Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Echvi_0343 Echvi_0343 Enoyl-CoA hydratase/carnithine racemase
Query= reanno::Pedo557:CA265_RS09125 (258 letters) >FitnessBrowser__Cola:Echvi_0343 Length = 258 Score = 239 bits (610), Expect = 4e-68 Identities = 123/258 (47%), Positives = 174/258 (67%) Query: 1 MENLVLYQVAERIATITINRPEKKNALNPQLIAELTAAFIKASEDDLVKVVILNANGDAF 60 ME V ++ RI + ++RPEK+NALN +++ L AA + + VKVVI+ A G F Sbjct: 1 MEEHVKFEQKGRIGYVILSRPEKRNALNAAMVSGLQAALDRCEAIETVKVVIIKAEGKVF 60 Query: 61 SAGADLAYLQQLQYNTFEENVADSNHLKKLFTTIYYLPKVVIAQVEGHAIAGGCGLATIC 120 +GADL ++++Q NTF+EN+ADS LKKLF +Y PKVVIAQV+GHA+AGGCGL ++C Sbjct: 61 CSGADLQDIERMQDNTFDENLADSEGLKKLFLRLYTFPKVVIAQVQGHALAGGCGLVSVC 120 Query: 121 DIVFATPESNFGYTEVKIGFVPAIVSCFLKEKVSESIAKEILLTGKIFSAEEALKYNLIN 180 D +A P + GYTEV+IGFVPA+V FL K+ E AKE+LLTG++ A A + LI Sbjct: 121 DFAYAVPTAKLGYTEVRIGFVPAMVLVFLVRKLGEGKAKELLLTGELLVAPAAKEIGLIQ 180 Query: 181 FVTNSSDIHQIVREFALSLCSGSSGNSLMITKQLITQTTNPLLEKCLETAVQINARVRES 240 V + + V+E A L S +SG S+ +TK++I + LE+ LE A ++NA+ RE+ Sbjct: 181 EVFEPAALDGAVQEIAERLISQNSGESMALTKKMIAAVQDLPLEEALEYAARMNAKARET 240 Query: 241 EDFKKGISSFLNKEKINW 258 ED K+GI++FL K+KI W Sbjct: 241 EDCKRGIAAFLGKKKIEW 258 Lambda K H 0.318 0.133 0.367 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: 163 Number of extensions: 4 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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 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