Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate 3607836 Dshi_1244 Dihydroxy-acid dehydratase (RefSeq)
Query= SwissProt::P9WKJ5 (575 letters) >FitnessBrowser__Dino:3607836 Length = 569 Score = 334 bits (856), Expect = 6e-96 Identities = 221/550 (40%), Positives = 312/550 (56%), Gaps = 31/550 (5%) Query: 34 RGMLRAVGMDDEDF-AKPQIGVASSWNEITPCNLSLDRLANAVKEGVFSAGGYPLEFGTI 92 R ++ G D F +P IG+ ++W+E+TPCN L LA VK GV+ AGG+P+EF + Sbjct: 22 RSWMKNQGFPDHVFDGRPVIGICNTWSELTPCNHGLRTLAEGVKRGVWEAGGFPVEFPVM 81 Query: 93 SVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKSLPGMLMAAARLD 152 S+ + M M F R ++A VE ++A +DG VLL GCDK+ PG LM AA +D Sbjct: 82 SLGE-TQMKPTAMLF----RNLLAMDVEESIRAYGMDGVVLLGGCDKTTPGQLMGAASVD 136 Query: 153 LAAVFLYAGSILPGRAKLSD-GSERDVTIIDAFEAVGACSRGLMSRADVDAIERAICPGE 211 L ++ + AG +L G+ + D GS DV EAV A G M+ AD E + Sbjct: 137 LPSIVVSAGPMLNGKYRGQDIGSGTDVWKFS--EAVRA---GEMTLADFMNAEAGMSRSA 191 Query: 212 GACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVELLRRGITARDI 271 G C M TA+TMAS EA+GMSLP +AA PA D RR A +G+ +VE++ + I Sbjct: 192 GVCMTMGTASTMASLVEAMGMSLPLNAALPAVDARRMALAHLTGKRIVEMVEEDLRPSAI 251 Query: 272 LTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSGVPHLADVKPFGR 331 LTK AFENAI A GGSTNAV+HLLA+A A V L+L+DF IG +P L + P G+ Sbjct: 252 LTKPAFENAILANAAVGGSTNAVMHLLALAGRAGVDLTLKDF-EIGGEIPLLVNCMPSGK 310 Query: 332 HVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITPPDP--DGKVLRALA 389 ++M D + GG+PVV+ L D L + +++AA T + V+ A Sbjct: 311 YLMEDFAYAGGMPVVLSELRDH-------LRPATTVLGKDIAAYTEGAECFNRDVIHAYD 363 Query: 390 NPIHPSGGITILHGSLAPEGAVVKTAGFDSDVF--EGTARVFDG---ERAALDALEDGTI 444 P+ P+ G+ +L GSLAP+GA+VK + + EG A VF+ +A +D +D I Sbjct: 364 APVKPAAGLRVLRGSLAPDGAIVKPSAATDALLEHEGPAFVFENIEDMKANIDR-DDLPI 422 Query: 445 TVGDAVVIRYEGPKGGPGMREM--LAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCVGHI 502 T +V++ GPKG PGM E+ + I + G+ +D++ ++D R SG G + H+ Sbjct: 423 TPDTILVLKGCGPKGYPGMPEVGNMPIPAKLVREGV-RDMIRVSDARMSGTAYGTVILHV 481 Query: 503 APEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTGVLSKYV 562 APEA GGP+AL++ GDRIR+ VLD+L D E A+R+ + P PP YT G Y+ Sbjct: 482 APEAQAGGPLALVKTGDRIRVSAREGVLDLLVDATELAARRAAWQPDPPHYTRGYAKLYI 541 Query: 563 KLVSSAAVGA 572 V A GA Sbjct: 542 DHVLQADRGA 551 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: 931 Number of extensions: 54 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: 575 Length of database: 569 Length adjustment: 36 Effective length of query: 539 Effective length of database: 533 Effective search space: 287287 Effective search space used: 287287 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