Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_010959409.1 MCA_RS00185 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000008325.1:WP_010959409.1 Length = 609 Score = 254 bits (649), Expect = 7e-72 Identities = 169/497 (34%), Positives = 266/497 (53%), Gaps = 30/497 (6%) Query: 32 PLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYS 90 P +G+ ++N+++ H ++ E +K R AG T G + A+CDG+ G GM S Sbjct: 68 PNLGIVTAYNDMLSAHQPYERYPEIIKDEARRAGVTAQVAGGVPAMCDGVTQGQTGMELS 127 Query: 91 LPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGV 149 L SR+VIA + + + DA + + CDKI PG L+AA R +P + + GPM+ G+ Sbjct: 128 LFSRDVIALSTAVALSHRVFDANLYLGVCDKIVPGLLIAALRFGHLPGVFVPAGPMVSGI 187 Query: 150 YGKERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLM 209 E+ + V GR + L + E ++ G+C TAN+ ML E MGL Sbjct: 188 SNSEKAKVRQQFAEGKV----GR-DALLESEMASYHSAGTCTFYGTANSNQMLLEIMGLQ 242 Query: 210 LPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPD--KILTRKALENAIAVDMALGGST 267 LPG+S V R + V + + P I+ + + NAI +A GGST Sbjct: 243 LPGSSFVNPGTPLRDALTRAATRVAVDLARDATAPALCHIVDERVIVNAIVGLLATGGST 302 Query: 268 NSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELG 327 N +HL A+A GI++ + F+++S VP +A + P+G+ V AGG+ +++EL Sbjct: 303 NHTIHLVAIARAAGIEVNWDDFNDLSAVVPLLARVYPNGKADVNHFHAAGGMGFLVRELL 362 Query: 328 EAGLIHKDALTV---------------TGKTVWENVKDAAVLDREVIRPLDNPYSPFGGL 372 +AGL+H+D T+ G W + + + D EV+ P P+SP GGL Sbjct: 363 DAGLLHEDVQTILGPGLRRWAEEPWLDNGTLAWRDAPEKS-HDPEVLAPAGEPFSPDGGL 421 Query: 373 AILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEG 432 ++ G++ V+K SAV E + A VF+ +++ + A + GE+E V V+R++G Sbjct: 422 RLVTGNI--GRGVIKVSAVAPENRVVRAPAIVFESQDELIAAFKRGELERDFVAVLRFQG 479 Query: 433 PRGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIAL 490 PR GM E+ T A+ +L G KVAL+TDGR SGA+ + PA H+SPEAA GGP+ L Sbjct: 480 PRAN-GMPELHQLTPALASLQDRGFKVALITDGRMSGASGKVPAAIHISPEAAMGGPLTL 538 Query: 491 VQDGDEIVIDIEKRRLD 507 ++ GD I++D + +L+ Sbjct: 539 LRTGDTILLDAVRGKLE 555 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: 895 Number of extensions: 48 Number of successful extensions: 7 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: 609 Length adjustment: 36 Effective length of query: 516 Effective length of database: 573 Effective search space: 295668 Effective search space used: 295668 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