Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 15969 b1851 phosphogluconate dehydratase (NCBI)
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Keio:15969 Length = 603 Score = 249 bits (637), Expect = 2e-70 Identities = 171/523 (32%), Positives = 267/523 (51%), Gaps = 49/523 (9%) Query: 27 EELRRPLIGVANSWNEIVPGHVHLDKVAEAVKAGI-------RMAGGTPLEFGTIAVCDG 79 + + R I + S+N+++ H + E ++ + ++AGG P A+CDG Sbjct: 61 KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVP------AMCDG 114 Query: 80 IAMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVI 138 + G +GM SL SREVIA + + + + D + + CDKI PG +AA +P + Sbjct: 115 VTQGQDGMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAV 174 Query: 139 LINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTEELRKLEESALP--GPGSCAGLFTA 196 + GPM G+ KE++ R+ L EG+ + + LE A PG+C TA Sbjct: 175 FVPSGPMASGLPNKEKV-------RIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTA 227 Query: 197 NTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKAL 253 NT M+ E MG+ LPG+S V R ++ +M G + K++ K + Sbjct: 228 NTNQMVVEFMGMQLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVV 287 Query: 254 ENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDL 313 N I +A GGSTN +HL A+A GI + + F ++S VP +A + P+G + Sbjct: 288 VNGIVALLATGGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHF 347 Query: 314 DRAGGIPAVLKELGEAGLIHKDALTV---------------TGKTVWENVKDAAVLDREV 358 AGG+P +++EL +AGL+H+D TV G+ W + + LD V Sbjct: 348 QAAGGVPVLVRELLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKS-LDSNV 406 Query: 359 IRPLDNPYSPFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGG 418 I + P+S GG +L G+L AV+K SAV E + A VF+ + D + A G Sbjct: 407 IASFEQPFSHHGGTKVLSGNL--GRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAG 464 Query: 419 EIEPGTVIVIRYEGPR--GGPGMREMLTATAAVMALGLGDKVALVTDGRFSGAT-RGPAI 475 ++ V+V+R++GP+ G P + +++ + L K+ALVTDGR SGA+ + P+ Sbjct: 465 LLDRDCVVVVRHQGPKANGMPELHKLMPPLGVL--LDRCFKIALVTDGRLSGASGKVPSA 522 Query: 476 GHVSPEAAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEER 518 HV+PEA GG +A V+DGD I ++ + L LLVDE EL R Sbjct: 523 IHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR 565 Lambda K H 0.319 0.138 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: 808 Number of extensions: 52 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: 552 Length of database: 603 Length adjustment: 36 Effective length of query: 516 Effective length of database: 567 Effective search space: 292572 Effective search space used: 292572 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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