Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_012277951.1 SHAL_RS14880 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_000019185.1:WP_012277951.1 Length = 269 Score = 152 bits (385), Expect = 5e-42 Identities = 92/243 (37%), Positives = 139/243 (57%), Gaps = 4/243 (1%) Query: 14 LLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RFFAAGADLNEMAEKD 72 ++++N P A N L +L ++ A + + VIT +FF+AGADL A+ D Sbjct: 26 VISMNNPPA-NTWTAQSLQELKQKVLALNENKEVYALVITAEGDKFFSAGADLKLFADGD 84 Query: 73 L--AATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPEI 130 AA + + + L F+ IAA+NGYA+G G E+AL CD+ + E A+ LPE Sbjct: 85 KQNAADMARYFGEAFETLSTFHGVSIAAINGYAMGGGLEVALACDLRICEEQAQMALPEA 144 Query: 131 TLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYALQL 190 T+G++P AGGTQ L VG+ A +M+L GE I A++A++ GLV +V A+ L Sbjct: 145 TVGLLPCAGGTQNLTALVGEGWAKRMILCGERINAEKAEKIGLVEEVVVQGNAFNAAMAL 204 Query: 191 ASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKRTP 250 A K+A SP +++A KQ ++ + + L ER+ F L TED+ EG+SAFL KR Sbjct: 205 AEKVANQSPSSVKACKQLVQAGRSMPRSQVLPLEREYFANLFDTEDQAEGVSAFLNKRKA 264 Query: 251 DFK 253 ++K Sbjct: 265 NWK 267 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: 117 Number of extensions: 4 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: 269 Length adjustment: 25 Effective length of query: 230 Effective length of database: 244 Effective search space: 56120 Effective search space used: 56120 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