Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate SM_b20890 SM_b20890 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Smeli:SM_b20890 Length = 579 Score = 389 bits (998), Expect = e-112 Identities = 219/546 (40%), Positives = 329/546 (60%), Gaps = 15/546 (2%) Query: 15 HRALWRASGL-IDEELRRPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73 HR+ + GL D RP+IG+ N+W+E+ P + HL +AE VK G+ AGG P+EF Sbjct: 27 HRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEFPV 86 Query: 74 IAVCDGIAMGHEGMR-YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAAR 132 + G +R ++ R + A VE + + +D VV++ CDK TP L+ AA Sbjct: 87 FST------GESTLRPTAMMFRNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAAS 140 Query: 133 LEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSC 190 +++P I+++GGPM+ G + + + + + + ++K G EE E+ GSC Sbjct: 141 VDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMARSAGSC 200 Query: 191 AGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTR 250 + TA+TM ++EA+G+ L G + +PAV+ARR ++LTG RIV+MV+E L P ILT+ Sbjct: 201 MTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPSDILTK 260 Query: 251 KALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFV 310 +A ENAI V+ A+GGSTN+VLHL ALA +G+DL L+ +D + R VP I ++ PSG++ + Sbjct: 261 EAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPSGKYLM 320 Query: 311 VDLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFG 370 + AGG+P V+K + E GL+H DA+TV+G T+W +VK + +VI P + + G Sbjct: 321 EEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGVVNYNEDVILPREKALTKSG 380 Query: 371 GLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGG--EIEPGTVIVI 428 G+A+L+G+LAP GAV+K SA L + KG A VF+ ED I +I+ ++V+ Sbjct: 381 GIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVL 440 Query: 429 RYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGG 486 +Y GP+G PGM E+ + V+ G+ D + ++D R SG G I H +PEAA GG Sbjct: 441 KYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIR-ISDARMSGTAYGTVILHTAPEAAEGG 499 Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSADK 546 P+ALV++GD I +DI R L L V ++EL RRA W VKPL G Y K + AD Sbjct: 500 PLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIKTVMQADA 559 Query: 547 GGALEY 552 G L++ Sbjct: 560 GADLDF 565 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: 832 Number of extensions: 42 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: 579 Length adjustment: 36 Effective length of query: 516 Effective length of database: 543 Effective search space: 280188 Effective search space used: 280188 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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