensions: 48 Number of successful extensions: 8 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: 552 Length of database: 608 Length adjustment: 36 Effective length of query: 516 Effective length of database: 572 Effective search space: 295152 Effective search space used: 295152 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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