Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate N515DRAFT_1164 N515DRAFT_1164 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__Dyella79:N515DRAFT_1164 Length = 260 Score = 192 bits (489), Expect = 4e-54 Identities = 107/260 (41%), Positives = 155/260 (59%), Gaps = 2/260 (0%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EK 59 MAY N+ + RG V ++T+NRP LNALN ++EL A + DDA+ +V+ G+ +K Sbjct: 1 MAYRNLDIGNRGAVRIITVNRPDKLNALNRDTLNELTLAFAQAAQDDAVRTVVLAGAGDK 60 Query: 60 AFAAGADIGMMSTYTYMDVYKGDYI-TRNWETVRSIRKPIIAAVAGFALGGGCELAMMCD 118 AF AGADI M+ YT + R ++ + KP++A + GFALGGG ELAM C Sbjct: 61 AFVAGADIAEMNGYTPVQAQGFSRAGQRLMSSIERLGKPVVARIQGFALGGGMELAMACH 120 Query: 119 IIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVS 178 + A++ A+FGQPEI LG++PG GGTQRL R + A++LCLT + A A G+V+ Sbjct: 121 LRVASEKARFGQPEINLGLIPGFGGTQRLLRLAGRGAALELCLTGAMVGAQRAYELGVVN 180 Query: 179 RVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATE 238 RV+ +L + A A +A A + +++ + E L +G+ FE + F F+TE Sbjct: 181 RVVAPEALDETVDALADQLAASAPLAAAGILDAILQGGEMALDQGLEFETQAFALAFSTE 240 Query: 239 DQKEGMAAFVEKRKPVFKHR 258 D +EG AF+EKRK FK R Sbjct: 241 DMREGTTAFLEKRKAEFKGR 260 Lambda K H 0.321 0.134 0.380 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: 184 Number of extensions: 9 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: 258 Length of database: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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