Align Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized)
to candidate YP_002826675.1 NGR_c21610 carnitinyl-CoA dehydratase
Query= SwissProt::G4V4T7 (265 letters) >NCBI__GCF_000018545.1:YP_002826675.1 Length = 260 Score = 159 bits (402), Expect = 6e-44 Identities = 95/253 (37%), Positives = 137/253 (54%), Gaps = 12/253 (4%) Query: 17 VTMDRPAVLNAMDRRMHEELAGIWDDVEADDDVRAVVLTGAGDRAFSVGQDLKERARLNE 76 VT+DRP NA+D + + I+ D D ++R ++TG G++ F G DLK A E Sbjct: 16 VTIDRPKA-NAIDLKTSRAMGEIFRDFRDDPELRVAIITGTGEKFFCPGWDLKAAA---E 71 Query: 77 SGVAPTTFGSGGQAGHPRLTDRFTLSKPVVARVRGYALGGGFELVLACDIVIAAEDAVFA 136 +G GG G L D L+KP++A V G GGG E+ L+ D+++AAE A FA Sbjct: 72 GDAVDGDYGVGGFGGMQELRD---LNKPIIAAVNGICCGGGLEIALSTDLILAAEHATFA 128 Query: 137 LPEVRLGLIAGAGGVFRLPRQLPQKVAMGYLLTGRRMDAATALRHGLVNEVVPAAELDQC 196 LPE+R G +A A + +LP+++P +AM LLTGR ++A A R G VNE++P L + Sbjct: 129 LPEIRSGTVADAASI-KLPKRIPYHIAMDMLLTGRWLEATEAHRWGFVNEILPTGRLMER 187 Query: 197 VADWTDSLVRAAPLSVRAIK----EAALRSVDLPLEEAFTTSYHWEERRRRSADAIEGVR 252 + L PL AIK EA R + + + + S D +EG R Sbjct: 188 AWELARLLESGPPLVYAAIKEVVREAEGRDFQATMNKITRRQFKTVDVLYSSEDQLEGAR 247 Query: 253 AFAEKRDPIWTGQ 265 AF+EKRDP+W G+ Sbjct: 248 AFSEKRDPVWKGR 260 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: 177 Number of extensions: 14 Number of successful extensions: 5 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: 260 Length adjustment: 25 Effective length of query: 240 Effective length of database: 235 Effective search space: 56400 Effective search space used: 56400 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 24 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