Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_057507562.1 ABB28_RS04910 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_001431535.1:WP_057507562.1 Length = 265 Score = 147 bits (372), Expect = 2e-40 Identities = 98/255 (38%), Positives = 137/255 (53%), Gaps = 8/255 (3%) Query: 4 LIVSRQQRVLLLTLNRPAARNALNNAL--LMQLVNELEAAATDTSISVCVITGNA-RFFA 60 L V V ++TL+ P A ++L L LV L A D SI VI+G +FF+ Sbjct: 12 LKVEADGHVAVITLHNPPAHTWTVHSLAALRDLVAALNA---DRSIYALVISGEGEKFFS 68 Query: 61 AGADLNEMAEKDLAATLNDTRP--QLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVV 118 AGADLN+ A D A R + + L F IAA+NGYA+G G E AL CD+ + Sbjct: 69 AGADLNQFASGDRGAAREAARRFGEAFEALSGFRGVSIAAINGYAMGGGLECALACDLRI 128 Query: 119 AGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVF 178 E+A+ LPE T+G++P AGGTQ L R VG+ A +M+L GE I A A + GL Sbjct: 129 IEEHAQVALPEATVGLLPCAGGTQNLPRLVGEGWAKRMILLGERIDADTAVRIGLAEQKA 188 Query: 179 PSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRH 238 AL+ A K + SP ++ A K ++ ++ A L ER+ F L + D+ Sbjct: 189 GKGEAKALALEWAKKAGKQSPTSIAACKTLVQSTRTGTHAAALVAEREAFVDLFDSADQV 248 Query: 239 EGISAFLQKRTPDFK 253 EG+SAFL+KR+ +K Sbjct: 249 EGVSAFLEKRSAQWK 263 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: 135 Number of extensions: 8 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: 265 Length adjustment: 24 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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