Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_000691145.1:WP_035704417.1 Length = 260 Score = 184 bits (467), Expect = 2e-51 Identities = 101/246 (41%), Positives = 155/246 (63%), Gaps = 5/246 (2%) Query: 14 LLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITG-NARFFAAGADLNE---MA 69 ++TLNRPA NAL+ A+L ++ ++ D +I ++TG A+ F AGADL E M Sbjct: 16 IMTLNRPAQANALSAAMLEEINQTIQEIKHDANIRCLLMTGAGAKVFCAGADLKERRLMT 75 Query: 70 EKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPE 129 E++ + T Q + +++ P+IA +NG+ALG G ELAL CD+ +A A GLPE Sbjct: 76 EQEAKEAVL-TIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRIARAGAALGLPE 134 Query: 130 ITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYALQ 189 L I+PGAGGTQRL R +G A +M+ +G S+ A++A Q GL+ + +D + A+ Sbjct: 135 TGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTADSLMNDAIT 194 Query: 190 LASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKRT 249 LA ++ ++ P+AL+ AKQA++ S + LQ GL +E + + L TEDR EG+ AF +KRT Sbjct: 195 LAKQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYLRLIHTEDRLEGLKAFQEKRT 254 Query: 250 PDFKGR 255 P ++G+ Sbjct: 255 PHYRGK 260 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: 101 Number of extensions: 2 Number of successful extensions: 1 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: 260 Length adjustment: 24 Effective length of query: 231 Effective length of database: 236 Effective search space: 54516 Effective search space used: 54516 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