Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_043880120.1 AZC_RS07250 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >NCBI__GCF_000010525.1:WP_043880120.1 Length = 571 Score = 357 bits (917), Expect = e-103 Identities = 217/539 (40%), Positives = 299/539 (55%), Gaps = 15/539 (2%) Query: 16 RALLRACGLTDEEMDRPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVETIA 75 +A ++A G +D+ +DRP + + NT+S+ P H ++ ++ EAVK G+ +AGG+P E T++ Sbjct: 33 KAFIKAAGYSDDALDRPIIGITNTFSDFNPCHGNVPRLIEAVKRGVMLAGGLPMEFPTVS 92 Query: 76 LCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARLDL 135 + + + T S+ R L+A E +I A D V I CDK VP LM A ++ Sbjct: 93 IHESFSNPT-----SMFLRNLMAMDTEEMIRAQPMDAVVLIGGCDKTVPAQLMGAVSANV 147 Query: 136 PAAIVTGGPMEPGCVDGERVDLI-DAFEAVGAYEEGEISEEELEELEQRACPGPGSCAGM 194 PA + GPM G GE + D G + G + EE++ L R P G+C M Sbjct: 148 PAIQLITGPMLVGHHKGEILGACTDCRRLWGQHRAGHLDAEEMDVLSGRLAPTQGTCMVM 207 Query: 195 FTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTREAF 254 TA+TM C+ E LG++ PAT A+++R A+ +G + V+ G T RD+LT AF Sbjct: 208 GTASTMGCLVEALGIALPWTGTIPATHADRIRAAEASGRQAVQLATHGPTPRDLLTPAAF 267 Query: 255 LDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMRDL 314 +A+ V A+GGSTN ++HL AIAR A + + LD FD + R P L ++P G + M Sbjct: 268 RNALTVLQAIGGSTNGLVHLAAIARRAGLSVDLDAFDAIGRSVPVLIDLKPSGDHYMEHF 327 Query: 315 YEAGGVPAVMKELADDLHLDRIDFAGRSMRERVERT-EVKDREVIRPKEDPVHEEGGIVV 373 + AGGVP +MKEL D L GR++ E + EV + +IRP P+ GG+ V Sbjct: 328 HWAGGVPKLMKELGDHLDRSAPTIDGRTIGEIADAAEEVPGQAIIRPASAPLKPFGGMAV 387 Query: 374 LYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAI--LGGDIDPGDVVVIRYEG 431 L GNLAP GAVIK +A SE + H G AVVFDS E+ I G D+ DV+V+R G Sbjct: 388 LRGNLAPGGAVIKHSAASEALLRHTGRAVVFDSVEDMVNRIDDPGLDVQADDVLVLRNAG 447 Query: 432 PAGGPGMRE--MLTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGGPIAV 489 P G PGM E L L G+ D V ++D R SG G V H++PEA GGP+ + Sbjct: 448 PKGAPGMPEAGYLPIPKKLAQAGVKDMVR-ISDARMSGTAFGTIVLHITPEAAVGGPLGL 506 Query: 490 VEEGDTIRLDVRERRLEVDVEDEELEARLEEWEPP---EDEVTGYLRRYRELVRGADEG 545 V GDTIRLDV R + + V DEELE R EW PP + GY Y V ADEG Sbjct: 507 VRSGDTIRLDVAAREIALLVPDEELERRRAEWTPPAHLAEAARGYQHLYLTHVLQADEG 565 Lambda K H 0.317 0.137 0.396 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: 902 Number of extensions: 48 Number of successful extensions: 6 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: 549 Length of database: 571 Length adjustment: 36 Effective length of query: 513 Effective length of database: 535 Effective search space: 274455 Effective search space used: 274455 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 (21.6 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