Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate BWI76_RS18100 BWI76_RS18100 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__Koxy:BWI76_RS18100 Length = 603 Score = 248 bits (633), Expect = 5e-70 Identities = 171/517 (33%), Positives = 264/517 (51%), Gaps = 35/517 (6%) Query: 27 EELRRPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHE 85 + + R I + S+N+++ H ++ + ++ + A G + A+CDG+ G + Sbjct: 61 KSMLRNNIAIITSYNDMLSAHQPYERYPDIIRKALHSANAVGQVAGGVPAMCDGVTQGQD 120 Query: 86 GMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGP 144 GM SL SREVIA + I + + D + + CDKI PG +AA +P I I GP Sbjct: 121 GMELSLLSREVIAMSAAIGLSHNMFDGALYLGVCDKIVPGLAMAALSFGHLPSIFIPSGP 180 Query: 145 MMPGVYGKERIDFKDLMERMNVLIKEGRTEELRKLEESALP--GPGSCAGLFTANTMNML 202 M G+ KE++ R+ L EG+ + + LE A PG+C TANT M+ Sbjct: 181 MASGLANKEKV-------RIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMV 233 Query: 203 SEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKALENAIAV 259 E MG+ LPG+S V R ++ ++ G + K+ K + N I Sbjct: 234 VEFMGMQLPGSSFVHPDAPLREALTAAAARQVTRLTGNGNEWMPLGKMFDEKVVVNGIVA 293 Query: 260 DMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGI 319 +A GGSTN +HL A+A GI + + F ++S VP +A + P+G + AGG+ Sbjct: 294 LLATGGSTNHTMHLVAMARAAGIIINWDDFSDLSDVVPLLARLYPNGPADINHFQAAGGV 353 Query: 320 PAVLKELGEAGLIHKDALTVTG-------KTVWENVKD-------AAVLDREVIRPLDNP 365 P +++EL + GL+H+D TV G W N + AA LD VI D P Sbjct: 354 PVLVRELLKGGLLHEDVHTVAGFGLSRYTMEPWLNNGELDWREGAAAPLDEAVIATFDKP 413 Query: 366 YSPFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTV 425 +S GG +L G+L AV+K SAV E + A VF+ + D + A G ++ V Sbjct: 414 FSRHGGTKVLSGNL--GRAVMKTSAVPVENQIIEAPAVVFESQHDVLPAFEAGLLDKDCV 471 Query: 426 IVIRYEGPR--GGPGMREMLTATAAVMALGLGDKVALVTDGRFSGAT-RGPAIGHVSPEA 482 +V+R++GP+ G P + +++ + L K+ALVTDGR SGA+ + P+ HV+PEA Sbjct: 472 VVVRHQGPKANGMPELHKLMPPLGVL--LDRRFKIALVTDGRLSGASGKVPSAIHVTPEA 529 Query: 483 AAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERR 519 GG +A V+DGD I ++ + L L VD+ EL R+ Sbjct: 530 YDGGLLAKVRDGDIIRVNGQTGELTLRVDDAELAARQ 566 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: 828 Number of extensions: 56 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 Apr 09 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