Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_090447193.1 BLS63_RS18160 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_900100495.1:WP_090447193.1 Length = 608 Score = 256 bits (654), Expect = 2e-72 Identities = 173/507 (34%), Positives = 261/507 (51%), Gaps = 31/507 (6%) Query: 34 IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYSLP 92 + + +++N+++ H + E +K +R G G + A+CDG+ G GM + Sbjct: 68 VAIVSAYNDMLSAHQPYEHFPEQIKQALREIGSVGQFAGGVPAMCDGVTQGEPGMELGIA 127 Query: 93 SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151 SREVIA + + + DA + + CDKI PG L+ A R +P + + GPM G+ Sbjct: 128 SREVIAMATAVALSHNMFDAALYLGICDKIVPGLLMGALRFGHLPSLFVPAGPMPSGLSN 187 Query: 152 KERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLMLP 211 KE+ D R + +EL + E +A PG+C TANT +L E MGL LP Sbjct: 188 KEKADV-----RQRYAEGKATRDELLEAEMAAYHSPGTCTFYGTANTNQLLMEVMGLHLP 242 Query: 212 GASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKALENAIAVDMALGGSTN 268 GAS V R + ++ ++ + + +I+ + L N+I A GGSTN Sbjct: 243 GASFVNPNTPLRDALTREAAQQVTRLTRQSGQFMPLGEIVDERCLVNSIVALSATGGSTN 302 Query: 269 SVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGE 328 LH+ A+A GI L + ++S P +A + P+G+ + AGG+ +++EL + Sbjct: 303 HTLHMPAIAQAAGIQLTWQDMADLSAVTPTLAHVYPNGKADINHFQAAGGMAFLIRELLD 362 Query: 329 AGLIHKDALTVT---------------GKTVWENVKDAAVLDREVIRPLDNPYSPFGGLA 373 AGL+H+D TV G+ VW + + D V+RP+ P+S GGL Sbjct: 363 AGLLHEDVNTVAGHGLSRYTREPFLEDGQLVWRDGPRKS-HDESVLRPVVRPFSAEGGLR 421 Query: 374 ILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEGP 433 +++G+L V+K SAV E + ARVF ++ A + GE+E V V+R++GP Sbjct: 422 LMQGNL--GRGVMKVSAVDPEHQLVEAPARVFHDQQALADAFKAGELERDFVAVMRFQGP 479 Query: 434 RGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIALV 491 R GM E+ T + L G KVALVTDGR SGA+ + PA HV PEA GGP+A V Sbjct: 480 RSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVCPEAYGGGPLARV 538 Query: 492 QDGDEIVIDIEKRRLDLLVDEKELEER 518 +DGD I +D + L LLV+ EL R Sbjct: 539 RDGDLIRVDGKTGELQLLVEAAELAAR 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: 836 Number of extensions: 49 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: 608 Length adjustment: 36 Effective length of query: 516 Effective length of database: 572 Effective search space: 295152 Effective search space used: 295152 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