Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate SMc00884 SMc00884 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Smeli:SMc00884 Length = 574 Score = 362 bits (930), Expect = e-104 Identities = 217/546 (39%), Positives = 318/546 (58%), Gaps = 17/546 (3%) Query: 15 HRALWRASGLIDEELR-RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73 HR+ + G D RP+IG+ N+W+E+ P + HL +AE VK G+ AGG P+EF Sbjct: 24 HRSWMKNQGFPDHVFDGRPIIGICNTWSELTPCNSHLRILAEGVKRGVWEAGGFPVEFPV 83 Query: 74 IAVCDGIAMGHEGMR-YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAAR 132 + +G MR ++ R ++A VE + A+ +D VV++ CDK TPG L+ AA Sbjct: 84 SS------LGETQMRPTAMLFRNLLAMDVEEAIRAYGIDGVVLLGGCDKTTPGQLMGAAS 137 Query: 133 LEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSC 190 +++P I+++ GPM+ G + + I + + + ++ G +E E PG C Sbjct: 138 VDLPTIVVSSGPMLNGKWKGKDIGSGTDVWKFSEAVRAGEMSLQEFMAAESGMSRSPGVC 197 Query: 191 AGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTR 250 + TA TM + EAMGL LP + +PAV+ARR+ + +TG RIV+MV E L KILT+ Sbjct: 198 MTMGTATTMASIVEAMGLSLPTNAALPAVDARRMALSHMTGKRIVEMVHEDLRLSKILTK 257 Query: 251 KALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFV 310 + EN I + A+GGSTN+V+H+ A+A GIDL LE FD + +VP I + PSG++ + Sbjct: 258 ENFENGIIANAAVGGSTNAVVHMLAIAGRAGIDLCLEDFDRVGGQVPCIVNCMPSGKYLI 317 Query: 311 VDLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFG 370 DL AGG+PAV+ + L+H DA TV G + + + A V + +VIRPLDNP Sbjct: 318 EDLAYAGGLPAVMNRIQH--LLHPDAPTVFGVPISKYWEAAEVYNDDVIRPLDNPLRAAA 375 Query: 371 GLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGE--IEPGTVIVI 428 G+ +LKG+LAPNGAV+K SA L +G A VFD ED I + + T++V+ Sbjct: 376 GIRVLKGNLAPNGAVIKPSAASEHLLAHEGPAYVFDTIEDLRAKIDDPDLPVTEDTILVL 435 Query: 429 RYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGG 486 + GP+G PGM E+ + ++ G+ D V ++D R SG G + HVSPEA AGG Sbjct: 436 KGCGPKGYPGMAEVGNMPIPRRLVEKGVRDMVR-ISDARMSGTAFGTVVLHVSPEANAGG 494 Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSADK 546 P+A+V+ GD I +D K L+LLV E+EL R A W+P + RG + Y L ADK Sbjct: 495 PLAIVRTGDRIRLDALKGELNLLVSEEELAARMAAWQPPEQKWHRGYYKLYHDTVLQADK 554 Query: 547 GGALEY 552 G L++ Sbjct: 555 GADLDF 560 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: 894 Number of extensions: 37 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: 574 Length adjustment: 36 Effective length of query: 516 Effective length of database: 538 Effective search space: 277608 Effective search space used: 277608 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