Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate BPHYT_RS25650 BPHYT_RS25650 dihydroxy-acid dehydratase
Query= SwissProt::P9WKJ5 (575 letters) >FitnessBrowser__BFirm:BPHYT_RS25650 Length = 588 Score = 496 bits (1277), Expect = e-144 Identities = 267/563 (47%), Positives = 355/563 (63%), Gaps = 9/563 (1%) Query: 18 KPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKE 77 K RSR VTDG+ +A R LRA G+DDE KP + + ++ E TPC++SL+++++ V+ Sbjct: 6 KHRSRRVTDGVTRAPHRAFLRATGLDDESMQKPFVAIVDTFGENTPCSMSLNQVSDNVRL 65 Query: 78 GVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGC 137 G+ + GG P+ ISVSDG SM H GM SLVSREV+ADSVE+ ++A D + +AGC Sbjct: 66 GIAAGGGVPIRGSAISVSDGTSMNHSGMRMSLVSREVVADSVELFVRAHNYDALIGVAGC 125 Query: 138 DKSLPGMLMAAARLDLAAVFLYAGSILPGRAK------LSDGSERDVTIIDAFEAVGACS 191 DK+LPG+LM R+++ VFL+ G++LPG A G +R TI+ EAVG Sbjct: 126 DKTLPGILMGMVRVNVPGVFLFGGAMLPGVAPGQLPGGAGTGLQRQSTILTTIEAVGTTQ 185 Query: 192 RGLMSRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFA 251 RG MSRA +DAIE+ P G+C G +TANTMA AE LG++ GSA PA R A Sbjct: 186 RGDMSRAQLDAIEKQCTPTAGSCPGQFTANTMAMVAETLGLAPLGSAMVPAVYSERIAIA 245 Query: 252 RRSGQAVVELLRRG-ITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSL 310 RR+G+ V+ +L +G RD++T E+ ENA A V A GGSTNA LH+ AIA+EA + +L Sbjct: 246 RRAGETVMRILTQGGPLPRDLVTMESLENACAAVAATGGSTNAALHIPAIANEAGIRFAL 305 Query: 311 QDFSRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAE 370 D R+ + +P + D++P GR++ D+ H GGVP V+ ALL G LHGD G T+AE Sbjct: 306 DDVQRVFAKIPLIGDLQPGGRYLAQDLHHAGGVPAVLNALLAGGFLHGDVPAFGGGTLAE 365 Query: 371 NLAAITPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFD 430 L+A + PDG V+R P+ +GG+ IL G+LAP+GA +K AG S F G RVF+ Sbjct: 366 ALSAFS--GPDGIVVRPCDEPLGENGGLVILRGNLAPDGACLKIAGLKSLSFTGAVRVFE 423 Query: 431 GERAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRF 490 E + + GD +VIR EGPKGGPGMREML +T AI G G+G+ V LLTDGRF Sbjct: 424 CEEDCMAVVAARDYREGDVLVIRNEGPKGGPGMREMLGVTAAIYGQGMGEKVALLTDGRF 483 Query: 491 SGGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPP 550 SG T G+C+G++ PEA GGPI LLRN DR+ +D +L V E A R+ D Sbjct: 484 SGATRGMCIGYVGPEAAAGGPIGLLRNDDRVHIDARAGILRVDLSDDELARRRADAPARA 543 Query: 551 PRYTTGVLSKYVKLVSSAAVGAV 573 R GVL KY LV A +GAV Sbjct: 544 SRRLAGVLEKYEALVRPAHLGAV 566 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: 1015 Number of extensions: 56 Number of successful extensions: 4 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: 588 Length adjustment: 36 Effective length of query: 539 Effective length of database: 552 Effective search space: 297528 Effective search space used: 297528 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 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