Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_017599121.1 D471_RS0113625 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000341125.1:WP_017599121.1 Length = 606 Score = 253 bits (646), Expect = 1e-71 Identities = 184/505 (36%), Positives = 263/505 (52%), Gaps = 37/505 (7%) Query: 32 PLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYS 90 P + + +++N+++ H L+ +KA + AGG G + A+CDG+ G GM S Sbjct: 73 PNVAIVSAYNDMLSAHQPLETYPAIIKAAVAEAGGVAQFAGGVPAMCDGVTQGRPGMELS 132 Query: 91 LPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGV 149 L SR+VIA + + DA +M+ CDKI PG L+ A +PV + GPM G+ Sbjct: 133 LFSRDVIAMATAVALSHEMFDAALMLGVCDKIVPGLLIGALSFGHLPVAFVPAGPMPSGL 192 Query: 150 YGKERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLM 209 K++ + V GRTE L + E +A PG+C TAN+ ML E MGL Sbjct: 193 PNKDKARVRQKFAEGKV----GRTE-LLQAESAAYHAPGTCTFYGTANSNQMLMEVMGLH 247 Query: 210 LPGAS-TVPAVEARRLWYAKLTGMRIVKMVEEG--LTP-DKILTRKALENAIAVDMALGG 265 LPGAS P R A+ G R++ G TP + + +A+ NA+ +A GG Sbjct: 248 LPGASFEQPGTPLREALTAE-AGRRVLAHTALGDDYTPVGEQVDERAIVNAVVALLATGG 306 Query: 266 STNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKE 325 STN LHL A+A GI L + F +S VP + + P+G V GG+ ++ Sbjct: 307 STNHTLHLVAIARAAGIQLTWDDFASLSEVVPLLTRMYPNGAADVNRFHEVGGMAYLIGS 366 Query: 326 LGEAGLIHKDALTVTGK----------------TVWENVKDAAVLDREVIRPLDNPYSPF 369 L +AGL+H+D TV G+ T + K++A D V+R ++ P++ Sbjct: 367 LLDAGLLHEDVRTVAGQGLGRYRETPRLEGSTLTWGDGPKESA--DTTVLRGVEEPFAAD 424 Query: 370 GGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIR 429 GGL +L G+L AV+K SAV E + ARVF + + A GE+ V V+R Sbjct: 425 GGLRMLSGNL--GRAVIKVSAVAPERHVVEAPARVFGDQAELQAAFSAGELTGDFVAVVR 482 Query: 430 YEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGG 486 ++GPR GM E+ LT AV+ G KVALVTDGR SGA+ + PA HVSPEA AGG Sbjct: 483 FQGPRAN-GMPELHKLTPPLAVLQ-DRGQKVALVTDGRMSGASGKVPAAIHVSPEAEAGG 540 Query: 487 PIALVQDGDEIVIDIEKRRLDLLVD 511 +A V+DGD I +D L++L D Sbjct: 541 ALAFVRDGDVIRLDAVAGTLEVLAD 565 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: 915 Number of extensions: 61 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 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