Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_028999114.1 H537_RS0119225 phosphogluconate dehydratase
Query= curated2:Q056W3 (617 letters) >NCBI__GCF_000430725.1:WP_028999114.1 Length = 602 Score = 176 bits (446), Expect = 3e-48 Identities = 148/526 (28%), Positives = 240/526 (45%), Gaps = 56/526 (10%) Query: 35 PIIAVVNSFTEFVPGHIHLRELGQLVSKEIEKSGGIAKEFNTI-AIDDGIAMGHSGMLYS 93 P I VV ++ + + H L+ E ++G + + A+ DG+ G GM S Sbjct: 66 PHIGVVTAYNDMLSAHQPYENYPALLRDEAHRNGATLQVAGGVPAMCDGVTQGTPGMELS 125 Query: 94 LPSRELIADSIEYMIQAHCVDAMVCISNCDKITPGMLLAALRL-NIPSVFVSGGPMESGK 152 L SR+ IA + DA + + CDKI PG+L+ AL ++P VFV GPM SG Sbjct: 126 LFSRDTIAMGTAIALTHDVFDAALLLGICDKIVPGLLIGALNFGHLPCVFVPAGPMSSGL 185 Query: 153 ILVNEKIIKIDLVDAMMHGANKNTSNKKLLNIEKSACPTCGSCSGMFTANSMNCLTEVLG 212 + ++ A +LL E +A G+C+ TANS L E +G Sbjct: 186 SNTEKSHVREQY-------AQGQVGRDELLQAESAAYHGPGTCTFYGTANSNQMLLEAMG 238 Query: 213 LSFPGNGSLLATHIDRKNLFLKAGKI---IVRNTKNYYENNDSSLLPRSIVTKENLKNAI 269 L PG + R++L +A + +V+ +N E D + + NA+ Sbjct: 239 LHVPGAAFIHPHDGLREDLSREAVRTALSLVQRKRNIGEQVDERV----------IVNAM 288 Query: 270 ILDISMGGSSNTVLHLLAMAYEANINFKMIDIDLLSRKVPHLCKISPSSSKYYMEDFHRA 329 + ++ GGS+N ++H +A+A A I D LS VP L ++ P+ S + F +A Sbjct: 289 VALLATGGSTNHLIHWVAVARAAGIRINWTDFAELSAVVPLLARVYPNGSA-DVNQFQQA 347 Query: 330 GGVFGILSELNKINLLNTSILNILRMSLEKTINKFDILKTKDKKIISFYSSGPGNKKTIY 389 GG +L EL + L+ +L + I Y+ P ++ Sbjct: 348 GGPGFVLRELLEAGCLHPDVLTVAEGG------------------IGAYTQVPVRQE--- 386 Query: 390 PFSQSFRWKKLDKDRIS-GCIRSKKYAYSKDGGLAVLTGNLAKNGSIIKTAAITNQSSKI 448 W L I +R+ +S GGL +LTGNL + S+IK +A+ Q + Sbjct: 387 ---GKLAWSALPPSPIDPSVVRTHGAPFSASGGLKLLTGNLGR--SVIKVSAVP-QDRHV 440 Query: 449 FSGPAKVYESQEDAVYAILNNYIKSGDIIVIRYEGPK--GGPGMQEMLYPTTYLKSMGLD 506 A+V++SQE + A ++ I V+R++GP+ G P + ++ P + G Sbjct: 441 VEASARVFDSQEALMAAFKAGELERDFIAVVRFQGPRANGMPELHKLTPPLAVQQGKGF- 499 Query: 507 KKCALITDGRFSGGTSGISIG-HISPEAANKGLIALVYDNDIININ 551 K AL+TDGR SG + + H++PEA + G +ALV D D+I ++ Sbjct: 500 -KVALVTDGRMSGASGKVPAAIHVTPEALDGGPLALVRDGDLIRLD 544 Lambda K H 0.318 0.135 0.384 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: 705 Number of extensions: 48 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 617 Length of database: 602 Length adjustment: 37 Effective length of query: 580 Effective length of database: 565 Effective search space: 327700 Effective search space used: 327700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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