Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 14407 b0269 CP4-6 prophage; predicted dehydratase (NCBI)
Query= curated2:C4Z566 (557 letters) >FitnessBrowser__Keio:14407 Length = 655 Score = 248 bits (634), Expect = 4e-70 Identities = 175/499 (35%), Positives = 253/499 (50%), Gaps = 47/499 (9%) Query: 46 GHMNIDKIVNAVKLGVAEAGGVPVVFPAIAVCDGIAMGHVGMKYSLVTR-DLIADSTECM 104 GH I + A + GG+P CDG + G GM SL R D + Sbjct: 88 GHWEIGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIVFRRLI 147 Query: 105 AIAHQFDGLVMVPNCDKNVPGLLMAAARLN-LPTVFVSGG---PMLAGHVKGKKRSLSSM 160 ++ V CDK +P ++A A ++ LPT+ V GG P G GK +++ + Sbjct: 148 RSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGATLPPTVGEDAGKVQTIGAR 207 Query: 161 FEAVGSYAAGTMTEEDVLEFEEKVCPTC----GSCSGMYTANSMNCLTEALGMGLRGNGT 216 F E + E E C C G C + TA + + EALG+ L + Sbjct: 208 F---------ANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQVVAEALGLALPHSAL 258 Query: 217 IPAVYSERIKLAKHAGMAVMDMVNKGITARDIITKDSIMNALTVDMALGCSTNSMLHLPA 276 P+ + +++A+ + AV ++ ++GIT RDI++ +I NA+ + A G STN +LH+PA Sbjct: 259 APSGQAVWLEIARQSARAVSELDSRGITTRDILSDKAIENAMVIHAAFGGSTNLLLHIPA 318 Query: 277 IAHEIGFDF-DIKFANPISEKTPNLCHLAPAGPTYMEDLNE--AGGVYAVMKELADIGLL 333 IAH G D++ I+ K P L + P GP Y + AGGV VM L D+GLL Sbjct: 319 IAHAAGCTIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFLAGGVPEVMLHLRDLGLL 378 Query: 334 NTDCLTVSGKTIGE----------------CIATAYNRDPE-VIRTVDNAYSK--TGGLA 374 + D +TV+G+T+GE C+ +P+ VI + A +K T + Sbjct: 379 HLDAMTVTGQTVGENLEWWQASERRARFRQCLREQDGVEPDDVILPPEKAKAKGLTSTVC 438 Query: 375 VLSGNLAPDGSVVKRSAVVPEMLV------HEGPARVFDSEEDAIAAIKGGKIVEGDVVV 428 +GN+AP+GSV+K +A+ P ++ H G RVF SE AI AIK +IV+GD++V Sbjct: 439 FPTGNIAPEGSVIKATAIDPSVVGEDGVYHHTGRVRVFVSEAQAIKAIKREEIVQGDIMV 498 Query: 429 IRYEGPKGGPGMREMLNPTSAIAGMGLGSSVALITDGRFSGASRGASIGHVSPEAAVGGP 488 + GP G GM E TSA+ + G +V+LITD RFSG S GA GHVSPEA GGP Sbjct: 499 VIGGGPSG-TGMEETYQLTSALKHISWGKTVSLITDARFSGVSTGACFGHVSPEALAGGP 557 Query: 489 IALVEEGDIISIDIPGLKL 507 I + + DII I + L L Sbjct: 558 IGKLRDNDIIEIAVDRLTL 576 Lambda K H 0.317 0.134 0.385 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: 924 Number of extensions: 50 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: 557 Length of database: 655 Length adjustment: 37 Effective length of query: 520 Effective length of database: 618 Effective search space: 321360 Effective search space used: 321360 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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