Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_028488076.1 Q394_RS0103620 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000621325.1:WP_028488076.1 Length = 611 Score = 256 bits (655), Expect = 1e-72 Identities = 183/498 (36%), Positives = 261/498 (52%), Gaps = 30/498 (6%) Query: 34 IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYSLP 92 +G+ ++N+++ H + +KA +R GT G + A+CDG+ G EGM SL Sbjct: 72 LGIVTAYNDMLSAHQPFVYYPDLIKAAVREVSGTAQVAGGVPAMCDGVTQGQEGMELSLF 131 Query: 93 SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151 SR+VIA + + + + DA + CDKI PG ++AAA +P I + GPM+ G+ Sbjct: 132 SRDVIAMSAAVALSHNVFDAAAFLGVCDKIVPGLVIAAASFGHLPCIFLPAGPMVSGLAN 191 Query: 152 KERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLMLP 211 D K + + K GR E L + E + G G+C TAN+ ML E MGL LP Sbjct: 192 ----DVKSKVRQQYAEGKVGRAE-LLQAEMQSYHGAGTCTFYGTANSNQMLMEFMGLQLP 246 Query: 212 GASTVPAVEARRLWYAKLTGMRIVKMVEEG--LTPD-KILTRKALENAIAVDMALGGSTN 268 G+S V + R R + M +G TP ILT A N I A GGSTN Sbjct: 247 GSSFVNPGTSLREALTVAGAQRALAMTAKGQDYTPAANILTVNAFVNGIVGLNATGGSTN 306 Query: 269 SVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGE 328 +LHL A+A GI L LE F ++S P IA + P+G V AGG+ V++EL Sbjct: 307 LLLHLVAMARAAGIVLCLEDFADLSAITPLIARVYPNGVADVNHFHAAGGLQFVIRELLA 366 Query: 329 AGLIHKDALTVTGKTVWENVKDAAVL---------------DREVIRPLDNPYSPFGGLA 373 AGL+H++ TV GK + ++A + D +V+RP+ P+ P GGL Sbjct: 367 AGLLHEEVDTVAGKGLHHYTQEAVLAADGTVTWREGASTSHDTDVLRPVVQPFQPSGGLV 426 Query: 374 ILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEGP 433 L G+L +V+K SAVK + + A+VF + A GE+E V V+R++GP Sbjct: 427 RLLGNL--GDSVIKVSAVKPDKHLIEAPAKVFHDQAAVKAAFEAGELEGDFVCVVRFQGP 484 Query: 434 RGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIALV 491 + GM E+ T + L G VALVTDGR SGA+ + PA HVSPEA GG IA + Sbjct: 485 KAN-GMPELHGLTPVLGLLQDRGQHVALVTDGRMSGASGKVPAAIHVSPEAMDGGAIAKI 543 Query: 492 QDGDEIVIDIEKRRLDLL 509 +DGD I +D++ L++L Sbjct: 544 RDGDLIRLDVDNGHLEVL 561 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: 803 Number of extensions: 52 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: 611 Length adjustment: 36 Effective length of query: 516 Effective length of database: 575 Effective search space: 296700 Effective search space used: 296700 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 10 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