Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011840931.1 RSPH17029_RS06605 phosphogluconate dehydratase
Query= curated2:Q5SIY0 (555 letters) >NCBI__GCF_000015985.1:WP_011840931.1 Length = 601 Score = 254 bits (650), Expect = 5e-72 Identities = 185/543 (34%), Positives = 269/543 (49%), Gaps = 33/543 (6%) Query: 32 PFVGVVNTFTDGMPCNFHLRELAQHLKAGLKEAGLFP-FEFGAPAISDGISMGTPGMRAS 90 P +G+V + D + + + + ++A + AG G PA+ DG++ G PGM S Sbjct: 67 PNLGIVTAYNDMLSAHQPYEDYPRLIRAAARRAGATAQVAGGVPAMCDGVTQGQPGMELS 126 Query: 91 LVSREVIADSVELIAQGYLYDGMVGLSACDKTIPGTAMGVIRSG-VPGMILYGGTIAPGE 149 L SR+VIA + + YD + L CDK +PG M G VP + + GG + G Sbjct: 127 LFSRDVIALAAGVSLSHNCYDAALFLGICDKIVPGLVMAAATFGHVPAVFVPGGPMTSGL 186 Query: 150 WQGRKLTIVEVFEAVGQRAAGKISEEELLEIERRAIPGPGACGGQYTANTMAMALEALGL 209 K + F A G++ E L+ E + GPG C TANT M +E +GL Sbjct: 187 PNDEKSRVRNQF------ATGEVGREALMAAEMASYHGPGTCTFYGTANTNQMLMEFMGL 240 Query: 210 SPVGYNAIPAVHPEKERATKEAGKILA--WAIAHDWKPK-DFLTRKSFLNAIAAVAATGG 266 G + + P +E T A + A A+ +D++P L ++F+N + + ATGG Sbjct: 241 HLPGASFVNPNTPLREALTVAAVERAAAITALGNDYRPVGQILDERAFVNGLVGLMATGG 300 Query: 267 STNAVLHLLALAKEAGVELSLDDFDQISRKTPVIADLRPWGTYTAWELYEAGGTALVFKR 326 STN VLHL A+A+ AGV L L+DF IS P++A + P G + AGG + + Sbjct: 301 STNLVLHLPAMARAAGVLLDLEDFADISEVVPLMAKVYPNGMADVNHFHAAGGLPYMIGQ 360 Query: 327 LLEAGLLFGEEKTLTGRTLA--------EEVERAYRE----QEGQKVVFPVEKALKPHGG 374 LL+AGLL E +T+ G L+ E +R+ + +++ P + +P GG Sbjct: 361 LLDAGLLHEEVQTVAGDGLSLYRREPVLTEDGLVWRDGPDASQNDRILRPATEPFQPSGG 420 Query: 375 LVVLKGNLAPKGAVLKLAGTERTYFEGPARVFDSEEAAMEKVLKGEIRPGDVVVIRYVGP 434 L L GNL + +R E PAR+F +EA GE VVV+R+ GP Sbjct: 421 LRQLSGNLGRGVMKVSAVAPDRHVIEAPARIFHDQEAVKAAFRAGEFTTDTVVVVRFQGP 480 Query: 435 KGAPGMPEMLSVTSAI-VGEGLGPEVALLTDGRFSGGTRGLMIG-HIAPEAFVGGPIALL 492 + A GMPE+ S+T + V + G VAL+TDGR SG + + H+APEA +GGP+A L Sbjct: 481 R-ANGMPELHSLTPVLSVLQDRGLRVALVTDGRMSGASGKVPSAIHVAPEAAMGGPLARL 539 Query: 493 EEGDRIRIDVEGRRLEVLLPEEELERRRARWRPRPPAFTHG----LFARYAALVRQADEG 548 GD +R+D RL+VL E R A HG LFA + A V A EG Sbjct: 540 RNGDLLRVDATTGRLDVLAEGFE---DRIPVEADLSASAHGIGRELFAAFRATVSSATEG 596 Query: 549 AVL 551 A + Sbjct: 597 AAV 599 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: 912 Number of extensions: 43 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: 601 Length adjustment: 36 Effective length of query: 519 Effective length of database: 565 Effective search space: 293235 Effective search space used: 293235 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