Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012852100.1 TCUR_RS08610 phosphogluconate dehydratase
Query= curated2:Q5SIY0 (555 letters) >NCBI__GCF_000024385.1:WP_012852100.1 Length = 613 Score = 285 bits (729), Expect = 4e-81 Identities = 190/543 (34%), Positives = 292/543 (53%), Gaps = 32/543 (5%) Query: 32 PFVGVVNTFTDGMPCNFHLRELAQHLKAGLKEAG-LFPFEFGAPAISDGISMGTPGMRAS 90 P + +V + D + + L++ LK + +AG G PA+ DG++ G GM S Sbjct: 77 PNIAIVTAYNDMLSAHQPLKDYPDLLKRAIGQAGGTAQVAGGVPAMCDGVTQGRAGMELS 136 Query: 91 LVSREVIADSVELIAQGYLYDGMVGLSACDKTIPGTAMGVIRSG-VPGMILYGGTIAPGE 149 L SR+V+A + + ++DG++ L CDK +PG +G + G +P +++ G +A G Sbjct: 137 LFSRDVVAMATAVALAHDMFDGVLLLGVCDKIVPGLVIGALAFGHLPAILVPAGPMASGL 196 Query: 150 WQGRKLTIVEVFEAVGQRAAGKISEEELLEIERRAIPGPGACGGQYTANTMAMALEALGL 209 +K + ++F A GK + EELLE E + PG C TAN+ + +E +GL Sbjct: 197 PNAQKAKVRKLF------AEGKATREELLEAEAASYHSPGTCTFYGTANSNQLLMEVMGL 250 Query: 210 SPVGYNAIPAVHPEKERATKEAGKILA--WAIAHDWKPK-DFLTRKSFLNAIAAVAATGG 266 G + +P +E T EAG+ + A+ + P + L ++F+N + A+ ATGG Sbjct: 251 HLPGASFVPPGTALREALTLEAGRRITELTALGGSYTPVGELLDERAFVNGVVALLATGG 310 Query: 267 STNAVLHLLALAKEAGVELSLDDFDQISRKTPVIADLRPWGTYTAWELYEAGGTALVFKR 326 STN LHL+A+A AG+EL+ DDFD++S TP++ L P G + AGGT + Sbjct: 311 STNHTLHLVAMAAAAGIELTWDDFDELSAVTPLLTRLYPNGGADVNHFHAAGGTGFLIGE 370 Query: 327 LLEAGLLFGEEKTLTGRT---------LAEEVERAY----REQEGQKVVFPVEKALKPHG 373 LLEAGLL + +T+ G+T L EE E + R+ V+ PV HG Sbjct: 371 LLEAGLLHADARTVGGKTLDDYRVTPELGEEGELVWRPAPRDSADTSVLRPVADPFDTHG 430 Query: 374 GLVVLKGNLAPKGAVLKLAGTERTY--FEGPARVFDSEEAAMEKVLKGEIRPGDVVVIRY 431 GL + GNL AV+K++ + + + PARVF S++ E GE+ VVV+R+ Sbjct: 431 GLRTVSGNLG--RAVVKVSAVDPAHRAVQAPARVFASQQELQEAFRAGELDGDVVVVVRH 488 Query: 432 VGPKGAPGMPEMLSVTSAI-VGEGLGPEVALLTDGRFSGGTRGLMIG-HIAPEAFVGGPI 489 GP+ A GMPE+ +T + V + G +VAL+TDGR SG + ++ H++PEA GGP+ Sbjct: 489 QGPR-ANGMPELHKLTPPLSVLQDRGHKVALVTDGRMSGASGSVLAAIHLSPEAAAGGPL 547 Query: 490 ALLEEGDRIRIDVEGRRLEVLLPEEELERRRARWRPRPPAFT-HGLFARYAALVRQADEG 548 A + +GD IR+D + L+VL+PEEEL R P T LFA + V A+ G Sbjct: 548 ARVRDGDLIRLDADEGVLQVLVPEEELAAREPAAAPGEQVGTGRELFAAFRRAVGPAERG 607 Query: 549 AVL 551 A + Sbjct: 608 AAV 610 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: 956 Number of extensions: 56 Number of successful extensions: 7 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: 613 Length adjustment: 36 Effective length of query: 519 Effective length of database: 577 Effective search space: 299463 Effective search space used: 299463 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