Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_005458787.1 SACCYDRAFT_RS19455 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >NCBI__GCF_000244975.1:WP_005458787.1 Length = 572 Score = 368 bits (944), Expect = e-106 Identities = 226/548 (41%), Positives = 314/548 (57%), Gaps = 23/548 (4%) Query: 16 RALLRACGLTDEEMDRPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVETIA 75 +A ++ G TD+ +DR V +V+T S P H + ++ EAVK G+ +AGG+P E TI+ Sbjct: 19 KAFIKGAGYTDDALDRTVVGIVDTGSGFNPCHGNAAQLVEAVKRGVLLAGGLPVEFPTIS 78 Query: 76 LCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARLDL 135 L + + T S+ R L++ E +I+A D V I CDK VP LM AA + Sbjct: 79 LHESFSNPT-----SMYLRNLMSMDTEEMIKALPLDAVVLIGGCDKTVPAQLMGAASAGI 133 Query: 136 PAAIVTGGPMEPGCVDGERVDLIDAFEAV-GAYEEGEISEEELEELEQRACPGPGSCAGM 194 PA + G M G G RV A G+Y GEI + E+ E+ R G+C+ M Sbjct: 134 PAIQLVTGSMLTGGYRGRRVGACTDCRAYWGSYRGGEIDDAEITEVNSRLVGSVGTCSVM 193 Query: 195 FTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTREAF 254 TA+TMAC++E +G++ A PA A++ RVA+ TG R V EG+T +LT +AF Sbjct: 194 GTASTMACVSEAMGIALPGSATPPAVTADRARVAEETGRRAVGLAAEGLTIDRILTEDAF 253 Query: 255 LDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMRDL 314 +A+RV +ALGGSTN ++HL AIA ++ LD FD LSRETP L ++P G + M DL Sbjct: 254 ENALRVLLALGGSTNGIVHLAAIAGRLGFDIDLDTFDALSRETPVLVNLKPAGSHYMEDL 313 Query: 315 YEAGGVPAVMKELADDLHLDRIDFAGRSMRERV-ERTEVKDREVIRPKEDPVHEEGGIVV 373 + AGGVP ++ EL D L+LD + GR++ E + ER E ++VIR +++PV+ GGI V Sbjct: 314 HRAGGVPRLLNELRDQLNLDALTVTGRTLGEELDERREDFPQDVIRTRDNPVYASGGIAV 373 Query: 374 LYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGGDID--PGDVVVIRYEG 431 L GNLAP GA++K AA S E+ EH G AVVF++ + I D+D DV+V++ G Sbjct: 374 LRGNLAPGGAIVKQAAASPELLEHRGRAVVFENSADLARRIDDDDLDVTADDVLVLKNIG 433 Query: 432 PAGGPGMRE--MLTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGGPIAV 489 P G PGM E + L G+ D V ++DGR SG G V HVSPEA GGP+ Sbjct: 434 PVGAPGMPEAGYIPIPKKLARAGVKDMVR-ISDGRMSGTAAGTIVLHVSPEAAVGGPLKH 492 Query: 490 VEEGDTIRLDVRERRLEVDVEDEELEARLE--------EWEPPEDEVTGYLRRYRELVRG 541 V GD +RL + ERRL+V++ EEL R + EPPE GY R + E V Sbjct: 493 VRTGDMVRLSISERRLDVEIPPEELRRREQADTSGTTAAVEPPE---RGYARLFVEQVTQ 549 Query: 542 ADEGAVLR 549 A+ G R Sbjct: 550 AEHGCDFR 557 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: 837 Number of extensions: 40 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: 572 Length adjustment: 36 Effective length of query: 513 Effective length of database: 536 Effective search space: 274968 Effective search space used: 274968 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