Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_050463927.1 AKL27_RS16435 phosphogluconate dehydratase
Query= curated2:Q5SIY0 (555 letters) >NCBI__GCF_001189915.1:WP_050463927.1 Length = 616 Score = 250 bits (639), Expect = 1e-70 Identities = 165/500 (33%), Positives = 253/500 (50%), Gaps = 26/500 (5%) Query: 34 VGVVNTFTDGMPCNFHLRELAQHLKAGLK-EAGLFPFEFGAPAISDGISMGTPGMRASLV 92 + +V+++ D + + Q LK ++ E G+ F G PA+ DGI+ G GM SL Sbjct: 70 IAIVSSYNDMLSAHQPFERFPQILKEAIRAEGGVAQFAGGVPAMCDGITQGQTGMELSLF 129 Query: 93 SREVIADSVELIAQGYLYDGMVGLSACDKTIPGTAMGVIRSG-VPGMILYGGTIAPGEWQ 151 SR+ IA S + ++D ++ L CDK +PG +G + G +P + + G + G Sbjct: 130 SRDTIAMSTAIALSHNMFDAVLYLGVCDKIVPGLLIGALHFGHLPAVFVPAGPMTSGMSN 189 Query: 152 GRKLTIVEVFEAVGQRAAGKISEEELLEIERRAIPGPGACGGQYTANTMAMALEALGLSP 211 K+ + +++ A GKI ELLE E ++ G C TAN+ M +EA+GL Sbjct: 190 SDKVKVRQLY------AEGKIGRTELLEAEAKSYHDAGTCTFYGTANSNQMLMEAMGLHL 243 Query: 212 VGYNAIPAVHPEKERATKEAGK--ILAWAIAHDWKPKDFLT-RKSFLNAIAAVAATGGST 268 G + P ++ T EAG+ + A+ + + P L KS +NAI A+ ATGGST Sbjct: 244 PGAAFVTPNTPMRDALTAEAGRQALKITALGNQYTPVGRLVDEKSIVNAIVALLATGGST 303 Query: 269 NAVLHLLALAKEAGVELSLDDFDQISRKTPVIADLRPWGTYTAWELYEAGGTALVFKRLL 328 N LHL+A+AK AG+ + DDF ++S P+I + P GT + AGGT V + LL Sbjct: 304 NHTLHLVAIAKAAGLIVDWDDFSKLSAVVPLITRIYPNGTADVNHFHAAGGTGFVIRELL 363 Query: 329 EAGLLFGEEKTLTGRTLAEEVER------------AYREQEGQKVVFPVEKALKPHGGLV 376 +AGL+ + T+ G+ L + E + V+ GGL Sbjct: 364 DAGLMHDDVMTILGQGLRAHCREPLLDGARPVWKDSPAESGDENVLRHAGNPFSADGGLK 423 Query: 377 VLKGNLAPKGAVLKLAGTERTYFEGPARVFDSEEAAMEKVLKGEIRPGDVVVIRYVGPKG 436 +L+GNL + E + PA VF S+EA M GE+ + V+ + GP+ Sbjct: 424 LLQGNLGRSVIKVSAVKHEHRAVQAPAIVFHSQEAFMHAFKAGELDKDFIAVLTFQGPR- 482 Query: 437 APGMPEMLSVTSAI-VGEGLGPEVALLTDGRFSGGTRGLMIG-HIAPEAFVGGPIALLEE 494 A GMPE+ ++T A+ + + G VAL+TDGR SG + + H+ PE GGP+ + Sbjct: 483 ANGMPELHALTPALGILQDKGRHVALVTDGRMSGASGKVPAAIHVTPEVLAGGPLGFVRT 542 Query: 495 GDRIRIDVEGRRLEVLLPEE 514 GD IR+D E LE L+P+E Sbjct: 543 GDMIRLDAEAGILEALVPQE 562 Lambda K H 0.318 0.138 0.405 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: 886 Number of extensions: 48 Number of successful extensions: 6 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: 555 Length of database: 616 Length adjustment: 37 Effective length of query: 518 Effective length of database: 579 Effective search space: 299922 Effective search space used: 299922 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 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