Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_051940866.1 BS73_RS27520 dihydroxy-acid dehydratase
Query= BRENDA::A0A481UJA7 (614 letters) >NCBI__GCF_000744815.1:WP_051940866.1 Length = 572 Score = 320 bits (820), Expect = 1e-91 Identities = 192/468 (41%), Positives = 275/468 (58%), Gaps = 24/468 (5%) Query: 135 GVSDAISMGTRGMCYSLQSRDLIADSIETVMSAQWYDGNISIPGCDKNMPGTIMAMGRLN 194 G+SD GT M YSL R+ D I + G I++ CDK GT+ A+ N Sbjct: 67 GISDGQRNGTPQMRYSLIGRETTNDGICLHLEGSDVRGAIAVVACDKPPVGTLAALLERN 126 Query: 195 RPSIMVYGGTIKPG--HYNGHSYDIISAFQAYGEYVNGSISDEDRKNVVHNSCPGAGACG 252 P++++ G+I+PG G DII+ FQA + ++R+ V + PG G+CG Sbjct: 127 VPAVIMSDGSIRPGVDSRTGERIDIITCFQA------AAAEPDERRRVALEASPGHGSCG 180 Query: 253 GMYTANTMASAIEAMGMCLPYSSSIPAENPLKLDECRLAGKYLLELL-KMDLKPQNIITP 311 GM+T NTM S I GM + S +E+P ++ E +L+LL + ++P++I+TP Sbjct: 181 GMFTYNTMQSFIATCGMEPLHMVSPASEDPRRIKEFPGQLLDVLQLLTERGIRPRDIVTP 240 Query: 312 QSLRNAMVVVMALGGSTNAVLHLIPIARSVGLE-----LTLEDFQKVSDEVPFLADLKPS 366 +LRNA +V +A+GGSTN VLH +AR+ G++ ++ ++F ++S +P L + P Sbjct: 241 AALRNATLVAIAMGGSTNVVLHAPELARAAGIDFWREVISQDEFNRMSRRLPVLVNAWPF 300 Query: 367 GKYVMEDVHKIGGTPAVLRYLLEHGFLDGDCLTVTGKTLAENVQNCPPLSEGQDIIRPLE 426 G+Y M D+ GG P ++ LL G LDG CLT TG+TLAE V P + D+I PL Sbjct: 301 GRYSMVDIDAKGGLPVIVNELLAAGMLDGSCLTCTGETLAEQVARLDPPAPDGDVIHPLS 360 Query: 427 NPIKKTGHIQILQGNLAPE-GSVAKI----TGKEGLYFSGPALVFEGEEAMLAAISENPM 481 P K TG +++L+GNLAPE G+V K+ +G E F G A VF+ E+A+L A++ P Sbjct: 361 APFKPTGGLRLLRGNLAPEGGAVIKLAGVESGMEDGRFVGRARVFDSEQALLDALTSAPE 420 Query: 482 NFKGK-VVVIRGEGPKGGPGMPEMLTPTSAI--MGAGLGKDCALLTDGRFSGGSHGFVVG 538 F+ + +VVIR EGP+G PGMPEML PTS I + G AL+TD RFSGGS G V+G Sbjct: 421 EFQDRDMVVIRYEGPRGAPGMPEMLDPTSRITALCRQRGITIALMTDARFSGGSVGLVIG 480 Query: 539 HICPEAQEGGPIGLVRNGDIIRIDVRERRIDVDVTDQ--EMEERRKNW 584 H+ PEA +GGPI L+ +GD I +DV + +D D EERR W Sbjct: 481 HVSPEAAQGGPIALIEDGDTIVVDVNQDTLDCTELDDPATAEERRARW 528 Lambda K H 0.316 0.135 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: 889 Number of extensions: 50 Number of successful extensions: 7 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: 614 Length of database: 572 Length adjustment: 37 Effective length of query: 577 Effective length of database: 535 Effective search space: 308695 Effective search space used: 308695 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 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