Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate YP_004144367.1 Mesci_5219 Dihydroxy-acid dehydratase
Query= curated2:A0Q0E8 (554 letters) >NCBI__GCF_000185905.1:YP_004144367.1 Length = 575 Score = 375 bits (963), Expect = e-108 Identities = 217/541 (40%), Positives = 325/541 (60%), Gaps = 13/541 (2%) Query: 15 HRSLFYAMGYTPEDLK-KPLIGIVNSHNEIIPGHFHLNEIVQAVKLGVASAGGTPIEIPS 73 HRS G + +P+IGI N+ +E+ P + HL + VK GV AGG P+E P Sbjct: 24 HRSWMKNQGIPADAFDGRPVIGICNTWSELTPCNAHLRALADHVKRGVYEAGGLPLEFPV 83 Query: 74 IGICDGISMNHSGMKYPLASRELIADSIEAMTIAHKFDALVLVGNCDKIVPGMLMGAARL 133 + + + +M + M + R L++ +E + D ++L+ CDK P +LMGAA Sbjct: 84 MSLGES-NMRPTAMLF----RNLVSMDVEESIRGNPIDGVILLVGCDKTTPALLMGAASC 138 Query: 134 NVPAIYVSGGPMLPGKLKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCA 193 N+P I VSGGPML GK +G+ I ++ G + D EQ + GSC Sbjct: 139 NLPTIAVSGGPMLNGKFRGQDIGSGTHVWKFAEEVKAGRMPVADFLAAEQGQSRSAGSCM 198 Query: 194 GLFTANSMNSLAEALGVALPGNGTIPAPYGRRKQLAKYAGVKIMELVKKKIKLRDILTKE 253 + TA++M S+ EALG+ +P N IPA RR LA+ AG +I++LV++ + + +ILT++ Sbjct: 199 TMGTASTMASMVEALGIGMPDNAAIPAVDSRRGVLAQMAGRQIVDLVRRDVTIAEILTRQ 258 Query: 254 AFKNAIALDMAIGGSSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHHMV 313 AF+NAI ++ AIGGS+N LHL+AIA+ V L+LED+D + R +P I L P+G M Sbjct: 259 AFENAIRVNGAIGGSTNAVLHLIAIANRIGVDLSLEDWDRLGRDVPTIVDLMPSGRFLME 318 Query: 314 DLDEAGGISAVLKELMDANLIFKDQLTVTGKTLEENIKNSLVLNDSVIRPLNNPYSNEGG 373 D AGG++AV+ L + L+ +D +TV+ KT+ E I + N VIRP++ P + EGG Sbjct: 319 DFYYAGGLAAVMASLDEVGLLHRDAMTVSAKTIGELIDGAPNYNSEVIRPMSEPLTKEGG 378 Query: 374 IAILRGNLAPDGAVVKQSAVEPEMLYHKGVARVFDGEELAFDAIMNKK--IHPGDVVVIR 431 I+ILRGNLAPDGAV+K SA PE++ H+G A VF+ E + I + + I V+V++ Sbjct: 379 ISILRGNLAPDGAVIKPSAATPELMQHRGKAVVFENIEHYYARIDDPELDIDATSVMVLK 438 Query: 432 YEGPKGCPGMREM--LSPTAAIIGLGLEKSTALITDGRFSGGTRGPCIGHISPEASEGGP 489 GP+G PGM E+ + A ++ LG+ I+D R SG G + H++PEA+ GG Sbjct: 439 NCGPRGYPGMAEVGNMPLPAKLLKLGI-SDMVRISDARMSGTAYGTVVLHVAPEAAAGGA 497 Query: 490 IALIEEGDLIEIDISNRRISLLVSPEELSKRKENWIQPPCKAPDGTYLKRYSKLVTSAST 549 +AL+ +GDLIE+D++ RR+ LLVS EEL+ R+ +W +PP +P+G Y Y + V A Sbjct: 498 LALVRDGDLIELDVAGRRLELLVSEEELAIRRRDW-KPPA-SPEGGYQSLYVERVLQADK 555 Query: 550 G 550 G Sbjct: 556 G 556 Lambda K H 0.317 0.136 0.392 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: 789 Number of extensions: 36 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: 554 Length of database: 575 Length adjustment: 36 Effective length of query: 518 Effective length of database: 539 Effective search space: 279202 Effective search space used: 279202 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