Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Ac3H11_4006 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4006 Length = 259 Score = 97.8 bits (242), Expect = 2e-25 Identities = 78/255 (30%), Positives = 127/255 (49%), Gaps = 13/255 (5%) Query: 1 MEYKKIKVEKD-ERVARIKIANPP-VNVLDMETMKEI---ISAIDEVEGVDVIVFSGEGK 55 M Y+ I+V + ++V I + P +N L+ + M E+ + A D E + ++ +G K Sbjct: 1 MAYETIEVRVEADKVGVITLNRPKQLNALNDQLMNELGAALKAFDADENIGCMIVTGSEK 60 Query: 56 SFSAGAEI----KEHFPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIAC 111 +F+AGA+I K F D + T+ + + + +AAV GFALGGG ELA+ C Sbjct: 61 AFAAGADIGAMAKYSFADTYKG--DYITRNWETIRSIRKPVIAAVSGFALGGGCELAMMC 118 Query: 112 DFVLASKNAKLGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLV 170 DF++A+ NA+ G PEI L P LPR +G A ++ LTG + A A GLV Sbjct: 119 DFIIAADNARFGQPEIKLGVIPGAGGTQRLPRAVGKSKAMDMALTGRMMDAAEAERAGLV 178 Query: 171 NKVFEDENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVK 230 ++V + + + S +A+ K+++ + E LS + L Sbjct: 179 SRVVPYDKLMDEALGAAIIVAGFSQLAVMAAKESVNRAFEGT-LSDGVMFERRLFHALFA 237 Query: 231 SEDAVEGLKAFLEKR 245 ++D EG+ AF+ KR Sbjct: 238 TQDQKEGMDAFMNKR 252 Lambda K H 0.318 0.136 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: 163 Number of extensions: 14 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: 252 Length of database: 259 Length adjustment: 24 Effective length of query: 228 Effective length of database: 235 Effective search space: 53580 Effective search space used: 53580 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