Align Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized)
to candidate WP_156424864.1 AQZ52_RS04030 enoyl-CoA hydratase
Query= SwissProt::G4V4T7 (265 letters) >NCBI__GCF_001519075.1:WP_156424864.1 Length = 277 Score = 198 bits (504), Expect = 9e-56 Identities = 117/267 (43%), Positives = 154/267 (57%), Gaps = 12/267 (4%) Query: 2 SETRVRYEKKDHVAYVTMDRPAVLNAMDRRMHEELAGIWDDVEADDDVRAVVLTGAGDRA 61 S + E++ V +T+ RPAVLNA++ RMHEEL ++ ADD V+TG G R Sbjct: 20 SMEHITVEQRGRVTRITLARPAVLNAINARMHEELEEAFNAFAADDGQWVAVVTGQG-RG 78 Query: 62 FSVGQDLKERARLNESGVAPTTFGSGGQAGHPRLTDRFTLSKPVVARVRGYALGGGFELV 121 F G DLK VA F S G+ L +RF KP++A V G ALGGGFE+ Sbjct: 79 FCAGSDLK--------AVAAEGFRSYPAHGYAGLIERFDCDKPIIAAVNGLALGGGFEVA 130 Query: 122 LACDIVIAAEDAVFALPEVRLGLIAGAGGVFRLPRQLPQKVAMGYLLTGRRMDAATALRH 181 LACD++IAAE A F LPE R+G +A GG+ RL RQ+ K AMG +L+ R +DAA R Sbjct: 131 LACDLIIAAESARFGLPEPRVGAVALGGGLHRLARQIGLKRAMGMILSARPVDAAEGERL 190 Query: 182 GLVNEVVPAAELDQCVADWTDSLVRAAPLSVRAIKEAALRSVD---LPLEEAFTTSYHWE 238 G V EVVP +L+ V W ++++ APLS+RA K+A +R +D + A Y Sbjct: 191 GFVTEVVPDTDLESAVERWVEAILLGAPLSIRASKQAVMRGLDEAGVAAAMAAQPGYPAF 250 Query: 239 ERRRRSADAIEGVRAFAEKRDPIWTGQ 265 SAD EG AFAEKR P+W G+ Sbjct: 251 AAWSASADLREGTTAFAEKRPPVWQGR 277 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: 221 Number of extensions: 14 Number of successful extensions: 3 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: 277 Length adjustment: 25 Effective length of query: 240 Effective length of database: 252 Effective search space: 60480 Effective search space used: 60480 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