Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_057509133.1 ABB28_RS13605 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_001431535.1:WP_057509133.1 Length = 262 Score = 115 bits (288), Expect = 9e-31 Identities = 89/259 (34%), Positives = 128/259 (49%), Gaps = 19/259 (7%) Query: 4 LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGA 63 L+V R +L L L+RPA NA ++ L+ +L + L+ A D S+ V+ G F+AGA Sbjct: 5 LLVERSGALLTLRLHRPALHNAFDDGLIAELTHALDQAGRDPSVRAVVLAGEGASFSAGA 64 Query: 64 DLNEMAEKDLAATLNDTR------PQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVV 117 DL M AA+ ++ R +L L KP +A V+G A G G L CD+ Sbjct: 65 DLQWMRGM-AAASESENRQDALALARLMRTLDELPKPTLARVHGSAFGGGVGLVACCDIA 123 Query: 118 VAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDV 177 +A ++ARFGL E LG++P A + +I ++G A + +GE A A + GLV V Sbjct: 124 IAADSARFGLTESRLGLLP-AVISPYVIAAIGTRQARRWFATGEQFDAATALRIGLVHAV 182 Query: 178 FPSD-LTLEYALQLASKMARHSPLALQAAKQALRQ-----SQEVALQAGLAQERQLFTLL 231 D L QLA MA P+A +AK +RQ + QA +L L Sbjct: 183 VADDQLDAAVEQQLALLMAA-GPVAAASAKALVRQVVVSHDPDARDQA----NAELIARL 237 Query: 232 AATEDRHEGISAFLQKRTP 250 + + EG+ AFL KR P Sbjct: 238 RVSAEGQEGLGAFLGKRRP 256 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: 106 Number of extensions: 5 Number of successful extensions: 4 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: 262 Length adjustment: 24 Effective length of query: 231 Effective length of database: 238 Effective search space: 54978 Effective search space used: 54978 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