Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_013092366.1 BC1002_RS22880 dihydroxy-acid dehydratase
Query= curated2:A0Q0E8 (554 letters) >NCBI__GCF_000092885.1:WP_013092366.1 Length = 578 Score = 342 bits (876), Expect = 3e-98 Identities = 205/528 (38%), Positives = 302/528 (57%), Gaps = 20/528 (3%) Query: 15 HRSLFYAMGYTPEDLK-KPLIGIVNSHNEIIPGHFHLNEIVQAVKLGVASAGGTPIEIPS 73 HRS MGY E+ KP+I I+N+ +EI P H H + V+ VK G+ AGG PIE+P Sbjct: 26 HRSRTAQMGYNREEYAGKPVIAILNTWSEINPCHTHFKQRVEEVKRGIWQAGGFPIELPV 85 Query: 74 IGICDGISMNHSGMKYPLASRELIADSIEAMTIAHKFDALVLVGNCDKIVPGMLMGAARL 133 + + + M Y R +A E M ++ D +VL+G CDK P +LMGA + Sbjct: 86 QTLSEPFQ-KPTTMLY----RNFLAMEAEEMLRSYPADGVVLMGGCDKTTPALLMGAISM 140 Query: 134 NVPAIYVSGGPMLPGKLKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCA 193 ++PAI++ GPML G G + ++ G L+ +D +E + G C Sbjct: 141 DLPAIFLPAGPMLRGNWNGVTLGSGSDSWRYWAELRAGTLTPEDWQGVEGSIARSPGHCM 200 Query: 194 GLFTANSMNSLAEALGVALPGNGTIPAPYGRRKQLAKYAGVKIMELVKKKIKLRDILTKE 253 + TA++M S AEALG LPG +IPA R Q+A G++I+E+V + +K D+LT Sbjct: 201 TMGTASTMTSAAEALGFTLPGFASIPAADSRHAQMAAKTGMRIVEMVWEDLKPSDLLTAA 260 Query: 254 AFKNAIALDMAIGGSSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHHMV 313 + NA+ +A+ GS+N+ +H++A+A A + LTL+ FD+I+RR P + + P G + M Sbjct: 261 SVDNAVTTCVALSGSTNSVVHMIALARRAGIALTLDRFDQIARRTPVLANIRPTGAYLME 320 Query: 314 DLDEAGGISAVLKELMDANLIFKDQLTVTGKTLEENIKNSLVLNDSVIRPLNNPYSNEGG 373 D AGG+ VL EL LI Q TV G+TL EN+ + + ND VIR NP + Sbjct: 321 DFFYAGGLRGVLAEL--GELIDGSQKTVNGRTLGENLAGAQIFNDDVIRRRTNPLLRDSS 378 Query: 374 IAILRGNLAPDGAVVKQSAVEPEMLYHKGVARVF-DGEELAF----DAIMNKKIHPGDVV 428 +A+LRGNLAPDGAV+K A EP +L H G A VF D ++A DA+ I V+ Sbjct: 379 LAVLRGNLAPDGAVIKPGAAEPHLLVHTGRAVVFSDYTDMAARIDDDAL---DIDESCVL 435 Query: 429 VIRYEGPKGCPGMRE--MLSPTAAIIGLGLEKSTALITDGRFSGGTRGPCIGHISPEASE 486 V+++ GP G GM E L ++ G+ + I+D R SG + G C+ H++PEA Sbjct: 436 VLQHAGPVGA-GMPEWGQLPIPRKLLQKGV-RDMVRISDARMSGTSYGACVLHVAPEAFV 493 Query: 487 GGPIALIEEGDLIEIDISNRRISLLVSPEELSKRKENWIQPPCKAPDG 534 GGP+AL+ GDLIE+D+ RR++LL+S EE ++RK W++P + G Sbjct: 494 GGPLALVRSGDLIELDVPRRRLNLLISDEEFARRKAAWVKPAARFERG 541 Lambda K H 0.317 0.136 0.392 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: 748 Number of extensions: 29 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: 554 Length of database: 578 Length adjustment: 36 Effective length of query: 518 Effective length of database: 542 Effective search space: 280756 Effective search space used: 280756 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