Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate PP_4030 PP_4030 Enoyl-CoA hydratase/isomerase family protein
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__Putida:PP_4030 Length = 280 Score = 126 bits (317), Expect = 4e-34 Identities = 83/265 (31%), Positives = 136/265 (51%), Gaps = 12/265 (4%) Query: 3 YENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFA 62 Y VE V V +NRP+ +NA+N A +E+ + D DA+ +V++G+ K F+ Sbjct: 14 YSAFKVELTDSVAHVQINRPEKVNAMNAAFWEEIVDIFQWIDDTDAVRVVVISGAGKHFS 73 Query: 63 AGADIGMMSTYTYM---DVYKGDYITR--------NWETVRSIRKPIIAAVAGFALGGGC 111 AG D+ M+++ DV + R ++ V + RKP++AAV G+ +GG Sbjct: 74 AGIDLMMLASLAGQMGKDVGRNARFLRKTIQRLQASFTAVDACRKPVLAAVQGYCIGGAI 133 Query: 112 ELAMMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEA 171 +L CD+ + + A+F EI +G+ G QRLPR + +L T R ++A EA Sbjct: 134 DLISACDMRYCSRDAQFSIKEIDMGMAADVGTLQRLPRIIGDGIMRELAFTGRNVEADEA 193 Query: 172 ERAGLVSRVI-PAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRL 230 R GLV+RV A+L+D A A IA AV KE ++ + + +G+ + Sbjct: 194 LRIGLVNRVYDDQAALMDGVFAIAREIAAKSPIAVAGTKEMLSYMRDHRIDDGLDYIATW 253 Query: 231 FHSLFATEDQKEGMAAFVEKRKPVF 255 ++ +ED + +AA + K+KP F Sbjct: 254 NAAMLQSEDLRVAVAAHMSKQKPTF 278 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: 161 Number of extensions: 7 Number of successful extensions: 3 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: 280 Length adjustment: 25 Effective length of query: 233 Effective length of database: 255 Effective search space: 59415 Effective search space used: 59415 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 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