Align Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized)
to candidate WP_075387689.1 BK574_RS07075 enoyl-CoA hydratase
Query= SwissProt::G4V4T7 (265 letters) >NCBI__GCF_002019605.1:WP_075387689.1 Length = 262 Score = 194 bits (493), Expect = 2e-54 Identities = 112/270 (41%), Positives = 158/270 (58%), Gaps = 15/270 (5%) Query: 1 MSETRVRYEKKDHVAYVTMDRPAVLNAMDRRMHEELAGIWDDVEADDDVRAVVLTGAGDR 60 M+ + +E++ VA +T++RP +NA++ + ++ + DD ++ VLTGAG++ Sbjct: 1 MNYEAIHFERRGSVALITLNRPNAMNAVNATLWNDVGHALESFSKDDSLQVAVLTGAGEK 60 Query: 61 AFSVGQDLKERARLNESGVAPT---TFGSGGQAGHPRLTDRFTLSKPVVARVRGYALGGG 117 AF G DLKE A + P +G GG H + KPV+A V G+ALGGG Sbjct: 61 AFCAGADLKEIAA--GRSIQPPGGEKWGFGGIVNH-------FVPKPVIAAVNGFALGGG 111 Query: 118 FELVLACDIVIAAEDAVFALPEVRLGLIAGAGGVFRLPRQLPQKVAMGYLLTGRRMDAAT 177 E+ LACD+V+A+E A F LPEV+ GLIA AGG+ RLPRQ+P K+AM +LTG + A Sbjct: 112 TEIALACDLVVASEKASFGLPEVKRGLIAAAGGLLRLPRQIPLKIAMEAVLTGDPLSAEE 171 Query: 178 ALRHGLVNEVVPAAELDQCVADWTDSLVRAAPLSVRAIKEAALRSVDLPLE---EAFTTS 234 AL+ GLVN+VVP ++ + + APLS++A KE R +D PL+ EA+ + Sbjct: 172 ALKWGLVNKVVPHEDVISTALALAEKISENAPLSLKASKEIVYRGLDRPLDHPPEAWEIN 231 Query: 235 YHWEERRRRSADAIEGVRAFAEKRDPIWTG 264 S D IEG AFAEKR PIW G Sbjct: 232 DEHTSVIMNSQDVIEGSSAFAEKRKPIWKG 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: 197 Number of extensions: 11 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: 262 Length adjustment: 25 Effective length of query: 240 Effective length of database: 237 Effective search space: 56880 Effective search space used: 56880 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