Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate RR42_RS18585 RR42_RS18585 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Cup4G11:RR42_RS18585 Length = 577 Score = 364 bits (935), Expect = e-105 Identities = 206/529 (38%), Positives = 318/529 (60%), Gaps = 16/529 (3%) Query: 31 RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGIAMGHEGMR-Y 89 RP+IG+ N+++E+ P + H +AE VK G+ AGG PLEF ++ +G +R Sbjct: 44 RPVIGICNTYSELTPCNSHFRTLAEQVKIGVWEAGGFPLEFPVMS------LGETMLRPT 97 Query: 90 SLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILINGGPMMPGV 149 ++ R + + VE + + +D VV++ CDK TP ++ AA ++P I ++GGPM+ G Sbjct: 98 AMLFRNLASMDVEESIRGNPIDGVVLLMGCDKTTPALMMGAASCDLPTIGVSGGPMLSGK 157 Query: 150 YGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAGLFTANTMNMLSEAMG 207 + + + +M+ ++ G+ E+ + E G C + TA+TM + EA+G Sbjct: 158 FRGGELGSGTDVWKMSEQVRAGQMSQEDFFEAESCMHRSHGHCMTMGTASTMASMVEALG 217 Query: 208 LMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIAVDMALGGST 267 + LPG + +PAV+ RR A+ +G RIV+MV++ L KILTR A ENAI V+ A+GGST Sbjct: 218 MSLPGNAAIPAVDGRRNVLARASGRRIVEMVKDNLVMSKILTRDAFENAIRVNAAIGGST 277 Query: 268 NSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELG 327 N+V+HL A+A +G++L LE +D + ++P + + PSGRH + D AGG+PAV++EL Sbjct: 278 NAVIHLLAIAGRIGVELKLEDWDALGHELPCLLDLQPSGRHLMEDFYYAGGLPAVIREL- 336 Query: 328 EAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAILKGSLAPNGAVVK 387 ++ +DALTV GKT+W+N KDA +REVI P+ G+A+L+G+L P+GAV+K Sbjct: 337 -ESVLARDALTVNGKTLWDNCKDAPNWNREVIHAFGAPFKANAGIAVLRGNLCPDGAVIK 395 Query: 388 ASAVKRELWKFKGVARVFDREEDAVKAI--RGGEIEPGTVIVIRYEGPRGGPGMREM--L 443 SA L K G A VF+ E + + +++ V+V++ GPRG PGM E + Sbjct: 396 PSAATPALLKHTGRAVVFENSEHMHQRLDDESLDVDETCVLVLKNCGPRGYPGMAEAGNM 455 Query: 444 TATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGGPIALVQDGDEIVIDIEK 503 V+ G+ D V V+D R SG G + HV+PEAAAGGP+ALV+DGD + +D+ Sbjct: 456 PLPPKVLRKGITDMVR-VSDARMSGTAYGTVVLHVAPEAAAGGPLALVKDGDMVELDVPM 514 Query: 504 RRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSADKGGALEY 552 R+L L VDE EL+ RRA W+ P+ RG R Y + A+ G +++ Sbjct: 515 RKLHLHVDEAELQRRRAAWQAPALPMARGWTRLYVEHVQQANLGADMDF 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: 849 Number of extensions: 41 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: 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