Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate YP_004139524.1 Mesci_0301 Dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000185905.1:YP_004139524.1 Length = 570 Score = 371 bits (953), Expect = e-107 Identities = 213/541 (39%), Positives = 319/541 (58%), Gaps = 13/541 (2%) Query: 15 HRSLLARCGLTDDDFE-KPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGVAFEFNT 73 HRS + GL DD F+ +P IGI N++++ P H+H R L E +K GV AGG+ EF Sbjct: 20 HRSWMKNNGLPDDAFDGRPVIGICNTFSEFTPCHVHFRGLIEHIKAGVLEAGGLPLEFPV 79 Query: 74 MAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAAARL 133 + C + M + R + + VE + +DG+VL+ CDK P ++M AA Sbjct: 80 FS-CGESNLRPTAMLF----RNLASMDVEEAIRGNPMDGVVLMAGCDKTTPSLVMGAASC 134 Query: 134 DIPAIVVTGGPMLPGEFKGRKVDL-INVYEGVGTVSAGEMSEDELEELERCACPGPRSCA 192 D+P+IV++GGPML G F+GR++ +V++ V AG MSE + E P C Sbjct: 135 DLPSIVISGGPMLNGRFQGREIGSGTDVWKFSEDVRAGVMSEQDFANAESAMSRSPGHCM 194 Query: 193 GLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLKPTMIMSQE 252 + TA+TMA + EALG++LPG A AV +R+ +IAR++G+RIVEMV ENL+P+ I+ +E Sbjct: 195 TMGTASTMASMVEALGLALPGNAAYPAVDARRSRIARMTGRRIVEMVNENLRPSAILKKE 254 Query: 253 AFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASISPAGEHMM 312 AF NA+ V+ A+GGSTN +H+ AIA + G + LD +D R +P I + P+G +M Sbjct: 255 AFANAIRVNGAIGGSTNAVVHLLAIAGRV-GTELTLDDWDRYGRDVPTILDLMPSGRFLM 313 Query: 313 LDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIRPLDSPVHSEGGL 372 D AGGIPAV+K + D ++ + +T TG+TV++NI + + + +VIRP D + GG+ Sbjct: 314 EDFCYAGGIPAVMKEIGDLLDLDVLTVTGKTVRDNIRDAENYNPEVIRPRDKALTPNGGI 373 Query: 373 AILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGR--IDEGDVIVIRY 430 A+LRGNLAP G+++K A + +M H G A F D+ + +DE ++V++ Sbjct: 374 AVLRGNLAPDGAIIKPSAASPALMKHRGRAVAFEDIDDYKARVDDPALDVDEASIMVLKN 433 Query: 431 EGPKGGPGMREMLNPT--SAIAGMGLERVALITDGRFSGGTRGPCVGHVSPEAMEDGPLA 488 GPKG PGM E+ N + G+ + I+D R SG G V H +PEA GPLA Sbjct: 434 CGPKGYPGMAEVGNMALPRKLLKQGVRDMIRISDARMSGTAFGTVVLHAAPEAAIGGPLA 493 Query: 489 AVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVK-GWLARYRKLAGSADTGAV 547 V GD I +D+ +RKL +D+S +E+ R +S + P +++ G+ Y AD GA Sbjct: 494 LVRSGDFIELDVEARKLHLDVSAQELARRRESWLPPVPAMRGGYQGLYVDRVLQADRGAD 553 Query: 548 L 548 L Sbjct: 554 L 554 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: 887 Number of extensions: 48 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: 549 Length of database: 570 Length adjustment: 36 Effective length of query: 513 Effective length of database: 534 Effective search space: 273942 Effective search space used: 273942 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