Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate N515DRAFT_3177 N515DRAFT_3177 6-phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Dyella79:N515DRAFT_3177 Length = 606 Score = 240 bits (612), Expect = 1e-67 Identities = 178/514 (34%), Positives = 263/514 (51%), Gaps = 40/514 (7%) Query: 32 PLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYS 90 P +G+ S+N+++ H ++ E ++ R +G T G + A+CDG+ G EGM S Sbjct: 70 PNLGIVTSYNDMLSAHQPYERYPELIRRIARESGITAQVAGGVPAMCDGVTQGREGMELS 129 Query: 91 LPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGV 149 L SR++IA + + D + + CDKI PG L+ A +P I + GGPM G+ Sbjct: 130 LFSRDLIAMATAVSLSHDMFDGTLYLGICDKIVPGLLIGALSFGHLPGIFVPGGPMPSGI 189 Query: 150 YGKERIDFKDLMERMNVLIKEGRTE--ELRKLEESALPGPGSCAGLFTANTMNMLSEAMG 207 +++ ++ EG+ EL + E +A PG+C TAN+ ML E MG Sbjct: 190 TNEQK-------SKVRQAYAEGKANRAELLEAEAAAYHAPGTCTFYGTANSNQMLMEIMG 242 Query: 208 LMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKALENAIAVDMALG 264 L LPGAS V R R+ + G L I+ +A+ N + A G Sbjct: 243 LHLPGASFVAPDTPLRDALTAEAVHRVAALSAHGDNHLPIGHIVDERAIINGVIGLHATG 302 Query: 265 GSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLK 324 GSTN +LHL A+A GI L + FD +S VP +A + P+G V AGG+ ++ Sbjct: 303 GSTNHLLHLVAMARAAGIQLRWDDFDALSSVVPLLARVYPNGYADVNQFHDAGGMAFLID 362 Query: 325 ELGEAGLIHKDALTV----------------TGKTVWENV-KDAAVLDREVIRPLDNPYS 367 +L AGL+H D TV +G W V K++ +R V+R + P+ Sbjct: 363 QLLGAGLLHGDVRTVFGTGLDGYAQVPSLDASGALQWTPVAKESG--NRGVLRGMAEPFR 420 Query: 368 PFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIV 427 GGL +L G+L AV+K S+V + + A VF +++ KA GE+ + V Sbjct: 421 ADGGLRMLAGNL--GRAVIKVSSVPDDRQVIEAPAVVFHDQDEVRKAFERGELNRDFIAV 478 Query: 428 IRYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAA 484 +R++GPR GM E+ LT T AV+ G ++AL+TDGR SGA+ R PA HV+PEA A Sbjct: 479 VRFQGPR-AIGMPELHKLTPTLAVLQ-DRGYRIALLTDGRMSGASGRVPAAIHVTPEAQA 536 Query: 485 GGPIALVQDGDEIVIDIEKRRLDLLVDEKELEER 518 G IA ++DGD I +D + LD+LVD E R Sbjct: 537 QGAIARIRDGDLIRLDATRGTLDVLVDASEFASR 570 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: 848 Number of extensions: 42 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: 606 Length adjustment: 36 Effective length of query: 516 Effective length of database: 570 Effective search space: 294120 Effective search space used: 294120 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 Aug 03 2021. The underlying query database was built on Aug 03 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