Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_089302713.1 CHB84_RS17445 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_900188115.1:WP_089302713.1 Length = 635 Score = 273 bits (699), Expect = 1e-77 Identities = 191/527 (36%), Positives = 276/527 (52%), Gaps = 44/527 (8%) Query: 30 RRPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMR 88 R+P I + +++N+++ H L+ A++ + GG G + A+CDGI G GM Sbjct: 75 RKPNIAIVSAYNDMLSAHKPLEDFPSALRKAVTDGGGIAQFAGGVPAMCDGITQGRAGME 134 Query: 89 YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMP 147 SL SR+VIA + + D +++ CDKI PG ++ A +P IL+ GPM Sbjct: 135 LSLFSRDVIAMATAVALSHDMFDGALLLGVCDKIVPGLVIGALSFGHLPTILVPAGPMTS 194 Query: 148 GVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAGLFTANTMNMLSEA 205 G+ E+ R+ L EG+ EEL + E ++ GPG+C TAN+ +L EA Sbjct: 195 GLPNSEK-------SRIRQLHAEGKVGREELLEAESASYHGPGTCTFYGTANSNQLLMEA 247 Query: 206 MGLMLPGASTVPAVEARRLWYAKLTGMRIVKMV--------EEGLTP-DKILTRKALENA 256 MGL LPG S V R G R+V + G TP ++ +A+ N Sbjct: 248 MGLHLPGTSFVNPGTDLRAALTHEAGRRVVGLTAPSGEDTAHPGYTPLADVVDERAVVNG 307 Query: 257 IAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRA 316 + +A GGSTN +HL A+A GIDL E F E+S P +A I P+G+ + A Sbjct: 308 VLALLATGGSTNHTMHLVAMAAAAGIDLRWEDFAELSAVTPLLARIYPNGQADINHFHAA 367 Query: 317 GGIPAVLKELGEAGLIHKDALTVTG----------------KTVWENVKDAAVLDREVIR 360 GG+ ++ +L +AGL+H D TV+G VW + A LD+ V+R Sbjct: 368 GGMGFLIGQLLDAGLLHPDTRTVSGHALSDAYRTEPALDGVSLVWRDA-PAESLDKTVLR 426 Query: 361 PLDNPYSPFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEI 420 + +P+SP GGL +L G+L AVVK SAV+ E + ARVFD + + A GE+ Sbjct: 427 GVSDPFSPEGGLRMLTGNL--GNAVVKTSAVRDEHRVVQAPARVFDDQSGFLAAFEAGEL 484 Query: 421 EPGTVIVIRYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGAT-RGPAIGH 477 + V V+R++GPR GM E+ LT T V+ G VALVTDGR SGA+ + PA H Sbjct: 485 DRDLVAVVRFQGPRAN-GMPELHKLTPTLGVLQ-DRGHTVALVTDGRMSGASGKVPAGIH 542 Query: 478 VSPEAAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKP 524 ++PEAA GG +A ++DGD I +D L++LVD E R A P Sbjct: 543 LTPEAADGGTLARLRDGDPIRLDTTSGTLEVLVDAHEFAAREADAAP 589 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: 949 Number of extensions: 59 Number of successful extensions: 9 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: 635 Length adjustment: 37 Effective length of query: 515 Effective length of database: 598 Effective search space: 307970 Effective search space used: 307970 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 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