Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 3608367 Dshi_1769 6-phosphogluconate dehydratase (RefSeq)
Query= curated2:Q5SIY0 (555 letters) >FitnessBrowser__Dino:3608367 Length = 601 Score = 249 bits (637), Expect = 2e-70 Identities = 182/539 (33%), Positives = 267/539 (49%), Gaps = 33/539 (6%) Query: 34 VGVVNTFTDGMPCNFHLRELAQHLKAGLKEAGLFP-FEFGAPAISDGISMGTPGMRASLV 92 +G+V + D + + ++ +K + AG G PA+ DG++ G GM SL Sbjct: 69 IGIVTAYNDMLSAHQPFKDYPDKIKEAARRAGATAQVAGGVPAMCDGVTQGQVGMELSLF 128 Query: 93 SREVIADSVELIAQGYLYDGMVGLSACDKTIPGTAMGVIRSG-VPGMILYGGTIAPGEWQ 151 SR+VIA + + +D L CDK +PG + G +PG+ + G + G Sbjct: 129 SRDVIALATGVALSHNTFDAAAYLGVCDKIVPGLVIAAATFGYLPGVFVPAGPMVSGLPN 188 Query: 152 GRKLTIVEVFEAVGQRAAGKISEEELLEIERRAIPGPGACGGQYTANTMAMALEALGLSP 211 +K + + F AAG+I ++L+E E + GPG C TAN+ M +E +GL Sbjct: 189 DQKAKVRQQF------AAGEIGRDKLMEAEMASYHGPGTCTFYGTANSNQMLMEFMGLHL 242 Query: 212 VGYNAIPAVHPEKERATKEAGKILA--WAIAHDWKPK-DFLTRKSFLNAIAAVAATGGST 268 G + + P +E T A + LA + ++++P D L K+F+N I + ATGGST Sbjct: 243 PGASFVNPGTPLREALTAAAAERLAAITQLGNEYRPVCDILDAKAFVNGIVGLMATGGST 302 Query: 269 NAVLHLLALAKEAGVELSLDDFDQISRKTPVIADLRPWGTYTAWELYEAGGTALVFKRLL 328 N V+HL A+A+ AGV L L DF IS TP++A + P G + AGG A + LL Sbjct: 303 NLVIHLPAMARAAGVILDLQDFADISEATPLMARVYPNGLADVNHFHAAGGLAYMIGELL 362 Query: 329 EAGLLFGEEKTLTGRTLAEE------VERAYREQEG------QKVVFPVEKALKPHGGLV 376 GLL + KT+ G LA+ ++ R ++G K++ P P GGL Sbjct: 363 SEGLLHPDTKTIAGDGLADYAREPKLIDGVLRWEDGPRRSLNAKILRPASDGFAPSGGLK 422 Query: 377 VLKGNLAPKGAVLKLAGTERTYFEGPARVFDSEEAAMEKVLKGEIRPGDVVVIRYVGPKG 436 LKGNL + ER E ARVF+ + A + GE VV++R+ GPK Sbjct: 423 ELKGNLGRGVMKVSAVAPERHVIEARARVFEDQGAVKDAFKAGEFTEDTVVIVRFQGPK- 481 Query: 437 APGMPEMLSVTSAI-VGEGLGPEVALLTDGRFSGGTRGLMIG-HIAPEAFVGGPIALLEE 494 A GMPE+ ++T + V + G +VAL+TDGR SG + + H+APEA GG +A + Sbjct: 482 ANGMPELHALTPVLAVLQDRGLKVALVTDGRMSGASGKVPAAIHVAPEALDGGLMAKVRT 541 Query: 495 GDRIRIDVEGRRLEVLLPEEELERRRARWRPRPPAFTHG----LFARYAALVRQADEGA 549 GD +R+D LEVL P E RA P +HG LF + V A GA Sbjct: 542 GDLVRVDAVAGVLEVLEPGVE---DRAPAMPDLSGNSHGIGRELFDVFRTTVGPASTGA 597 Lambda K H 0.318 0.138 0.405 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: 950 Number of extensions: 50 Number of successful extensions: 6 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: 555 Length of database: 601 Length adjustment: 36 Effective length of query: 519 Effective length of database: 565 Effective search space: 293235 Effective search space used: 293235 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: 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