Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30355 Length = 264 Score = 150 bits (379), Expect = 3e-41 Identities = 96/264 (36%), Positives = 145/264 (54%), Gaps = 9/264 (3%) Query: 1 MSELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFA 60 MS+L VS RV++ LNRP +NAL+ ++L L L AA + I VITG F Sbjct: 1 MSDLEVSTVGRVMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGDAFC 60 Query: 61 AGADLN----EMAEKDLAAT-----LNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELA 111 +G DL E AE D L Q+ ++ F KPLIAAVNG A+GAG +L+ Sbjct: 61 SGGDLGRRAAESAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLS 120 Query: 112 LLCDVVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQA 171 L CD+ A E+ARF I +G++PG GG L R VG + A +++ +G+ ++A++A Sbjct: 121 LQCDMRFASESARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALAL 180 Query: 172 GLVSDVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLL 231 G+V+ VF D ++ L A+++A P+ ++ K+ L QS L+ L ++ Sbjct: 181 GIVNRVFSDDELMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAVV 240 Query: 232 AATEDRHEGISAFLQKRTPDFKGR 255 +T+D E I A+ +KR P F G+ Sbjct: 241 QSTDDYKEAIKAYKEKRKPRFIGK 264 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: 97 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: 264 Length adjustment: 24 Effective length of query: 231 Effective length of database: 240 Effective search space: 55440 Effective search space used: 55440 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 Apr 09 2024. 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