Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate Dsui_0502 Dsui_0502 enoyl-CoA hydratase/carnithine racemase
Query= curated2:P24162 (257 letters) >FitnessBrowser__PS:Dsui_0502 Length = 263 Score = 155 bits (392), Expect = 8e-43 Identities = 103/259 (39%), Positives = 136/259 (52%), Gaps = 10/259 (3%) Query: 5 TIRYEISEGLAVITLDRPEVMNALNAAMRHELTAALHRAR-GEARAIVLTGSGRAFCSGQ 63 T+ + +G+ +TL+RPE +NALN AM +L AA RA EA V+ G F +G Sbjct: 3 TVLSHLEDGVLTLTLNRPEALNALNLAMIEDLRAATARAEHDEAVGAVVLRGGEHFMAGG 62 Query: 64 DLGDGAAEGLNLETVLREE-YEPLLQAIYSCPL-------PVLAAVNGAAAGAGANLALA 115 DL ++ L L R+ +E + A+++ L PV+A+V+GAAAG G +L LA Sbjct: 63 DLKWFHSQ-LALPPAERQALFEQTIAAVHATTLQVRRMGKPVVASVSGAAAGFGLSLMLA 121 Query: 116 ADVVIAAQSAAFMQAFTRIGLMPDAGGTWWLPRQVGMARAMGMALFAEKIGAEEAARMGL 175 D+ +AA +A F A+ IGL PD G TW+LPR VG RA +AL ++ A +A GL Sbjct: 122 CDLAVAADNAYFTLAYCHIGLSPDGGATWFLPRAVGAKRAAEIALLGDRFDAAQAREWGL 181 Query: 176 IWEAVPDVDFEHHWRARAAHLARGPSAAFAAVKKAFHAGLSNPLPAQLALEARLQGELGQ 235 I VP + E A LA GP A A K A N LP QL E Sbjct: 182 INRVVPAAELEAESAKLARRLAAGPRQALARTKALLQASSGNSLPEQLFAEQGNFAACSV 241 Query: 236 SADFREGVQAFLEKRPPHF 254 DF EG+ AFLEKR P F Sbjct: 242 HPDFAEGLGAFLEKRKPAF 260 Lambda K H 0.321 0.133 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: 145 Number of extensions: 7 Number of successful extensions: 2 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: 257 Length of database: 263 Length adjustment: 24 Effective length of query: 233 Effective length of database: 239 Effective search space: 55687 Effective search space used: 55687 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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