Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011801097.1 PNAP_RS08485 dihydroxy-acid dehydratase
Query= curated2:A6UUU2 (550 letters) >NCBI__GCF_000015505.1:WP_011801097.1 Length = 579 Score = 334 bits (856), Expect = 6e-96 Identities = 190/541 (35%), Positives = 312/541 (57%), Gaps = 15/541 (2%) Query: 15 NRSLLKACGYTDEEIE-KPFIGIVNSFTEVVPGHIHLNTLAEAAKKGVYANGGTPFEFNT 73 +RS + GY ++ E KP I I+N+++++ H H E K+GV GG P E Sbjct: 25 HRSRVMQLGYGPQDWEGKPVIAIINTWSDIGTCHGHFKQRVEDVKRGVLQAGGFPLELPA 84 Query: 74 MAVCDGIAMGHEGMRYSLPSREIIADTVESMAKAHGFDGLVLIPSCDKIVPGMIMGALRL 133 +++ + + M Y R ++A VE + ++H DG VL+ CDK PG+++GAL Sbjct: 85 LSLSESLVKPTT-MLY----RNMLAMEVEELLRSHPIDGAVLMGGCDKTTPGLVLGALSA 139 Query: 134 NIPFIVITGGPMQPGELHGKKYDLIS-VFEGVGEYNVGKITKEELMEIETCACPGAGSCA 192 +PFI + GPM G + GK S ++ E GKI + +E+E G C Sbjct: 140 GVPFIYMPAGPMLRGNVKGKVLGSGSDTWKYWDERRAGKINATQWLEVEGGIARSHGHCM 199 Query: 193 GLFTANSMACLTETLGLSLPMCATTHATDAEKVRIAKRSGMKIVDLVKEDIKPTDLLTKE 252 + TA++M + E +GLSLP ++ A D+ +R+A G +IV +V ED+ P +L++ Sbjct: 200 TMGTASTMTGIAEAIGLSLPGASSIPAVDSNHIRMATECGRRIVSMVWEDLTPARMLSRA 259 Query: 253 SFENAILVDLALGGSSNTTLHIPALAYEIAPE-FITLDDFDRLCDEVPHIASLRPGGD-H 310 SFENAI V +A+G S+N +H+ A++ + LDDFD VP IA++RP GD + Sbjct: 260 SFENAITVAMAMGCSTNAIIHLVAMSRRAGEHCAVGLDDFDAASRRVPVIANIRPSGDTY 319 Query: 311 FISDLHRAGGIPAVLKILEQKIR-DANTVSGKSIKEIINEVKYIDYNIIRPVDKPVHETA 369 + D + AGG+ ++ +L+ ++ DA TV+GK + + + + ++++IRP+D P++ Sbjct: 320 LMEDFYYAGGMLGMMSVLKDHLKLDALTVTGKPLGDNLVGAEVYNHDVIRPLDNPIYAQG 379 Query: 370 GLRILKGNIAPDGCVVKISAVNPKMYKHEGPARVFNSEEETIDAI--LGGDIKEGDVVVI 427 L +L+GN+APDGCV+K SA P+ ++H GPA VF+ A+ D+ ++++ Sbjct: 380 ALAVLRGNLAPDGCVIKPSACAPQFFQHTGPALVFDDYPSMKAAVDDENLDVTADHIMIL 439 Query: 428 RYEGPAGGPGMRE--MLSPTSAICGMGLDDSVALITDGRFSGGSRGPCIGHISPEAMAGG 485 R GP GGPGM E ML + G+ D + I+D R SG S G CI H++PEA GG Sbjct: 440 RNAGPQGGPGMPEWGMLPIPLKLVKQGVKDMLR-ISDARMSGTSYGACILHVAPEAYIGG 498 Query: 486 PIAIIEEGDIIAIDMMAKEINLKISEEEIKERLANWKKPEIKVKKGYISRYAKLVSSANE 545 P+A+++ GD+I++D+ A+ I+L++S++E+ R A W P + ++GY A+ + A+ Sbjct: 499 PLALVKTGDLISVDVPARSIHLEVSDDELALRRAAWTAPPKRFERGYGWMSARHIQQADT 558 Query: 546 G 546 G Sbjct: 559 G 559 Lambda K H 0.317 0.138 0.400 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: 803 Number of extensions: 32 Number of successful extensions: 8 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: 550 Length of database: 579 Length adjustment: 36 Effective length of query: 514 Effective length of database: 543 Effective search space: 279102 Effective search space used: 279102 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 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