Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012331253.1 M446_RS06245 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >NCBI__GCF_000019365.1:WP_012331253.1 Length = 575 Score = 334 bits (856), Expect = 6e-96 Identities = 209/540 (38%), Positives = 297/540 (55%), Gaps = 16/540 (2%) Query: 16 RALLRACGLTDEEMDRPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVETIA 75 +A ++A G +D+ ++RP V + NT+S+ P H + + EA K G+ +AG +P TI+ Sbjct: 27 KAFIKAMGYSDDALNRPIVGITNTFSDYNPCHGNAPALIEAAKRGVMLAGAMPMVFPTIS 86 Query: 76 LCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARLDL 135 + + A T S+ R L+A E +I A D + I CDK +P +MAAA +DL Sbjct: 87 IHESFAHPT-----SMFLRNLMAMDTEEMIRAQPMDAVIVIGGCDKTLPAQIMAAASVDL 141 Query: 136 PAAIVTGGPMEPGCVDGERVDLI-DAFEAVGAYEEGEISEEELEELEQRACPGPGSCAGM 194 P ++ GPM G GE + D A+ GEI E E+E + R P G+C M Sbjct: 142 PTVVIPVGPMVVGHHKGEVLGACTDCRRLWAAHRAGEIDEAEIEVVNGRLAPSVGTCMVM 201 Query: 195 FTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVE-AIEEGITARDVLTREA 253 TA+TMACM E +G++ PA AE++R+A+ +G R A+ G +LT + Sbjct: 202 GTASTMACMIEAMGLALPYAGTIPAPHAERVRLAEASGRRAAAMAVAGGPRPSALLTPAS 261 Query: 254 FLDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMRD 313 +A V A+GGSTN ++HL A+A + LD FD + RE P L ++P G + M Sbjct: 262 LRNAQVVLQAIGGSTNGLIHLTAMANRVGARIDLDAFDAVGREVPVLVDLKPSGAHYMEH 321 Query: 314 LYEAGGVPAVMKELADDLHLDRIDFAGRSMRERVERT-EVKDREVIRPKEDPVHEEGGIV 372 + AGGVP +++EL D + LD AG +R+ V EV + VIR DP+ GG+ Sbjct: 322 FHHAGGVPKLLRELGDLIDLDAPTVAGGCLRDVVAAAEEVPGQTVIRSPADPIKAAGGLA 381 Query: 373 VLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGGDIDPG--DVVVIRYE 430 VL GNLAP+GA+IK AA S + +H G AVVF+S + I D+D G DV+V+R Sbjct: 382 VLRGNLAPRGALIKHAAASPRLLQHTGRAVVFESIPDMAARIDAPDLDVGADDVLVLRNA 441 Query: 431 GPAGGPGMRE--MLTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGGPIA 488 GP G PGM E L L G+ D V ++D R SG G V HV+PE+ GGP+A Sbjct: 442 GPKGAPGMPEAGYLPIPKKLARQGVKDMVR-ISDARMSGTAFGTIVLHVTPESAVGGPLA 500 Query: 489 VVEEGDTIRLDVRERRLEVDVEDEEL---EARLEEWEPPEDEVTGYLRRYRELVRGADEG 545 +V GD IRLDV RR+++ V++ EL +A L E P GY R + + V ADEG Sbjct: 501 LVRTGDAIRLDVAGRRIDLLVDEAELARRQAALPEAPRPAWARRGYARLFHDTVTQADEG 560 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: 871 Number of extensions: 39 Number of successful extensions: 9 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: 575 Length adjustment: 36 Effective length of query: 513 Effective length of database: 539 Effective search space: 276507 Effective search space used: 276507 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