Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 18321 b4297 KpLE2 phage-like element; predicted dehydratase (NCBI)
Query= curated2:A8LKN5 (577 letters) >FitnessBrowser__Keio:18321 Length = 655 Score = 251 bits (641), Expect = 6e-71 Identities = 182/513 (35%), Positives = 264/513 (51%), Gaps = 46/513 (8%) Query: 60 LSRQAQAVKMGVKQASGTPREFTTITVTDGIAMGHEGMRSSLASREAIADTVELTMRG-H 118 L Q +A +K P DG G GM SL R + + +R Sbjct: 92 LDIQMKAAAEVIKANHALPYAVYVSDPCDGRTQGTTGMFDSLPYRNDASMVMRRLIRSLP 151 Query: 119 CYDAIVGLAGCDKSLPGMMMAMV-RLNVPSVFIYGGSILPGRLNGEDVTVQDVFEAVGKH 177 A++G+A CDK LP MMA+ + N+ +V + GG+ LP + +GED + +G Sbjct: 152 DAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGATLPAK-DGED---NGKVQTIGAR 207 Query: 178 QAGNYTDAELEVLERVACPSAGACGG--QF--TANTMACVSEAIGLALPNSAGAPAPYES 233 A + L+ R C + + GG QF TA T V+E +GLA+P+SA AP+ Sbjct: 208 FANG--ELSLQDARRAGCKACASSGGGCQFLGTAGTSQVVAEGLGLAIPHSALAPSGEPV 265 Query: 234 RDQYGEASGRAVMDLIEKGIRARDIVTRKSLENAARIVACTGGSTNAGLHLPAIAHEAGI 293 + AS RA ++L +KGI R+I+T K++ENA + A GGSTN LH+PAIAH+AG Sbjct: 266 WREIARASARAALNLSQKGITTREILTDKAIENAMTVHAAFGGSTNLLLHIPAIAHQAGC 325 Query: 294 EF-TLQDVCDIFRDTPYFVDLKPGGK--YVAKDMYEAGGVPVVMRELRRAGLIHEDCMTV 350 T+ D I + P V + P G + + + AGGVP VM LR GL+HED MTV Sbjct: 326 HIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAFMAGGVPEVMLHLRSLGLLHEDVMTV 385 Query: 351 TGYSIGEE-----------------LDKVTLEADGRVIYPVDTPL-STTGGVVGLEGNLA 392 TG ++ E LD+ + AD ++ P T + GN+A Sbjct: 386 TGSTLKENLDWWEHSERRQRFKQLLLDQEQINADEVIMSPQQAKARGLTSTITFPVGNIA 445 Query: 393 PEGAIVKIA----GMSDDQLVF--TGPARVFECEEDAFEAVQNRAYAEGDVFVIRNEGPA 446 PEG+++K M D+Q ++ G A+V+ E+ A +++ GD+ VI GP+ Sbjct: 446 PEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAGDILVIIGVGPS 505 Query: 447 GGPGMREMLATTAALSGQGMGKKVALITDGRFSGATRGFCVGHVGPEAAHGGPIAMLKDG 506 G GM E T+AL GK V+LITD RFSG + G C+GHVGPEA GGPI L+ G Sbjct: 506 -GTGMEETYQVTSALKHLSYGKHVSLITDARFSGVSTGACIGHVGPEALAGGPIGKLRTG 564 Query: 507 DMITID----ALKGELSV--ALSEDELAARKDA 533 D+I I L GE++ S+++L ++++A Sbjct: 565 DLIEIKIDCRELHGEVNFLGTRSDEQLPSQEEA 597 Lambda K H 0.317 0.135 0.397 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: 989 Number of extensions: 53 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: 577 Length of database: 655 Length adjustment: 37 Effective length of query: 540 Effective length of database: 618 Effective search space: 333720 Effective search space used: 333720 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 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