Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011157710.1 TX73_RS10980 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >NCBI__GCF_000195775.1:WP_011157710.1 Length = 568 Score = 339 bits (869), Expect = 2e-97 Identities = 209/540 (38%), Positives = 301/540 (55%), Gaps = 17/540 (3%) Query: 16 RALLRACGLTDEEMDRPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVETIA 75 +A ++A G +D+ +DRP V + NT+S+ P H + ++ EAVK G+ +AG +P TI+ Sbjct: 23 KAFIKAMGYSDDALDRPIVGITNTHSDYNPCHGNAPQIIEAVKRGVMLAGAMPMVFPTIS 82 Query: 76 LCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARLDL 135 + + A T S+ R L+A E +I A D V I CDK +P +MAA DL Sbjct: 83 IAESFAHPT-----SMYLRNLMAMDTEEMIRAQPMDAVVVIGGCDKTLPAQVMAAVSADL 137 Query: 136 PAAIVTGGPMEPGCVDGERVDLI-DAFEAVGAYEEGEISEEELEELEQRACPGPGSCAGM 194 P ++ GPM G GE + D Y GEI + E+E + R P G+C M Sbjct: 138 PTVVIPVGPMVVGHHKGEVLGACTDCRRLWAKYRAGEIDDAEIEAVNGRLAPSVGTCMVM 197 Query: 195 FTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEE--GITARDVLTRE 252 TA+TMACM E +G+S A PA AE+ R A+ +G R+ A+ + G ++LT Sbjct: 198 GTASTMACMIEAMGLSLPMSATIPAPHAERFRSAEASG-RVAAAMAKAKGPRPSEILTPA 256 Query: 253 AFLDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMR 312 AF +A V A+GGSTN ++HL AIA + LDDFD + R+ P L ++P G + M Sbjct: 257 AFRNAQVVLQAIGGSTNGLIHLTAIAGRVPHRIDLDDFDAIGRKVPVLVDLKPSGAHYME 316 Query: 313 DLYEAGGVPAVMKELADDLHLDRIDFAGRSMRERVERTE-VKDREVIRPKEDPVHEEGGI 371 + AGGVP +M +L D + LD G ++RE V + E V ++VIR +++P+ EGG+ Sbjct: 317 HFHHAGGVPKLMAQLGDLIELDASTVTGATLREVVAQAEDVPGQDVIRSRDNPIRCEGGL 376 Query: 372 VVLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGGDID--PGDVVVIRY 429 VL+GNLAP+GA+IK AA S + +H G AVVF++ E+ I D+D DV+V+R Sbjct: 377 AVLHGNLAPRGALIKHAAASPGLLQHTGRAVVFETLEDMARRIDDPDLDVAADDVLVLRN 436 Query: 430 EGPAGGPGMRE--MLTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGGPI 487 GP G PGM E L L G+ D V ++D R SG G V H++PE+ GGP+ Sbjct: 437 AGPKGAPGMPEAGYLPIPLKLARAGVKDMVR-ISDARMSGTAFGTIVLHITPESAEGGPL 495 Query: 488 AVVEEGDTIRLDVRERRLEVDVEDEELEARLEEWEPPE--DEVTGYLRRYRELVRGADEG 545 A+V+ GD I LDV RR+++ V+D EL R GY + + + V ADEG Sbjct: 496 ALVQTGDRIALDVAARRIDLLVDDAELTRRRTALPATTAIRPARGYAQLFHDAVLQADEG 555 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: 805 Number of extensions: 36 Number of successful extensions: 7 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: 568 Length adjustment: 36 Effective length of query: 513 Effective length of database: 532 Effective search space: 272916 Effective search space used: 272916 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