Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_004315431.1 C665_RS13940 enoyl-CoA hydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2193 (272 letters) >NCBI__GCF_000310185.1:WP_004315431.1 Length = 263 Score = 223 bits (567), Expect = 4e-63 Identities = 118/263 (44%), Positives = 168/263 (63%), Gaps = 1/263 (0%) Query: 3 NFNTLELHSDPRGVATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRGKH 62 ++ TLE+ GVAT+W++R +NAFNA++I +L A + +D +R +++ GRGK Sbjct: 2 SYETLEIVR-AAGVATIWMNRPDVHNAFNAQLIADLTTACIELDADEAVRAVVLAGRGKS 60 Query: 63 FSAGADLAWMQQSAELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLISA 122 FSAGADL WM+ + E N DA LA ++ LA++ PT+A V GAA GG +GL SA Sbjct: 61 FSAGADLNWMKAAGEASEAENFADAMRLAGMLRTLAEMNKPTIARVHGAALGGGMGLASA 120 Query: 123 CDMAIGADEAQFCLSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGLL 182 CD+ I D+A F SEV+ G+ P+ ISP+V++AIGER A RY TAER RA E+GL Sbjct: 121 CDICIAGDKAVFATSEVKFGIIPSAISPYVIRAIGERQATRYFQTAERIGAARAAELGLA 180 Query: 183 SESYPAEVLDQQVEQWIDNLLLNSPAAMRASKELLREVGNGALTPALRRYTENAIARIRV 242 E+ +E LD +V++ ++ LL P + A+K+L+R V N L+ AL T IA +R Sbjct: 181 HEAVASEELDAKVKEVVEALLQGGPKSQAAAKDLIRAVANRPLSDALVEDTARRIASLRA 240 Query: 243 SPEGQEGLRAFLQKRAPNWQAES 265 +PE +EGL AFL KR W A++ Sbjct: 241 TPEAKEGLAAFLDKRPAAWIAQA 263 Lambda K H 0.318 0.133 0.382 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: 183 Number of extensions: 9 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: 272 Length of database: 263 Length adjustment: 25 Effective length of query: 247 Effective length of database: 238 Effective search space: 58786 Effective search space used: 58786 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 (21.7 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