Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate H281DRAFT_06137 H281DRAFT_06137 dihydroxyacid dehydratase (EC 4.2.1.9)
Query= curated2:B9MPM8 (552 letters) >FitnessBrowser__Burk376:H281DRAFT_06137 Length = 583 Score = 362 bits (928), Expect = e-104 Identities = 212/547 (38%), Positives = 314/547 (57%), Gaps = 14/547 (2%) Query: 8 KGFEKAPQRSLFKAMGYTDEEIRRPLIAVVNSWNEVVPGHIHLDRIAEAVKAGIRLAGAT 67 +GF +++ K GYTD+ + RP+I +VN+ + H ++ ++ EAVK G+ LAG Sbjct: 27 QGFSLFLRKAFIKGAGYTDQALDRPVIGIVNTGSGFNACHGNMPQLVEAVKRGVMLAGGL 86 Query: 68 PMEFNVIGVCDGIAMGHIGMKYSLITRELIADSIEAMVMAHQFDGMVLIPNCDKIVPGML 127 P++F I V + + S+ R L++ E M+ A D +VLI CDK VP L Sbjct: 87 PVDFPTISVHESFSS-----PTSMYLRNLMSMDTEEMIRAQPMDAVVLIGGCDKTVPAQL 141 Query: 128 IAAARVNIPAILISGGPMLAGKI-GDKVCDLNSVFEGVGAYSAGKISEEDLYALEENACP 186 + AA IPAI + G ML G ++V G + A +I +E++ + Sbjct: 142 MGAASAEIPAIQLVTGSMLTGSHRSERVGACTDCRRYWGKFRASEIDQEEINDVNNQLVA 201 Query: 187 GCGSCSGMFTANTMNCLSEVLGLALPGNGTIPAVMAARIRLAKMAGMKIVELVEKDIKPS 246 G+CS M TA+TM C++E LG+ +PG T PAV A RIR+A+ G V+L + + Sbjct: 202 SVGTCSVMGTASTMACIAEALGMTVPGGATPPAVTADRIRVAEQTGTTAVKLASERLTID 261 Query: 247 DILTVEAFENALAVDMALGGSTNTILHLPAIANEVGIKLNLDIINAISDRTPNLCKLSPA 306 ILT +AFENA+ V +A+GGSTN I+HL A+A +G K+ LD ++ + TP L L P Sbjct: 262 KILTPKAFENAMRVLLAIGGSTNAIVHLSAVAGRLGHKIGLDSLDRMGKETPVLLDLKPT 321 Query: 307 GQHHIEDLYFAGGVQAVMNELSKKGLLHLNLMTVTGKTVGENIKDANVK-NYNVIRPIDN 365 GQH++ED + AGGV ++ EL K LLHL+ MTV+G T+GE I+ + + +V+R Sbjct: 322 GQHYMEDFHKAGGVATLLREL--KPLLHLDAMTVSGHTLGEQIEASGPGFSQDVVRSFSQ 379 Query: 366 PYSETGGLVIVRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAILKGK--IQK 423 P GGL +VRGNLAP GA++K+SA PKLM+H G A VFE+ E++ + ++ Sbjct: 380 PIYPQGGLAVVRGNLAPGGAIIKQSAADPKLMEHEGRAVVFENLEDLINRVDDESLDVKA 439 Query: 424 GDVIVIRYEGPKGGPGMRE--MLSPTSALAGVGLIEDVALITDGRFSGATRGACFGHVSP 481 DV+V++ GP G PGM E + LA G ++D+ I+DGR SG G HV+P Sbjct: 440 DDVLVLKNIGPVGAPGMPEAGYIPIPRKLARAG-VKDMVRISDGRMSGTAFGTIVLHVTP 498 Query: 482 EAAERGPIAAVQDGDMISIDIENKTLTLEVPEEEIKRRLEILPPFEPKVKKGYLYRYSKL 541 EAA GP A VQ+GD I + + N+ ++L V +E++K+R P P +GY + + Sbjct: 499 EAAAGGPFAYVQNGDRIRLSVSNREVSLLVSDEKLKQRAADKPIKRPTADRGYRKLFLQT 558 Query: 542 VRSASTG 548 V A G Sbjct: 559 VTQADEG 565 Lambda K H 0.318 0.137 0.394 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: 806 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: 552 Length of database: 583 Length adjustment: 36 Effective length of query: 516 Effective length of database: 547 Effective search space: 282252 Effective search space used: 282252 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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