Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate Ga0059261_0354 Ga0059261_0354 6-phosphogluconate dehydratase (EC 4.2.1.12)
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Korea:Ga0059261_0354 Length = 608 Score = 268 bits (686), Expect = 3e-76 Identities = 181/518 (34%), Positives = 278/518 (53%), Gaps = 41/518 (7%) Query: 34 IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYSLP 92 IG+ ++N+++ H + E +K AG T G + A+CDG+ G+ GM SL Sbjct: 71 IGIVTAYNDMLSAHAPYYRYPEQMKIWALEAGATAQVAGGVPAMCDGVTQGYAGMELSLF 130 Query: 93 SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151 SR+ IA + + + + + ++ CDKI PG L+ A R +P++LI GG M G+ Sbjct: 131 SRDTIAMSTAVALSHNTFEGAALLGICDKIVPGLLMGALRFGHLPMVLIPGGAMPTGIAN 190 Query: 152 KERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLM 209 KE+ R+ L EG+ EEL E +A G G+C TAN+ M+ EAMGL Sbjct: 191 KEKA-------RVRELYAEGKASREELLDSEIAAYHGKGTCTFYGTANSNQMMVEAMGLH 243 Query: 210 LPGASTV-PAVEARRLWYAKLTGMRIVKMVEEGLTPD------KILTRKALENAIAVDMA 262 +PGA+ + P + R+ LT + ++ E G + +I+ +A+ NA V +A Sbjct: 244 MPGAAFIHPGTKLRQA----LTRAAVQRLPEIGWDSNDYRPIGEIVDERAIVNAAVVLLA 299 Query: 263 LGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAV 322 GGSTN ++HL A+A G+ + + FD +SR VP +A + P+G V + AGG V Sbjct: 300 TGGSTNHLIHLPAIARCAGVLIDWDDFDRLSRVVPLLARVYPNGSADVNGFEDAGGPTFV 359 Query: 323 LKELGEAGLIHKDALTVTGKTVWENVK--------------DAAVLDREVIRPLDNPYSP 368 ++EL + G++H D LTV G ++ + V+ A D ++R +D P+S Sbjct: 360 IRELIKGGVLHGDTLTVAGDSLADYVRRPVLEDDTLVWKDHGAKSGDDSILRTIDAPFSE 419 Query: 369 FGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVI 428 GG IL G+L A +K SAV+R+ W + RVF +++ A + GE++ V+V+ Sbjct: 420 EGGFRILSGNL--GRACIKVSAVERDRWTIEAPCRVFATQQEVQDAFKAGELDRDVVVVV 477 Query: 429 RYEGPRGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGG 486 R++GPR GM E+ T + L G +VALVTDGR SGA+ + PA H+SPEA GG Sbjct: 478 RFQGPRAN-GMPELHKLTPPLGVLQNKGFRVALVTDGRMSGASGKVPAAIHLSPEAIGGG 536 Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKP 524 PI ++DGD + + E+ L LV+ E E R P Sbjct: 537 PIGKLRDGDVVRLCAEEGILQALVEPAEWEARELAAAP 574 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: 902 Number of extensions: 54 Number of successful extensions: 9 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