Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_013819526.1 METME_RS14635 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000214665.1:WP_013819526.1 Length = 606 Score = 246 bits (629), Expect = 1e-69 Identities = 174/512 (33%), Positives = 259/512 (50%), Gaps = 36/512 (7%) Query: 34 IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYSLP 92 +G+ +S+N+++ H E +K +R GG G + A+CDGI G GM SL Sbjct: 68 VGIISSYNDMLSAHEPYQHYPELIKQAVREVGGVAQFAGGVPAMCDGITQGMPGMELSLF 127 Query: 93 SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151 SR+VIA I + + DA + + CDKI PG LL +P + + GPM G+ Sbjct: 128 SRDVIALATAIGLSHNMFDAALYLGVCDKIVPGLLLGGLSFGHIPAVFVPAGPMTTGISN 187 Query: 152 KERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLM 209 KE+ R +G+ +EL + E A PG+C TAN+ M+ E MGL Sbjct: 188 KEK-------SRARQKFADGKIGEKELLESESKAYHSPGTCTFYGTANSNQMMVEIMGLH 240 Query: 210 LPGASTVPAVEARRLWYAKLTGMRIVKMVEEG--LTP-DKILTRKALENAIAVDMALGGS 266 LPG+S V R K +++K G P ++ KA+ NAI +A GGS Sbjct: 241 LPGSSFVNPYTPLRDELTKAAAKQVLKFTSLGNDFRPLGHMVNEKAIVNAIIGLLATGGS 300 Query: 267 TNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKEL 326 TN +HL A+A G+ + + FD +S+ +P + I P+G V AGG+ ++ EL Sbjct: 301 TNHTIHLIAIARAAGVIINWDDFDNLSKVIPLLTKIYPNGPADVNQFHSAGGMGILIGEL 360 Query: 327 GEAGLIHKDALTV----------------TGKTVWENVKDAAVLDREVIRPLDNPYSPFG 370 GL+H D LTV G+ WE + LD E+I ++ P++ G Sbjct: 361 LNHGLLHGDILTVGDQRGMAQYSQVPTLANGQLRWEPGPTQS-LDPEIIASVEKPFATGG 419 Query: 371 GLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRY 430 GL ++ G+L V K SAV + A VFD + D V A + GE+E ++V+R+ Sbjct: 420 GLHVIHGNL--GRGVTKVSAVAEKHQVVTAPAMVFDDQLDVVAAFKRGELEKDVIVVLRF 477 Query: 431 EGPRGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPI 488 +GP+ GM E+ T + L G VAL+TDGR SGA+ + P+ H+ PE GGP+ Sbjct: 478 QGPKAN-GMPELHKLTPIMGLLQDKGFHVALLTDGRMSGASGKVPSAIHMWPECIDGGPL 536 Query: 489 ALVQDGDEIVIDIEKRRLDLLVDEKELEERRA 520 A V+DGD IV++ + +++ VD E E R A Sbjct: 537 AKVRDGDIIVLNTQTGEVNVQVDAAEFEARVA 568 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: 834 Number of extensions: 51 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: 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