Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012334621.1 M446_RS23595 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000019365.1:WP_012334621.1 Length = 603 Score = 300 bits (767), Expect = 1e-85 Identities = 190/512 (37%), Positives = 285/512 (55%), Gaps = 22/512 (4%) Query: 24 LIDEELRRPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGIAMG 83 L + + +PLIG+A + +++ P + H ++A+ V+ GI AGG EF C I Sbjct: 43 LAELQAGKPLIGIAQTGSDLSPCNRHHMELAKRVRDGITAAGGVAFEFP----CHPIQET 98 Query: 84 HEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILINGG 143 + +L VE++ + LD VV++T CDK P L+AAA + +P I +N G Sbjct: 99 GKRPTAALDRNLAYLSLVEVLY-GYPLDGVVLLTGCDKTMPACLMAAATVNIPAISLNVG 157 Query: 144 PMMPGVYGKERIDFKDLMERMNVLIKEGRTEELRKLE--ESALPGPGSCAGLFTANTMNM 201 PM+ G ER ++ + G + + L+ S+ P G C + TA+TMN Sbjct: 158 PMLNGWSRGERTGSGTVVWKARERHAAGDIDYQQFLDIVASSAPSTGHCNTMGTASTMNA 217 Query: 202 LSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIAVDM 261 L+EA+G+ LPG++ +PA R A TG RIV+MV E L P ILTR+A ENAI + Sbjct: 218 LAEALGMALPGSAAIPAPYRERGQAAYATGQRIVEMVWEDLKPSDILTREAFENAIVANT 277 Query: 262 ALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPA 321 A+GGSTN+ +H+ A+A +G+ L + ++ + +P + ++ P+G + + RAGG+PA Sbjct: 278 AIGGSTNAPIHINAIAKLIGVPLSCDDWERVGYDIPLLVNMQPAGAYLGEEYYRAGGLPA 337 Query: 322 VLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAILKGSLAP 381 VL EL EAG IH DALT G+TV EN ++A DREVI+P P G LKG+L Sbjct: 338 VLAELIEAGKIHADALTCNGRTVGENCREARTWDREVIKPYSEPLRERAGFLNLKGTLF- 396 Query: 382 NGAVVKASAVKREL-----------WKFKGVARVFDREEDAVKAIRGG--EIEPGTVIVI 428 + A++K S + RE + F+G VFD ED I +I+ TV+++ Sbjct: 397 DSAIMKTSVISREFYDRYLSNPGDPYAFEGRVVVFDGPEDYHHRIDDPALDIDENTVLIM 456 Query: 429 RYEGPRGGPGMREMLTATAAVMALGLGD-KVALVTDGRFSGATRGPAIGHVSPEAAAGGP 487 R GP G PG E++ + G + + DGR SG + P+I + SPEAAAGG Sbjct: 457 RGAGPIGYPGAAEVVNMQPPGALIRRGVLSLPCIGDGRQSGTSGTPSILNASPEAAAGGG 516 Query: 488 IALVQDGDEIVIDIEKRRLDLLVDEKELEERR 519 +AL+Q+GD + ID+ RR D+L+ ++EL RR Sbjct: 517 LALLQNGDRVRIDLNTRRADILLPDEELARRR 548 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: 880 Number of extensions: 45 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: 603 Length adjustment: 36 Effective length of query: 516 Effective length of database: 567 Effective search space: 292572 Effective search space used: 292572 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