Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate H281DRAFT_02329 H281DRAFT_02329 dihydroxyacid dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Burk376:H281DRAFT_02329 Length = 577 Score = 395 bits (1014), Expect = e-114 Identities = 224/546 (41%), Positives = 332/546 (60%), Gaps = 17/546 (3%) Query: 15 HRALWRASGLIDEELR-RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73 HR+ + G+ +E RP+IG+ N+W+E+ P + H ++AE VK G+ AGG PLEF Sbjct: 27 HRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAEYVKKGVHEAGGLPLEFPV 86 Query: 74 IAVCDGIAMGHEGMR-YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAAR 132 ++ +G +R ++ R + + VE + + +D V+++ CDK TP L+ AA Sbjct: 87 MS------LGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCDKTTPALLMGAAS 140 Query: 133 LEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSC 190 +P + ++GGPM+ G + + I + +M+ ++ G EE + E G C Sbjct: 141 CNLPALAVSGGPMLNGRFRGKHIGSGTGVWQMSEEVRAGSMTQEEFTEAESCMNRSRGHC 200 Query: 191 AGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTR 250 + TA+TM + E++G+ LP + +PAV+ARR A L G RIV MV E LT DKILTR Sbjct: 201 MTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMVREDLTMDKILTR 260 Query: 251 KALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFV 310 +A ENAI + A+GGSTN+V+HL ALA +G++L LE + E+ VP + ++ PSG + + Sbjct: 261 QAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-ELGSNVPCLVNLQPSGEYLM 319 Query: 311 VDLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFG 370 D AGG+PAVLK+LGE GL+H++ALTV GKT+W+NV++A D +VI P+ P Sbjct: 320 EDFYYAGGLPAVLKQLGEQGLLHREALTVNGKTIWDNVRNAPNHDEKVITTFAEPFKPKA 379 Query: 371 GLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAI--RGGEIEPGTVIVI 428 G+A+LKG+LAPNGAV+K SA EL K +G A VF+ E+ I +I+ ++V+ Sbjct: 380 GIAVLKGNLAPNGAVIKPSAATAELLKHRGRAVVFENIEELHAKIDDESLDIDENCIMVL 439 Query: 429 RYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGG 486 + GP+G PG E+ + V+ G+ D V ++DGR SG G + HVSPEAAAGG Sbjct: 440 KGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVR-ISDGRMSGTAYGAVVLHVSPEAAAGG 498 Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSADK 546 P+A VQ GD I +D+E RRL L V + EL RRA W+ P +RG + Y + L AD+ Sbjct: 499 PLAFVQTGDMIELDVEARRLHLDVSDDELARRRAAWQAPESP-KRGYYKLYVEHVLQADQ 557 Query: 547 GGALEY 552 G L++ Sbjct: 558 GADLDF 563 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: 824 Number of extensions: 37 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: 552 Length of database: 577 Length adjustment: 36 Effective length of query: 516 Effective length of database: 541 Effective search space: 279156 Effective search space used: 279156 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 09 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