Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012405897.1 BPHY_RS33425 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >NCBI__GCF_000020045.1:WP_012405897.1 Length = 577 Score = 355 bits (911), Expect = e-102 Identities = 221/544 (40%), Positives = 310/544 (56%), Gaps = 16/544 (2%) Query: 15 HRALLRACGLTDEEMD-RPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVET 73 +R+ ++ G+ D E D RP + + NT+SE+ P + H K+ E VK GI AGG P E Sbjct: 24 YRSWMKNQGIPDHEFDGRPVIGICNTWSELTPCNAHFRKIAEHVKRGIYEAGGFPVEFPV 83 Query: 74 IALCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARL 133 + + T ++ +R L A +E I + D V + CDK P LM AA Sbjct: 84 FSNGESNLRPT-----AMLTRNLAAMDVEEAIRGNPIDAVVLLTGCDKTTPALLMGAASC 138 Query: 134 DLPAAIVTGGPMEPGCVDGERVDLIDA-FEAVGAYEEGEISEEELEELEQRACPGPGSCA 192 D+PA +VTGGPM G +DG+ + A ++ + + GEI + E G+C Sbjct: 139 DVPAIVVTGGPMLNGKLDGKDIGSGTAVWQLHESLKAGEIDLHKFLSAEAGMSRSAGTCN 198 Query: 193 GMFTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTRE 252 M TA+TMACM E LG S + AA PA ++ + +A ++GMRIVE EG+T +LTRE Sbjct: 199 TMGTASTMACMAEALGTSLPHNAAIPAVDSRRYVLAHMSGMRIVEMAHEGLTLSKILTRE 258 Query: 253 AFLDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMR 312 AFL+AIRV+ A+GGSTN V+HL AIA V+L LDD+ + R TP + + P G + M Sbjct: 259 AFLNAIRVNAAIGGSTNAVIHLKAIAGRIGVKLDLDDWVRIGRNTPTIVDLMPSGRFLME 318 Query: 313 DLYEAGGVPAVMKELAD-DL--HLDRIDFAGRSMRERVERTEVKDREVIRPKEDPVHEEG 369 + Y AGG+PAV++ L + DL H + G+++ V + + EVIRP + P+ ++G Sbjct: 319 EFYYAGGLPAVLRRLGEADLLPHPGAMTANGKALWHNVMDAPIYNDEVIRPLDKPLVKDG 378 Query: 370 GIVVLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGG--DIDPGDVVVI 427 GI VL GNLAP+GAV+K +A + + +H G AVVF++ E E I+ D+D V+V+ Sbjct: 379 GIRVLRGNLAPRGAVLKPSAATPALLKHRGRAVVFENFEHYKERIVDETLDVDANSVLVM 438 Query: 428 RYEGPAGGPGMREM--LTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGG 485 + GP G PGM E+ + L G+ D V ++D R SG G V HV+PEA GG Sbjct: 439 KNCGPKGYPGMAEVGNMGLPPKLLRQGVKDMVR-ISDARMSGTAYGTVVLHVTPEAADGG 497 Query: 486 PIAVVEEGDTIRLDVRERRLEVDVEDEELEARLEEWEPPEDEV-TGYLRRYRELVRGADE 544 P+A V++GD I LD L VD+ DEEL RLE PPE GY R Y + V ADE Sbjct: 498 PLAAVQDGDWIELDCDAGTLRVDIGDEELARRLERHTPPEMPAGGGYQRLYIDHVLQADE 557 Query: 545 GAVL 548 G L Sbjct: 558 GCDL 561 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: 855 Number of extensions: 41 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: 577 Length adjustment: 36 Effective length of query: 513 Effective length of database: 541 Effective search space: 277533 Effective search space used: 277533 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