Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 201628 SO2487 6-phosphogluconate dehydratase (NCBI ptt file)
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__MR1:201628 Length = 608 Score = 239 bits (609), Expect = 3e-67 Identities = 170/522 (32%), Positives = 266/522 (50%), Gaps = 45/522 (8%) Query: 28 ELRRPLIGVANSWNEIVPGHVH-------LDKVAEAVKAGIRMAGGTPLEFGTIAVCDGI 80 +L + IG+ ++N+++ H L K + V + ++AGG P A+CDG+ Sbjct: 62 QLTKANIGIITAFNDMLSAHQPYETYPDLLKKACQEVGSVAQVAGGVP------AMCDGV 115 Query: 81 AMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVIL 139 G GM SL SREVIA + + + D +++ CDKI PG L+ A +P++ Sbjct: 116 TQGQPGMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLF 175 Query: 140 INGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTEELRKLEESALP--GPGSCAGLFTAN 197 + GPM G+ KE+ R+ +G+ + + LE A G+C TAN Sbjct: 176 VPAGPMKSGIPNKEKA-------RIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTAN 228 Query: 198 TMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPD---KILTRKALE 254 + ++ E MGL LPG+S V + R K+ ++ ++ E G +++ K++ Sbjct: 229 SNQLMLEVMGLQLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSIV 288 Query: 255 NAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLD 314 N I +A GGSTN +H+ A A GI + + F E+S VP +A + P+G + Sbjct: 289 NGIVALLATGGSTNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFH 348 Query: 315 RAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAV--------------LDREVIR 360 AGG+ ++KEL +AGL+H+D TV G + ++ + LD EV+ Sbjct: 349 AAGGMAFLIKELLDAGLLHEDVNTVAGYGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLT 408 Query: 361 PLDNPYSPFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEI 420 + P+ GGL +LKG+L AV+K SAV+ + + A V D + + G + Sbjct: 409 SVATPFQNNGGLKLLKGNL--GRAVIKVSAVQPQHRVVEAPAVVIDDQNKLDALFKSGAL 466 Query: 421 EPGTVIVIRYEGPRGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHV 478 + V+V++ +GP+ GM E+ T + +L G KVAL+TDGR SGA+ + PA H+ Sbjct: 467 DRDCVVVVKGQGPKAN-GMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHL 525 Query: 479 SPEAAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRA 520 +PEA GG IA VQDGD I +D L LLV + EL R A Sbjct: 526 TPEAIDGGLIAKVQDGDLIRVDALTGELSLLVSDTELATRTA 567 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: 794 Number of extensions: 49 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