Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate NP_350187.1 CA_C3604 dihydroxyacid dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000008765.1:NP_350187.1 Length = 572 Score = 400 bits (1027), Expect = e-116 Identities = 231/559 (41%), Positives = 333/559 (59%), Gaps = 36/559 (6%) Query: 22 SGLIDEELRRPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGIA 81 SG EEL + I + +S+ PG HLD + + I GG ++ +CDG Sbjct: 21 SGWKSEELNKAQIIIESSFGHSHPGSAHLDTLVDEAFKSIDDNGGRGAKYFVTDICDGET 80 Query: 82 MGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILIN 141 GH+GM YSL SR+++ + +EI V+A DA + + +CDK P L+A ARL++P IL+ Sbjct: 81 QGHDGMNYSLASRDIMTNLMEIHVQATPFDAGIFIASCDKAVPAHLMAIARLDMPSILVP 140 Query: 142 GGPMM--PGVYGKERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTM 199 GG M P + E+I + + KE + +++A P G+C+ + TA+TM Sbjct: 141 GGIMNAGPNMLTLEQIGTYNAQYERGEITKE----QYEHYKQNACPSCGACSFMGTASTM 196 Query: 200 NMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIAV 259 ++SEA+G+ LPG + +P AK G +I+K++E + P +I+T+KA ENAI V Sbjct: 197 QVMSEALGIALPGTALIPVTSKELKLAAKNAGKQILKLIELNIKPSEIMTKKAFENAIMV 256 Query: 260 DMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGI 319 A+ GS+N +LH+ A+A+ELG+D+ E+FDEI +K+P+I +I PSG + AGG+ Sbjct: 257 HAAIAGSSNCLLHIPAIAHELGMDIEPELFDEIHKKIPYILNIRPSGFYPGSYFWNAGGV 316 Query: 320 PAVLKELGEAGLIHKDALTVTGKTVWENVKDA----------------AVLDREVIRPLD 363 PA+++E+ E +H D +TVTGKT+ EN++D + +VIR + Sbjct: 317 PAIMEEIKE--FLHLDVMTVTGKTLGENLEDLKNSGYYEEHDKLITSLGIKKEDVIRTKE 374 Query: 364 NPYSPFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPG 423 NP G +AILKG+LAP GAVVK SA+ ++L + ARVF+ EEDA+K++ I+PG Sbjct: 375 NPIQSQGAIAILKGNLAPGGAVVKHSAISKKLMQVVLKARVFNCEEDAIKSVLTKNIKPG 434 Query: 424 TVIVIRYEGPRGGPGMREMLTATAAVMA-LGLGDKVALVTDGRFSGATRGPAIGHVSPEA 482 + +RYEGP+G GM EM T A+ + L D AL+TDGRFSGATRGPAIGHVSPEA Sbjct: 435 DAVFVRYEGPKGS-GMPEMFYTTEAIASDHELVDSTALITDGRFSGATRGPAIGHVSPEA 493 Query: 483 AAGGPIALVQDGDEIVIDIEKRRLDLL------VDEKELE----ERRARWKPKVKPLRRG 532 + GGPIA VQ+GD I IDI R+LD++ EKE+E ER W +G Sbjct: 494 SEGGPIAFVQEGDLIKIDIPARKLDIIGTNGIEKSEKEIENILKERSQNWVKPAPRYTKG 553 Query: 533 ILRRYAKMALSADKGGALE 551 IL Y + A S KGG +E Sbjct: 554 ILGLYTRCASSPMKGGYME 572 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: 874 Number of extensions: 41 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: 552 Length of database: 572 Length adjustment: 36 Effective length of query: 516 Effective length of database: 536 Effective search space: 276576 Effective search space used: 276576 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