Align Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized)
to candidate WP_036263857.1 DL86_RS15400 enoyl-CoA hydratase/isomerase family protein
Query= SwissProt::G4V4T7 (265 letters) >NCBI__GCF_000746085.1:WP_036263857.1 Length = 259 Score = 95.5 bits (236), Expect = 1e-24 Identities = 80/257 (31%), Positives = 112/257 (43%), Gaps = 17/257 (6%) Query: 14 VAYVTMDRPAVLNAMDRRMHEELAGIWDDVEADDDVRAVVLTGAGDRAFSVGQDLKERAR 73 +A V +RP NA+ M+E LA I V+AD ++ ++LTGAGD+AF+ G D+ E + Sbjct: 13 IAQVVFNRPRTRNALTSGMYEGLAAICAKVDADPAIKVLILTGAGDQAFASGTDIAEFRQ 72 Query: 74 LNESGVAPTTFGSGGQAGHPRLTDRFTLSKPVVARVRGYALGGGFELVLACDIVIAAEDA 133 +P + L+ +A + G GGG + CD+ I + Sbjct: 73 F----ASPDDVLAYEARIEAALSALERCRASTIAAIAGVCTGGGAMIAACCDLRIGEPET 128 Query: 134 VFALPEVR-LGLIAGAGGVFRLPRQLPQKVAMGYLLTGRRMDAATALRHGLVNEVV-PAA 191 +P R LG RL + +LT R + A A+ GL+NE V Sbjct: 129 KLGMPIARTLGNCLSMSNYARLAGLIGPARVKDLILTARLVGAKEAIAMGLLNEAVDQTK 188 Query: 192 ELDQCVADWTDSLVRAAPLSVRAIKEAALR----SVDLPLEEAFTTSYHWEERRRRSADA 247 EL D + APLS+RA KEA LR + E+ Y E+ R Sbjct: 189 ELLPRAHDLGRRVAGHAPLSLRATKEALLRMRGQAPQSAAEDLVLMCYLSEDFR------ 242 Query: 248 IEGVRAFAEKRDPIWTG 264 EGV AF EKR P W G Sbjct: 243 -EGVAAFLEKRSPRWRG 258 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: 175 Number of extensions: 13 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: 259 Length adjustment: 25 Effective length of query: 240 Effective length of database: 234 Effective search space: 56160 Effective search space used: 56160 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 Apr 09 2024. 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