Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012755650.1 RLEG_RS26495 dihydroxy-acid dehydratase
Query= curated2:B5YKD5 (550 letters) >NCBI__GCF_000023185.1:WP_012755650.1 Length = 578 Score = 338 bits (866), Expect = 4e-97 Identities = 195/540 (36%), Positives = 304/540 (56%), Gaps = 15/540 (2%) Query: 15 HRALLFATGI-PKSEMNKPFIGVATSFTDIIPGHISMKELERFIEKGIHTGGGYPFFFGI 73 HR+ G P+ KP I V +++D P H+ +E ++++GI GG+P Sbjct: 26 HRSRTMQMGYAPEDWQGKPIIAVINTWSDAQPCHMHFRERAEWVKRGILQSGGFPMELPA 85 Query: 74 PGICDGIAMGHKGMKYSLPSRELIADIIECIVEAHQFDGIVLLTNCDKITPGMLMAAARL 133 + + ++ R ++A E ++ +H DG VL+ CDK TPG++M A + Sbjct: 86 LSLSENFVK-----PTTMLYRNMLAMETEELLRSHPVDGAVLMGGCDKTTPGLVMGAVSM 140 Query: 134 DIPAIVLTAGPMLAGYYKGQRRNLTSDTFEAIGKFKKGVLTEKDLEALELCACPGAGSCQ 193 IP I L AGPML G Y G+ +D F+ + + G +T+++ + +E G C Sbjct: 141 GIPFIYLPAGPMLRGNYAGKTLGSGTDGFKYWDERRAGTITQEEWQGIEGGIARSYGHCM 200 Query: 194 GMYTANTMACVTEALGMSLPGTAATPAVMSEKRRLAFETGVKIVELVRKKINARQILTKE 253 M TA+TM + EA+G++LPG ++ PA + +R++ G +IV++V + + QI+T Sbjct: 201 TMGTASTMTAIAEAMGLTLPGASSIPAADANHQRMSAACGRRIVDMVWEDLTPDQIITPA 260 Query: 254 AFYNAIAVDMALGGSTNTVLHIKAIANEAGINLPLEVFDEISRKTPHLVNIIPSGEHY-M 312 A NA+ V MA G STN ++H+ A+A AG+ L L+ D I R TP L NI PSG Y M Sbjct: 261 AVDNAVTVAMATGCSTNAIIHLIAMARRAGVPLELDDLDRIGRTTPVLANIRPSGSTYLM 320 Query: 313 EDLYKAGGIPAVLKRLKDKIYSNP-TVSGIDIKEIAQKAEIYDENVIRSIKKAYHKEGGV 371 ED + AGG+ A++K+L DK+ TV G + + + +IY+++VIR + + EG + Sbjct: 321 EDFFYAGGLRALMKQLGDKLDPTAITVMGKPLVDGLDQVKIYNDDVIRPLSNPVYHEGSL 380 Query: 372 AILKGNLAPDGAVVKQTAVSSKMLKFEGIARCFDSEENAMKAILDG---KIKEGDVIIIR 428 A+LKGNL PDGAV+K A K + G A DS MK I+D + V+++R Sbjct: 381 AVLKGNLCPDGAVIKPAACDPKFHRHRGPALVADSYAE-MKKIIDDPDYPLTPDTVLVLR 439 Query: 429 YEGPSGGPGMRE--MLSPTSAITGMGLNESVALITDGRFSGGTRGPCIGHVSPEAARGGP 486 GP GGPGM E M+ A+ +GL + V I+D R SG + G C+ HV+PE+ GGP Sbjct: 440 NAGPQGGPGMPEWGMIPMPKALLKLGLRDMVR-ISDARMSGTSFGACVLHVAPESYVGGP 498 Query: 487 IAIVKDGDKILIDIPKRKIEILISESEIKKRLKNWKPPKQKIEKGYLLRYARNVSSADKG 546 +A+++ GD + +DIP R + +L++E EI R W P + E+GY ++ ++ ADKG Sbjct: 499 LALLRTGDMVELDIPARSLNMLVAEEEITARRAAWVAPTRHYERGYGFMFSGHIEQADKG 558 Lambda K H 0.318 0.137 0.395 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: 751 Number of extensions: 31 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: 550 Length of database: 578 Length adjustment: 36 Effective length of query: 514 Effective length of database: 542 Effective search space: 278588 Effective search space used: 278588 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 (21.7 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