Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_029001945.1 H537_RS0137420 IlvD/Edd family dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000430725.1:WP_029001945.1 Length = 578 Score = 367 bits (942), Expect = e-106 Identities = 213/530 (40%), Positives = 315/530 (59%), Gaps = 15/530 (2%) Query: 31 RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGIAMGHEGMR-Y 89 RP+IG+ N+W+E+ P + H K+AE VK G+ AGG P+EF + G +R Sbjct: 42 RPVIGICNTWSELTPCNAHFRKLAEHVKRGVYEAGGFPVEFPVFS------NGESNLRPT 95 Query: 90 SLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILINGGPMMPGV 149 ++ +R + A VE + + +DAVV++ CDK TP L+ AA +VP I+++GGPM+ G Sbjct: 96 AMLTRNLAAMDVEEAIRGNPIDAVVLLAGCDKTTPALLMGAASCDVPAIVVSGGPMLNGK 155 Query: 150 YGKERIDFKDLMERMNVLIKEGRTE--ELRKLEESALPGPGSCAGLFTANTMNMLSEAMG 207 + I + +++ +K G + E G+C + TA+TM ++EA+G Sbjct: 156 LEGKNIGSGTAVWQLHESLKAGEINLHQFLSAEAGMSRSAGTCNTMGTASTMACMAEALG 215 Query: 208 LMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIAVDMALGGST 267 LP + +PAV+ARR A ++G RIV+M EGLT KILTR+A ENAI + A+GGST Sbjct: 216 TSLPHNAAIPAVDARRYVLAHMSGQRIVQMALEGLTLSKILTREAFENAIRANAAIGGST 275 Query: 268 NSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELG 327 N+V+HL+A+A +G+ L LE + I R P I + PSGR + + AGG+PAVL+ LG Sbjct: 276 NAVIHLKAIAGRIGVPLELEDWTRIGRDTPTIVDLMPSGRFLMEEFYYAGGLPAVLRRLG 335 Query: 328 EAG-LIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAILKGSLAPNGAVV 386 EAG L H ALTV G ++W+NV++A + D EVIRPL P GG+ +L+G+LAP GAV+ Sbjct: 336 EAGRLPHPGALTVNGHSLWDNVREAPITDDEVIRPLQRPLIDDGGIRVLRGNLAPRGAVL 395 Query: 387 KASAVKRELWKFKGVARVFDREEDAVKAI--RGGEIEPGTVIVIRYEGPRGGPGMREM-- 442 K SA EL + +G A VF+ E + I ++ +V+V++ GPRG PGM E+ Sbjct: 396 KPSAASPELLRHRGRAVVFENLEHYKERIVDESLAVDASSVLVLKNCGPRGYPGMAEVGN 455 Query: 443 LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGGPIALVQDGDEIVIDIE 502 + ++ G+ D V ++D R SG G + HV+PEAAAGGP+A V+DGD I +D E Sbjct: 456 MGLPPKLLRAGVKDMVR-ISDARMSGTAYGTVVLHVAPEAAAGGPLAAVRDGDWIELDCE 514 Query: 503 KRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSADKGGALEY 552 L L + ++EL R + +P P G + Y L AD+G L++ Sbjct: 515 AGTLRLDIPDEELARRLSDVQPLPAPADGGYRKLYVNHVLQADEGCDLDF 564 Lambda K H 0.319 0.138 0.401 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: 863 Number of extensions: 40 Number of successful extensions: 6 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: 552 Length of database: 578 Length adjustment: 36 Effective length of query: 516 Effective length of database: 542 Effective search space: 279672 Effective search space used: 279672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Jul 25 2024. The underlying query database was built on Jul 25 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