Align Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized)
to candidate 5210229 Shew_2672 carnitinyl-CoA dehydratase (RefSeq)
Query= SwissProt::G4V4T7 (265 letters) >FitnessBrowser__PV4:5210229 Length = 261 Score = 186 bits (473), Expect = 3e-52 Identities = 109/270 (40%), Positives = 159/270 (58%), Gaps = 14/270 (5%) Query: 1 MSETRVRYEKKDHVAYVTMDRPAVLNAMDRRMHEELAGIWDDVEADDDVRAVVLTGAGDR 60 MSE+ + + + + +DRP NA+D + E+ ++ D ++R ++TGAG R Sbjct: 1 MSES-LHVTRNGSILEIVLDRPKA-NAIDAKTSYEMGEVFLAFRDDPELRVAIITGAGAR 58 Query: 61 AFSVGQDLKERARLNESGVAPTT-FGSGGQAGHPRLTDRFTLSKPVVARVRGYALGGGFE 119 FS G DLK A G AP FG GG AG LT+ F L KPV+A V GYA GGGFE Sbjct: 59 FFSAGWDLKAAAE----GEAPDADFGPGGFAG---LTELFDLDKPVIAAVNGYAFGGGFE 111 Query: 120 LVLACDIVIAAEDAVFALPEVRLGLIAGAGGVFRLPRQLPQKVAMGYLLTGRRMDAATAL 179 L LA D+++ A++A FALPE +LG++ +GG+ RLP+ LP + ++TGR MDA AL Sbjct: 112 LALAADLIVCADNASFALPEAKLGIVPDSGGMLRLPKLLPAPIVNELMMTGRSMDAQEAL 171 Query: 180 RHGLVNEVVPAAELDQCVADWTDSLVRAAPLSVRAIKEAALRSVDLPLEEAFTTSYHWEE 239 R G+VN VV L + + + + ++APL++ AIKE + +L +E+ + + Sbjct: 172 RWGVVNRVVEQEALMETARELANEISQSAPLALAAIKEIYRETGELSVEQGYAHIRGGQL 231 Query: 240 RR----RRSADAIEGVRAFAEKRDPIWTGQ 265 + S DA+EG AFAEKRDP+W G+ Sbjct: 232 KHYPSVLHSEDALEGPAAFAEKRDPVWQGK 261 Lambda K H 0.320 0.136 0.399 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: 192 Number of extensions: 11 Number of successful extensions: 4 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: 265 Length of database: 261 Length adjustment: 25 Effective length of query: 240 Effective length of database: 236 Effective search space: 56640 Effective search space used: 56640 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 (21.8 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