Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012113038.1 XAUT_RS05120 phosphogluconate dehydratase
Query= curated2:Q8TW40 (549 letters) >NCBI__GCF_000017645.1:WP_012113038.1 Length = 619 Score = 236 bits (603), Expect = 1e-66 Identities = 171/510 (33%), Positives = 253/510 (49%), Gaps = 37/510 (7%) Query: 34 VAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVETI-ALCDGIAMNTPGMKYSLP 92 + +V Y++++ H ++ E ++ R GGV + A+CDG+ GM+ SL Sbjct: 80 LGIVTAYNDMLSAHQPYERYPELLREAARGVGGVALVAGGVPAMCDGVTQGEAGMELSLF 139 Query: 93 SRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARLD-LPAAIVTGGPMEPGCVD 151 SR+++A + + FD V + CDK+VPG ++ A LPA + GPM G + Sbjct: 140 SRDVIALSTAVALSHQTFDAAVFLGICDKIVPGLVIGALSFGHLPAVFIPSGPMTSGLSN 199 Query: 152 GERVDLIDAFEAVGAYEEGEISEEELEELEQRACPGPGSCAGMFTANTMACMTEVLGM-- 209 E+ + F EG++ + L E E ++ GPG+C TANT + E++G+ Sbjct: 200 TEKSKIRQLFA------EGKVGRDALLEAESKSYHGPGTCTFYGTANTNQMLMEIMGLHL 253 Query: 210 --SEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTREAFLDAIRVDMALGGS 267 + F TP +A R A + I + I A +L +AF++ I A GGS Sbjct: 254 PGASFVTPDTPLRDA-LTRAAAQRALAITALGNDYIPAGRMLDEKAFVNGIVGLHATGGS 312 Query: 268 TNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMRDLYEAGGVPAVMKEL 327 TN LHL+A+A + L+ DF +L+ TP L + P G + + AGG+ V++EL Sbjct: 313 TNHTLHLVAMAAAGGIALTWQDFSDLAEVTPLLTRVYPNGTADVNHFHAAGGMAFVIREL 372 Query: 328 --ADDLHLDRIDFAGR---------------SMRERVERTEVKDREVIRPKEDPVHEEGG 370 A LH D GR S+ R D +V+R DP GG Sbjct: 373 LGAGLLHADAETILGRGLAAYTKEPVLAEDGSLAWRDGPAVTGDAKVLRTAADPFQATGG 432 Query: 371 IVVLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGGDIDPGDVVVIRYE 430 + VL GN+ AVIKT+A++ E + E PA VF ++EE A G++ V V+R++ Sbjct: 433 LKVLDGNIG--RAVIKTSAVAPERHVIEAPARVFHAQEELQAAFKAGELTGDMVAVLRFQ 490 Query: 431 GPA--GGPGMREMLTPTAALCGMGLDDSVALVTDGRFSGGT-RGPCVGHVSPEAYRGGPI 487 GP G P + +++ P L GL VALVTDGR SG + + P HV+PEA GG I Sbjct: 491 GPKANGMPELHKLMPPLGVLQDRGL--KVALVTDGRLSGASGKVPSAIHVTPEAVDGGAI 548 Query: 488 AVVEEGDTIRLDVRERRLEVDVEDEELEAR 517 A V +GD IR+D LEV V E AR Sbjct: 549 AKVRDGDLIRVDAVAGTLEVLVPAAEWAAR 578 Lambda K H 0.317 0.137 0.396 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: 954 Number of extensions: 55 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: 549 Length of database: 619 Length adjustment: 36 Effective length of query: 513 Effective length of database: 583 Effective search space: 299079 Effective search space used: 299079 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