Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011952465.1 SWIT_RS08210 phosphogluconate dehydratase
Query= curated2:Q1ILZ0 (573 letters) >NCBI__GCF_000016765.1:WP_011952465.1 Length = 606 Score = 225 bits (573), Expect = 5e-63 Identities = 170/538 (31%), Positives = 260/538 (48%), Gaps = 32/538 (5%) Query: 43 IGIANTWIEIGPCNLHLRELAEHIKQGVREAGGTPMEFNTV-SISDGITMGSEGMKASLV 101 IGI + ++ + + +K REAG T V ++ DG+T G GM+ SL Sbjct: 69 IGIVTAYNDMLSAHQPYGGYPDRMKLWAREAGITAQVAGGVPAMCDGVTQGQRGMELSLF 128 Query: 102 SREVIADSIELVARGNLFDGLIALSGCDKTIPGTIMALERLD-IPGLMLYGGSIAPGKFH 160 SR+ IA S + +F+G L CDK +PG ++ R +P +++ G + G + Sbjct: 129 SRDTIALSTAVALSHGMFEGAALLGICDKIVPGLLIGALRFGHLPTILVPAGPMPSGLAN 188 Query: 161 AQKVTIQDVFEAVGTHARGKMSDADLEELEHNACPGAGACGGQFTANTMSMCGEFLGISP 220 +K ++ ++ A GK A+L E E + GAG C TAN+ M E +G+ Sbjct: 189 KEKQRVRQLY------AEGKAGRAELLEAESASYHGAGTCTFYGTANSNQMMMEVMGLHM 242 Query: 221 MGANSVPAMTVEKQQVARRCGHLVMELV--RRDIRPSQI-ITRKAIENAIASVAASGGST 277 GA V T +Q++ R H + E+ D RP + + KAI NA + A+GGST Sbjct: 243 PGAAFVNPGTKLRQELTRAAVHRLGEIGWDGGDYRPLGLCVDEKAIVNAAVGLLATGGST 302 Query: 278 NAVLHLLAIAHEMDVELNIEDFDKISSRTPLLCELKPAGRFTATDLHDAGGIPLVAQRLL 337 N V+HL AIA + ++ ED D++S+ PL+ + P G AGG+ V LL Sbjct: 303 NHVIHLPAIARAAGIMIDWEDIDRLSAAVPLIARVYPNGAGDVNHFQAAGGMAYVIATLL 362 Query: 338 EANLLHADALTVTGKTIAEEAKQ------------AKETP-GQEVVRPLTDPIKATGGLM 384 + LH D LTV G + A++ A P ++R DP + GG+ Sbjct: 363 DGGYLHRDILTVAGDDLGAYAREPLLDGEALVWTDAPAAPLDPAMLRSHADPFQPDGGMR 422 Query: 385 ILKGNLASEGCVVKLVGHKKLFFEGPARVFESEEEAFAGVEDRTIQAGEVVVVRYEGPKG 444 +++GNL V + E P R+F+ +++ A + VVVVR++GP+ Sbjct: 423 LVRGNLGRGTFKTSAVDRSRWTIEAPVRLFDDQDQVTAAFRAGELDRDVVVVVRFQGPRA 482 Query: 445 GPGMREMLGVTAAIAG-TELAETVALITDGRFSGATRGLSVG-HVAPEAANGGAIAVVRN 502 GM E+ +T + + VAL+TDGR SGA+ + H+ PEA GG IA +R+ Sbjct: 483 N-GMPELHKLTPPLGVLQDKGHKVALVTDGRMSGASGKVPAAIHLTPEAFAGGPIAKLRD 541 Query: 503 GDIITLDVERRELRVHLTDAELEARLRNWRAPEPRYK---RGVFAKYASTVSSASFGA 557 GD++ L ER E+ + AE EA R AP PR R +FA + +A GA Sbjct: 542 GDVVRLCAERGEILALVDAAEWEA--REPAAPPPRQPGTGRELFAFMRAGADTAERGA 597 Lambda K H 0.317 0.134 0.381 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: 908 Number of extensions: 53 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: 573 Length of database: 606 Length adjustment: 37 Effective length of query: 536 Effective length of database: 569 Effective search space: 304984 Effective search space used: 304984 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