Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_013420676.1 RVAN_RS15600 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000166055.1:WP_013420676.1 Length = 609 Score = 273 bits (698), Expect = 1e-77 Identities = 193/528 (36%), Positives = 276/528 (52%), Gaps = 42/528 (7%) Query: 21 ASGLIDEEL----RRPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTP-LEFGTIA 75 A G ID+E R P +G+ ++N+++ H ++ ++ R AG T + GT A Sbjct: 53 ACGPIDKERLREGRTPNLGIVTAYNDMLSAHQPYERFPPLIREAAREAGATAQVAGGTPA 112 Query: 76 VCDGIAMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-E 134 +CDGI G EGM SL SR+VIA + + + DA VM+ CDKI PG + AA Sbjct: 113 MCDGITQGFEGMDLSLFSRDVIALSTAVALSHQTFDATVMLGICDKIVPGLFIGAASFGH 172 Query: 135 VPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAG 192 +P + I GPM G+ E+ R+ L EG+ +EL E PG+C Sbjct: 173 LPTVFIPSGPMTSGLPNPEK-------SRIRQLYAEGKVGRDELLAAEAECYHAPGTCTF 225 Query: 193 LFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEG--LTP-DKILT 249 TANT M+ E MG+ +PGAS V A R + R + M G TP ++ Sbjct: 226 YGTANTNQMVMEMMGVHIPGASFVNANTPLRDALTREGVRRALAMTALGNEYTPFGAMVD 285 Query: 250 RKALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHF 309 ++ NAIA +A GGSTN LHL A++ +GI L + FD +S VP +A + PSG Sbjct: 286 ERSFVNAIAGVLATGGSTNHTLHLLAMSSAMGITLTWDDFDALSPVVPLVAHVYPSGAAD 345 Query: 310 VVDLDRAGGIPAVLKELGEAGLIHKDALTVTGKT----------------VWENVKDAAV 353 V AGG+P V++EL AGL+H D TV G T VW + + + Sbjct: 346 VNQFAAAGGLPFVIRELLAAGLLHGDIKTVWGTTLDAYAIEPGLDAEGQLVWRDAAEKSG 405 Query: 354 LDREVIRPLDNPYSPFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVK 413 D +++R +D P+S GG+ +L G+L AV+K SA+ E +G AR+F +E Sbjct: 406 -DEKILRSVDQPFSVEGGIRVLDGNL--GRAVMKTSALAPERLAIEGPARIFHSQEALQD 462 Query: 414 AIRGGEIEPGTVIVIRYEGPR--GGPGMREMLTATAAVMALGLGDKVALVTDGRFSGAT- 470 A + G + V V+R++GP+ G P + ++L + G +VAL+TDGR SGA+ Sbjct: 463 AFKAGALTGDFVAVVRFQGPKANGMPELHKLLPPLGVLQ--DRGQRVALLTDGRMSGASG 520 Query: 471 RGPAIGHVSPEAAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEER 518 + P+ HV+PEA AGGPIA ++DGD I ID L LV EKE R Sbjct: 521 KVPSAIHVTPEAVAGGPIARIRDGDIIRIDAVSGTLAALVGEKEWAAR 568 Lambda K H 0.319 0.138 0.401 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: 906 Number of extensions: 51 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: 552 Length of database: 609 Length adjustment: 36 Effective length of query: 516 Effective length of database: 573 Effective search space: 295668 Effective search space used: 295668 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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