Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate SMc04144 SMc04144 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >FitnessBrowser__Smeli:SMc04144 Length = 574 Score = 372 bits (956), Expect = e-107 Identities = 217/538 (40%), Positives = 308/538 (57%), Gaps = 14/538 (2%) Query: 15 HRALLRACGLTDEEM-DRPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVET 73 HR+ L G E+ ++P +A++NT+S++ P H HL E VK G+ AGG P E+ Sbjct: 26 HRSRLYQMGYDHAELANKPVIAIINTWSDINPCHAHLRARAEEVKRGVWQAGGFPIELPA 85 Query: 74 IALCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARL 133 ++L + T M Y R +A +E +I +H DG V + CDK PG +M A ++ Sbjct: 86 MSLAETYVKPTT-MLY----RNFLAMEVEELIRSHPVDGVVLLAGCDKTTPGTIMGAIQV 140 Query: 134 DLPAAIVTGGPMEPGCVDGERVDL-IDAFEAVGAYEEGEISEEELEELEQRACPGPGSCA 192 DLP V GPM G G + D ++ E G ++E E E+E+ G+C Sbjct: 141 DLPTIFVPAGPMLRGNYRGRMLGSGSDVWKYWAEKEAGRVTENEWSEMERGIARSFGTCM 200 Query: 193 GMFTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTRE 252 M TA+TM + + LG+S +A PA +A R+A L+G RIVE + E + D+LT + Sbjct: 201 TMGTASTMTALADTLGLSLPGASAIPAADAGHARMAALSGARIVEMVFEDLKPSDILTAK 260 Query: 253 AFLDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMR 312 AF +A+ V MA+ GSTN ++HL+AIAR V L+LDDFD +S E P LC +RP G + M Sbjct: 261 AFENALAVHMAMAGSTNAMIHLIAIARRCGVPLTLDDFDRVSAEVPVLCNIRPTGEFLME 320 Query: 313 DLYEAGGVPAVMKELADDLHLDRIDFAGRSMRERVERTEVKDREVIRPKEDPVHEEGGIV 372 D Y AGG+ A+ K+L LH + G ++ ++ EV EVIRP + PV GG Sbjct: 321 DFYYAGGLIALWKQLKPLLHTGERNVIG-TIGGALDEAEVHLPEVIRPLDRPVAARGGTA 379 Query: 373 VLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGGDID--PGDVVVIRYE 430 +L GNLAP+G V+K AA + +H GPA+VFD + +A+ D+D V+++R Sbjct: 380 ILKGNLAPQGCVMKPAAADPALLQHRGPALVFDDYDAMMKAVNDDDLDVTADTVMILRNA 439 Query: 431 GPAGGPGMRE--MLTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGGPIA 488 GP GGPGM E ML L G+ D V ++D R SG + G C+ HV+PEAY GGP+A Sbjct: 440 GPVGGPGMPEWGMLPIPRKLLKEGVRDMVR-ISDARMSGTSYGACILHVAPEAYVGGPLA 498 Query: 489 VVEEGDTIRLDVRERRLEVDVEDEELEARLEEWEPPE-DEVTGYLRRYRELVRGADEG 545 V GD I LDV R + ++V+ E+E RL EW PPE D GYL+ + E ++ A EG Sbjct: 499 AVRNGDIIALDVARRTITLEVDQAEIERRLAEWRPPERDYSRGYLKMHAEHIQQAPEG 556 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: 828 Number of extensions: 38 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: 549 Length of database: 574 Length adjustment: 36 Effective length of query: 513 Effective length of database: 538 Effective search space: 275994 Effective search space used: 275994 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 09 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