Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 14407 b0269 CP4-6 prophage; predicted dehydratase (NCBI)
Query= curated2:A8LKN5 (577 letters) >FitnessBrowser__Keio:14407 Length = 655 Score = 247 bits (631), Expect = 9e-70 Identities = 178/483 (36%), Positives = 239/483 (49%), Gaps = 36/483 (7%) Query: 60 LSRQAQAVKMGVKQASGTPREFTTITVTDGIAMGHEGMRSSLASREAIADTVELTMRG-H 118 + Q QA + + G P DG + G GM SL R A +R Sbjct: 92 IGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIVFRRLIRSLP 151 Query: 119 CYDAIVGLAGCDKSLPGMMMAMVRLN-VPSVFIYGGSILPGRLNGEDVTVQDVFEAVGKH 177 A++G+A CDK LP M+A+ ++ +P++ + GG+ LP + + VQ + H Sbjct: 152 TRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGATLPPTVGEDAGKVQTIGARFANH 211 Query: 178 QAGNYTDAELEVLERVACPSAGACGGQFTANTMACVSEAIGLALPNSAGAPAPYESRDQY 237 + AEL R G C TA T V+EA+GLALP+SA AP+ + Sbjct: 212 ELSLQEAAELGC--RACASPGGGCQFLGTAGTSQVVAEALGLALPHSALAPSGQAVWLEI 269 Query: 238 GEASGRAVMDLIEKGIRARDIVTRKSLENAARIVACTGGSTNAGLHLPAIAHEAGIEFTL 297 S RAV +L +GI RDI++ K++ENA I A GGSTN LH+PAIAH AG T+ Sbjct: 270 ARQSARAVSELDSRGITTRDILSDKAIENAMVIHAAFGGSTNLLLHIPAIAHAAGC--TI 327 Query: 298 QDV---CDIFRDTPYFVDLKPGGK--YVAKDMYEAGGVPVVMRELRRAGLIHEDCMTVTG 352 DV I R P V + P G + + AGGVP VM LR GL+H D MTVTG Sbjct: 328 PDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFLAGGVPEVMLHLRDLGLLHLDAMTVTG 387 Query: 353 YSIGEELD------------KVTLEADG----RVIYPVDTPLS--TTGGVVGLEGNLAPE 394 ++GE L+ + E DG VI P + + T V GN+APE Sbjct: 388 QTVGENLEWWQASERRARFRQCLREQDGVEPDDVILPPEKAKAKGLTSTVCFPTGNIAPE 447 Query: 395 GAIVKIAGM------SDDQLVFTGPARVFECEEDAFEAVQNRAYAEGDVFVIRNEGPAGG 448 G+++K + D TG RVF E A +A++ +GD+ V+ GP+ G Sbjct: 448 GSVIKATAIDPSVVGEDGVYHHTGRVRVFVSEAQAIKAIKREEIVQGDIMVVIGGGPS-G 506 Query: 449 PGMREMLATTAALSGQGMGKKVALITDGRFSGATRGFCVGHVGPEAAHGGPIAMLKDGDM 508 GM E T+AL GK V+LITD RFSG + G C GHV PEA GGPI L+D D+ Sbjct: 507 TGMEETYQLTSALKHISWGKTVSLITDARFSGVSTGACFGHVSPEALAGGPIGKLRDNDI 566 Query: 509 ITI 511 I I Sbjct: 567 IEI 569 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: 998 Number of extensions: 59 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: 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