Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate RR42_RS33305 RR42_RS33305 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >FitnessBrowser__Cup4G11:RR42_RS33305 Length = 579 Score = 353 bits (905), Expect = e-101 Identities = 204/539 (37%), Positives = 308/539 (57%), Gaps = 14/539 (2%) Query: 15 HRALLRACGLT-DEEMDRPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVET 73 HR+ + G + DE +DRP +A++NT+S++ P H H + + VK GI AGG P E+ Sbjct: 27 HRSRIMQMGYSPDEWLDRPIIAIINTWSDINPCHSHFKQRVDDVKRGILQAGGFPIELPA 86 Query: 74 IALCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARL 133 I+L + A+ M Y R ++A E +I +H DG V + CDK PG LM A+ Sbjct: 87 ISLSES-AVKPTTMLY----RNMLAMEAEELIRSHPVDGAVLMGGCDKTTPGLLMGASSA 141 Query: 134 DLPAAIVTGGPMEPGCVDGERVDL-IDAFEAVGAYEEGEISEEELEELEQRACPGPGSCA 192 +PA V GPM G G + DA++ G IS+ E +E G+C Sbjct: 142 GVPAIYVPAGPMLRGNWKGNVLGSGSDAWKFWDERRAGNISKTEWIGIEGGIARSHGTCM 201 Query: 193 GMFTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTRE 252 M TA+TM + E +GM+ ++ PA +A +R+ G RIV+ + E +T + + TR Sbjct: 202 TMGTASTMTAIAEAIGMTLPGASSIPAADANHIRMCSEAGRRIVDMVWEDLTPQRIQTRA 261 Query: 253 AFLDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGP-YTM 311 +F +AI V MA+G STN ++H++A+AR A ++ L+DFD+ SR P + +RP G Y M Sbjct: 262 SFENAIAVAMAMGCSTNAIIHVIAMARRAGHDIGLEDFDKTSRHVPVIANIRPSGDKYLM 321 Query: 312 RDLYEAGGVPAVMKELADDLHLDRIDFAGRSMRERVERTEVKDREVIRPKEDPVHEEGGI 371 D + AGG+PA+M ++D L+LD + GR++ E + EV + +VIR KE+ +++EG + Sbjct: 322 EDFFYAGGLPALMNRISDKLNLDALTVTGRTLGENIAGAEVYNDDVIRTKENALYQEGAL 381 Query: 372 VVLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGGDID--PGDVVVIRY 429 VL GN+AP G VIK +A + ++H GPA+VFD EA+ D+D ++++R Sbjct: 382 AVLKGNIAPDGCVIKPSACEKRFFKHTGPALVFDDYPSMKEAVERDDLDVTADHILILRN 441 Query: 430 EGPAGGPGMRE--MLTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGGPI 487 GP GGPGM E ML L G+ D + + +D R SG + G C+ HVSPE+Y GGP Sbjct: 442 AGPQGGPGMPEWGMLPIPKKLVQQGVRDMLRM-SDARMSGTSYGACILHVSPESYIGGPF 500 Query: 488 AVVEEGDTIRLDVRERRLEVDVEDEELEARLEEWEPPEDEV-TGYLRRYRELVRGADEG 545 A+V GD I +D+ R + ++V DEEL R W PP GY + + +R A++G Sbjct: 501 ALVRTGDMISVDIDRRSIHLEVSDEELARRKAAWTPPPPRFGRGYGWMFSKHIRQANDG 559 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: 801 Number of extensions: 30 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: 579 Length adjustment: 36 Effective length of query: 513 Effective length of database: 543 Effective search space: 278559 Effective search space used: 278559 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