Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_086511017.1 BZY95_RS16650 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_002151265.1:WP_086511017.1 Length = 599 Score = 295 bits (756), Expect = 3e-84 Identities = 189/521 (36%), Positives = 288/521 (55%), Gaps = 32/521 (6%) Query: 23 GLIDEELR--RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGI 80 G+ EEL +P+IG+ S +++ P + H ++ + VK GIR AGG P EF + Sbjct: 37 GITLEELAGGKPIIGICQSGSDLTPCNRHHIELVKRVKEGIRAAGGVPFEFPLHPI---- 92 Query: 81 AMGHEGMRY---SLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPV 137 HE R +L VE++ + LD VV+ T CDK TP L+AAA + +P Sbjct: 93 ---HENARRPTAALDRNLAYLGLVEVL-HGYPLDGVVLTTGCDKTTPASLMAAATVNIPA 148 Query: 138 ILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGR---TEELRKLEESALPGPGSCAGLF 194 I+++GGPM+ G G +R+ ++ + + G E L + +SA P G C + Sbjct: 149 IVLSGGPMLNGWRGPDRVGSGTIIWELRKRLAAGDIDYAEFLARATDSA-PSVGHCNTMG 207 Query: 195 TANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALE 254 TA+TMN ++EA+G+ LPG++ +PA R A TG RIV MV + L P ILTR+A E Sbjct: 208 TASTMNSMAEALGMSLPGSAMIPAPYKERAMVAYDTGARIVDMVWQDLRPSDILTRQAFE 267 Query: 255 NAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLD 314 NAI V ALGGS+N+ +H+ A+A G++L + + + +P +A++ P+G + + Sbjct: 268 NAIVVCSALGGSSNAPIHINAIARHSGVELTNDDWQALGHAIPLLANVMPAGAYLSEEFY 327 Query: 315 RAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAI 374 RAGG+PAV+ EL AG +H +ALTV G+T+ +N D EVIR DNP G Sbjct: 328 RAGGVPAVVNELLGAGKLHGEALTVNGRTLADNCAGRETQDPEVIRRYDNPLVEQAGFLN 387 Query: 375 LKGSLAPNGAVVKASAVKRELW-----------KFKGVARVFDREEDAVKAIRGG--EIE 421 LKG+L + A++K S + + F+G VFD ED I +I+ Sbjct: 388 LKGNLF-DSALMKTSVISADFRARFLSNPDDPNAFEGKVVVFDGSEDYHARIDDPALDID 446 Query: 422 PGTVIVIRYEGPRGGPGMREMLTATAAVMALGLG-DKVALVTDGRFSGATRGPAIGHVSP 480 T++V+R GP G PG E++ + G + + + DGR SG + P+I + +P Sbjct: 447 EHTILVMRGAGPVGHPGGAEVVNMQPPEALIKRGIESLPCLGDGRQSGTSGSPSILNAAP 506 Query: 481 EAAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRAR 521 EAA GG +AL++DGD + +D+ + + LLVD+ EL+ RR R Sbjct: 507 EAATGGGLALLEDGDRLRVDLNRGEVRLLVDDAELQARRER 547 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: 931 Number of extensions: 47 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: 599 Length adjustment: 36 Effective length of query: 516 Effective length of database: 563 Effective search space: 290508 Effective search space used: 290508 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