Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_090447542.1 BLS63_RS19940 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_900100495.1:WP_090447542.1 Length = 257 Score = 120 bits (300), Expect = 4e-32 Identities = 80/254 (31%), Positives = 132/254 (51%), Gaps = 3/254 (1%) Query: 1 MSE-LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFF 59 MSE L + R+ +L L LNR +NAL A+ + L+ A D S+ ++TG F Sbjct: 1 MSEHLHIEREPGLLTLRLNRLDKKNALTRAMYSGMAEVLKQAEQDPSVRAVLLTGGESCF 60 Query: 60 AAGADLNEMAEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVA 119 +G D+ + + LN Q L F+KP++AAV+G A+G G L L CD+V Sbjct: 61 TSGNDVADFIQAPPGG-LNSEVFQFMLALFDFSKPVVAAVSGPAVGIGTTLLLHCDLVYV 119 Query: 120 GENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFP 179 +A +P + LG+ P G + L R +G + A++++L GES + +QA G+ + Sbjct: 120 SRDALLKMPFVNLGLCPEYGSSLILPRLLGHARAAELLLLGESFSGEQAAAWGIANQALD 179 Query: 180 SD-LTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRH 238 TL A ++A + + +P A+ +K+ +R L+ + +E LF + + Sbjct: 180 DGAATLARAREMALRFQQLAPSAVADSKRLMRAPGREELRRVIEEEGALFGQRLRSPEAI 239 Query: 239 EGISAFLQKRTPDF 252 E +SAF+Q+R PDF Sbjct: 240 EALSAFMQRRAPDF 253 Lambda K H 0.318 0.130 0.356 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: 115 Number of extensions: 5 Number of successful extensions: 2 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: 255 Length of database: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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