Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 6937208 Sama_1378 enoyl-CoA hydratase (RefSeq)
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__SB2B:6937208 Length = 257 Score = 159 bits (403), Expect = 4e-44 Identities = 99/258 (38%), Positives = 145/258 (56%), Gaps = 4/258 (1%) Query: 1 MSELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RFF 59 M+ LI + +LT++ P A N L +L ++ + I V+TG +FF Sbjct: 1 MAFLIERIEGNTAILTISNPPA-NTWTRESLNELKEKVLELNDNNEIYALVLTGEGEKFF 59 Query: 60 AAGADLNEMAEKDL--AATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVV 117 +AGADL A+ D AAT+ + + L AF IAA+NGYA+G G E+AL CD+ Sbjct: 60 SAGADLKLFADGDKGNAATMAKAFGEAFETLSAFRGVSIAAINGYAMGGGLEVALACDIR 119 Query: 118 VAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDV 177 +A A LPE T+G++P AGGTQ L VG+ A +M+L GE I A +A GLV +V Sbjct: 120 IAEIQAVMALPEATVGLLPCAGGTQNLTALVGEGWAKRMILCGERIDATKALNLGLVEEV 179 Query: 178 FPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDR 237 +L A+ LA+K+A+ SP A+ K+ ++ + + L ER+LF L TED+ Sbjct: 180 VEKGESLSAAIALAAKVAKQSPSAVAVCKKLIQSGRNMPRTQALPLERELFVGLFDTEDQ 239 Query: 238 HEGISAFLQKRTPDFKGR 255 EG++AFL+KR +K R Sbjct: 240 AEGVNAFLEKRAAQWKNR 257 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: 131 Number of extensions: 3 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: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 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 17 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