Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_046009536.1 OLEAN_RS12750 phosphogluconate dehydratase
Query= curated2:A0Q0E8 (554 letters) >NCBI__GCF_000967895.1:WP_046009536.1 Length = 620 Score = 240 bits (612), Expect = 1e-67 Identities = 168/507 (33%), Positives = 266/507 (52%), Gaps = 44/507 (8%) Query: 34 IGIVNSHNEIIPGHFHLNEIVQAVKLGVASAGGTPIEIPSI-GICDGISMNHSGMKYPLA 92 IGI+N++N+I+ H + Q +K +A G + +CDGI+ SGM+ L Sbjct: 72 IGIINAYNDILSAHQPYKDYPQQIKSHLAELGHVAQMAAGVPAMCDGITQGQSGMELSLF 131 Query: 93 SRELIADSIEAMTIAHK-FDALVLVGNCDKIVPGMLMGAARL-NVPAIYVSGGPMLPGKL 150 SR+ IA S A+ ++H FD +VL+G CDKIVPG+LM A R ++PA+++ GPM G Sbjct: 132 SRDTIALST-AIGLSHDVFDGVVLLGICDKIVPGLLMAALRFGHLPAVFLPSGPMASGIT 190 Query: 151 KGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCAGLFTANSMNSLAEALGV 210 K + +A G + D+L + E S + G+C TANS L E +G+ Sbjct: 191 NSAKA-------KTRQKFAAGEVGKDELLESELKSYHSAGTCTFYGTANSNQMLLEIMGL 243 Query: 211 ALPGNGTIPAPYGRRKQLAKYAGVKIME---LVKKKIKLRDILTKEAFKNAIALDMAIGG 267 LPG+ I R L +YA ++ + + + I L +L +++F NAI +A GG Sbjct: 244 QLPGSSFIHPEDPLRPLLNQYALEQLTQHTAIEQDYIPLGQMLNEKSFVNAIVGLLATGG 303 Query: 268 SSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHHMVDLDEAGGISAVLKE 327 S+N ++HL+AIA A + L +D E+S +P +T++ P G + +AGG+ +++E Sbjct: 304 STNHSIHLVAIAKMAGIILDWQDISELSDVVPLLTRIYPNGEGDVNHFQQAGGMGFLIRE 363 Query: 328 LMDANLIFKDQLTVTG--------------KTLEENIK---------NSLVLNDSVIRPL 364 L+D L+ KD T+ G KTLE + N LN V+ P Sbjct: 364 LLDEGLLHKDVQTLLGKDLSAYCQEPYLVIKTLENGDQEAQLAWQDVNKESLNLDVLAPA 423 Query: 365 NNPYSNEGGIAILRGNLAPDGAVVKQSAVEPEMLYHKGVARVFDGEELAFDAIMNKKIHP 424 + P+ EGG+ +L GN+ ++K SAV Y K A+VF + A +++ Sbjct: 424 HAPFMREGGLKLLSGNIG--RGLIKISAVPESRWYTKAPAKVFTDQASVQQAYQRGELNC 481 Query: 425 GDVVVIRYEGPK--GCPGMREMLSPTAAIIGLGLEKSTALITDGRFSGGT-RGPCIGHIS 481 V+V++++GPK G P + +++ A + G + AL+TDGR SG + + P + H+ Sbjct: 482 DCVIVVKFQGPKANGMPELHKLMPVMANLQDAGF--NVALLTDGRLSGASGKVPAVLHLC 539 Query: 482 PEASEGGPIALIEEGDLIEIDISNRRI 508 PEA GG I I EGD+IEID ++ Sbjct: 540 PEALLGGAIDRIREGDIIEIDAHKAKV 566 Lambda K H 0.317 0.136 0.392 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: 779 Number of extensions: 41 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: 554 Length of database: 620 Length adjustment: 37 Effective length of query: 517 Effective length of database: 583 Effective search space: 301411 Effective search space used: 301411 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 (21.6 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