Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_086014462.1 SWIT_RS08390 dihydroxy-acid dehydratase
Query= SwissProt::P9WKJ5 (575 letters) >NCBI__GCF_000016765.1:WP_086014462.1 Length = 571 Score = 483 bits (1243), Expect = e-141 Identities = 258/559 (46%), Positives = 353/559 (63%), Gaps = 10/559 (1%) Query: 18 KPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKE 77 K RS + +G+ + R L A+G DDED +P + V + E++PCN +L A K Sbjct: 8 KFRSEIIREGVVRTTTRSFLYALGEDDEDLRQPHVAVIHTGGEMSPCNTTLRDQALHAKT 67 Query: 78 GVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGC 137 G+++ GG E +SVSDG+S+ H GM FSL+SRE+IADSVE +++ + DG + + GC Sbjct: 68 GIYAGGGTAHECPVVSVSDGLSVAHSGMRFSLISRELIADSVEATVRSHQWDGVLAVGGC 127 Query: 138 DKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSR 197 DK++PG++M R ++ +VFLY G+ LPG RDV I+D +E +G G ++ Sbjct: 128 DKNMPGLMMGIVRCNVPSVFLYGGAALPGHL-----GGRDVNIVDTYEMIGRVLAGEATQ 182 Query: 198 ADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQA 257 +++ + RA P GAC G YTANTM +EALG++L GS+ PA R AR++G+ Sbjct: 183 GELEDMARACLPTAGACAGQYTANTMGMVSEALGLALLGSSMIPAVYAARAPMARKAGKV 242 Query: 258 VVE-LLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRI 316 ++ +L G RDI+T++A ENA AVV A GGSTNA LHL AIA+EA + L D + + Sbjct: 243 LMRAVLGGGPLPRDIVTRKALENACAVVAATGGSTNAPLHLPAIANEAGIDFDLDDVAAV 302 Query: 317 GSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAIT 376 + P +AD+KP GR + DV IGG PV++KALLD G LHGDC+TVTG T+AE+LA + Sbjct: 303 LARTPLIADLKPGGRFLAKDVFEIGGTPVILKALLDGGHLHGDCMTVTGRTLAEDLAKVC 362 Query: 377 PPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAAL 436 PPD G V+R PI PSGG+T+L G+LAP+GA++KTAG G ARVF+ E L Sbjct: 363 PPD--GAVVRDCGMPIAPSGGVTVLKGNLAPDGALLKTAGLKKLEHRGPARVFESEEQCL 420 Query: 437 DALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTG 496 A+ GD +VIR EGP+GGPGMREML IT + G G+G+ V L+TDGRFSG T G Sbjct: 421 SAVRAMAYAAGDVIVIRNEGPRGGPGMREMLGITALLYGQGMGEKVALITDGRFSGATRG 480 Query: 497 LCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRV--LDVLADPAEFASRQQDFSPPPPRYT 554 +C+G+I+PEA GPI L+R+GD I +D + L V E +R+ P R Sbjct: 481 MCIGYISPEAASDGPIGLVRDGDLIAIDARDGIVSLQVELPKGELEARRALPRPARVRPK 540 Query: 555 TGVLSKYVKLVSSAAVGAV 573 GVL KY +V A GAV Sbjct: 541 GGVLEKYAAIVGPANKGAV 559 Lambda K H 0.318 0.136 0.393 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: 1043 Number of extensions: 54 Number of successful extensions: 5 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: 575 Length of database: 571 Length adjustment: 36 Effective length of query: 539 Effective length of database: 535 Effective search space: 288365 Effective search space used: 288365 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