Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_028998224.1 H537_RS0112690 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000430725.1:WP_028998224.1 Length = 566 Score = 356 bits (914), Expect = e-102 Identities = 215/531 (40%), Positives = 303/531 (57%), Gaps = 6/531 (1%) Query: 23 GLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGVAFEFNTMAICDGIAM 82 G+ ++D +KP I + NS +++ + HL ++A+ VKE + AAGGV FE T A D + Sbjct: 32 GIPEEDCDKPKIAVVNSSSELAACYSHLDQVAKVVKEAIRAAGGVPFEIRTAAPSDFVTG 91 Query: 83 NHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAAARLDIPAIVVTG 142 Y LA+R++V + +E LDG+V L +CDK VPG LMAAARL++P I+V Sbjct: 92 AGARGAYMLAARDLVTNDIEVAVEGAQLDGMVCLTSCDKTVPGQLMAAARLNVPTILVPC 151 Query: 143 GPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEELERCACPGPRSCAGLFTANTMAC 202 G GE+KG VD+ V+ V +E+ E+ RCA P C+GL TANTM Sbjct: 152 GYQASGEYKGAHVDIEEVFIHSMHVVTANKPAEEVVEMSRCAIRSPGVCSGLGTANTMHV 211 Query: 203 LTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLKPTMIMSQEAFENAVMVDL 262 EALG++LPG A A+S + Q AR +G RIV+MV ++LKP I+S+ AF NAV L Sbjct: 212 ACEALGLALPGSAPVRALSDKMFQDARAAGARIVQMVWDDLKPRDILSEGAFANAVKAVL 271 Query: 263 ALGGSTNTTLHIPAIAAEIDGLNINL-DLFDELSRVIPHIASISPAGEHMMLDLDRAGGI 321 A+GGS N H+ A+A E G +I++ +F+ P +A I P GE + + + AGG Sbjct: 272 AIGGSLNAVKHLQAVATEA-GSDIDVYAMFERFGPETPVVAGIRPIGERFIEEFEDAGGC 330 Query: 322 PAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIRPLDSPVHSEGGLAILRGNLAP 381 V+K L ++ +T +G TV +N+ V+V +VIRP PV + +LRGNLAP Sbjct: 331 RGVMKQLGALMDTTALTVSGATVADNLGTVQVRDEEVIRPASRPVAPRPAVVLLRGNLAP 390 Query: 382 RGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRIDEGDVIVIRYEGPKGGPGM-R 440 ++ K G V + GPA F++ DE + A+ GR+ G VIV+R G GGP M Sbjct: 391 EAALSKPGIVERKVRRFSGPAICFSTSDEALAAMNDGRVRPGQVIVMRGAGACGGPAMGG 450 Query: 441 EMLNPTSAIAGMGL-ERVALITDGRFSG-GTRGPCVGHVSPEAMEDGPLAAVNDGDIIRI 498 I G GL ++VA++TDG SG +G V V+PEA GPLA V DGD I I Sbjct: 451 GASRVVFGIDGKGLGDQVAMLTDGHLSGLVCKGLVVAEVAPEAALGGPLALVRDGDTITI 510 Query: 499 DIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWLARYRKLAGSADTGAVL 548 D+ +R+++VDLS E+ +R P +GWL YR+ G GAVL Sbjct: 511 DLDTRRVDVDLSDAELAQRRAQWQPPAPLFDRGWLQIYRRNVGPLSQGAVL 561 Lambda K H 0.319 0.136 0.397 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: 846 Number of extensions: 43 Number of successful extensions: 4 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: 549 Length of database: 566 Length adjustment: 36 Effective length of query: 513 Effective length of database: 530 Effective search space: 271890 Effective search space used: 271890 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 Jul 25 2024. The underlying query database was built on Jul 25 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