Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_086510991.1 BZY95_RS16565 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_002151265.1:WP_086510991.1 Length = 581 Score = 368 bits (945), Expect = e-106 Identities = 215/545 (39%), Positives = 325/545 (59%), Gaps = 18/545 (3%) Query: 15 HRALWRASGLIDEELR-RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73 +R+ + G+ D E +P+IG+ N+W+E+ P + H K+AE VK G+ AGG P+EF Sbjct: 24 YRSWMKNQGIPDHEFEGKPIIGICNTWSELTPCNAHFRKLAEHVKKGVLEAGGFPVEFPV 83 Query: 74 IAVCDGIAMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL 133 + + + +L S +V E + + LDAVV++ CDK TP L+ AA Sbjct: 84 FSNGESLLRPTAMFTRNLASMDV-----EESIRGNPLDAVVLLVGCDKTTPALLMGAASC 138 Query: 134 EVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTE--ELRKLEESALPGPGSCA 191 ++P I+++GGPM+ G + I ++ +++ +K G+ E E G+C Sbjct: 139 DIPTIVVSGGPMLNGKHEGRDIGSGTVVWQLSEQVKAGKISIHEFMSAEAGMSRSAGTCN 198 Query: 192 GLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRK 251 + TA+TM ++EA+G LP + +PAV+ARR A L+G RIV+MVEE L K+LTR+ Sbjct: 199 TMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHLSGNRIVEMVEEDLRLSKVLTRQ 258 Query: 252 ALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVV 311 A ENAI + A+GGSTN+V+HL+A+A +G++L L+ + I R P + + PSGR + Sbjct: 259 AFENAIRTNAAIGGSTNAVIHLKAIAGRIGVELDLDDWSRIGRGTPTLVDLQPSGRFLME 318 Query: 312 DLDRAGGIPAVLKELGEAG-LIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFG 370 + AGG+PAVL+ LGEA L H++ALTV G+T+W+NVK+A + + EVIRPL+ P G Sbjct: 319 EFYYAGGLPAVLRRLGEADRLPHREALTVNGRTLWDNVKEAPLYNDEVIRPLERPLREDG 378 Query: 371 GLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGG--EIEPGTVIVI 428 G+ +L+G+LAP GAV+K SA EL +G A VF+ +D I E++ +V+V+ Sbjct: 379 GMCVLRGNLAPRGAVLKPSAASPELMIHRGRAVVFEDFDDYKARINDPDLEVDASSVLVM 438 Query: 429 RYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGG 486 + GPRG GM E+ + A ++ G+ D V ++D R SG G + HV+PE+AAGG Sbjct: 439 KNCGPRGYHGMAEVGNMGLPAKLLEQGVTDMVR-ISDARMSGTAYGTVVLHVAPESAAGG 497 Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLR----RGILRRYAKMAL 542 P+A V+DGD I +D + L L VD+ ELE R A P + R G + Y + L Sbjct: 498 PLAAVRDGDWIELDCDAGTLHLEVDDAELEARLAERDPTAESRRIASDGGYRQLYIERVL 557 Query: 543 SADKG 547 AD+G Sbjct: 558 QADEG 562 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: 810 Number of extensions: 49 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: 552 Length of database: 581 Length adjustment: 36 Effective length of query: 516 Effective length of database: 545 Effective search space: 281220 Effective search space used: 281220 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 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