Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011653082.1 RL_RS18610 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >NCBI__GCF_000009265.1:WP_011653082.1 Length = 579 Score = 357 bits (917), Expect = e-103 Identities = 218/545 (40%), Positives = 310/545 (56%), Gaps = 19/545 (3%) Query: 15 HRALLRACGLTDEEMD-RPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVET 73 HR L+ G + D RP + ++NT+S++ P + HL ++ E VKAG+ AGG P EV Sbjct: 27 HRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPV 86 Query: 74 IALCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARL 133 + + T M Y R L A +E I DG V +V CDK P +M AA Sbjct: 87 FSASENTFRPT-AMMY----RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLIMGAASC 141 Query: 134 DLPAAIVTGGPMEPGCVDGERVDL-IDAFEAVGAYEEGEISEEELEELEQRACPGPGSCA 192 DLP+ +VTGGPM G GERV ++ + GE+++ E E E G+C Sbjct: 142 DLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCN 201 Query: 193 GMFTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTRE 252 M TA+TMA M E LGM+ AA P ++ + +A+LTG RIV+ +++ + +++T++ Sbjct: 202 TMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQ 261 Query: 253 AFLDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMR 312 AF +AIR + A+GGSTN V+HLLAIA ++LSLDD+D R+ P + + P G Y M Sbjct: 262 AFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLME 321 Query: 313 DLYEAGGVPAVMKELADD--LHLDRIDFAGRSMRERVERTEVKDREVIRPKEDPVHEEGG 370 + + AGG+P V+K L + LH D + +G ++ + V+ + +VI P E + GG Sbjct: 322 EFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDVILPAEKALTASGG 381 Query: 371 IVVLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGG--DIDPGDVVVIR 428 IVVL GNLAPKGAV+K +A S + H G AVVF+ ++ I DID ++V++ Sbjct: 382 IVVLRGNLAPKGAVLKPSAASPHLLVHRGRAVVFEDIDDYKAKINDDNLDIDETCIMVMK 441 Query: 429 YEGPAGGPGMREM----LTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRG 484 GP G PGM E+ L P G+ LD + ++D R SG G V H SPEA G Sbjct: 442 NCGPKGYPGMAEVGNMGLPPKVLKKGI-LD--MVRISDARMSGTAYGTVVLHTSPEAAVG 498 Query: 485 GPIAVVEEGDTIRLDVRERRLEVDVEDEELEARLEEWEPPED-EVTGYLRRYRELVRGAD 543 GP+AVV+ GD I LDV RRL +D+ DEE+ RL EW+P D +GY +++ V GAD Sbjct: 499 GPLAVVKNGDMIELDVPNRRLHLDISDEEMARRLAEWQPNHDLPTSGYAFLHQQHVEGAD 558 Query: 544 EGAVL 548 GA L Sbjct: 559 TGADL 563 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: 813 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: 549 Length of database: 579 Length adjustment: 36 Effective length of query: 513 Effective length of database: 543 Effective search space: 278559 Effective search space used: 278559 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