Align Putative enoyl-CoA hydratase protein; EC 4.2.1.17 (characterized, see rationale)
to candidate PP_3283 PP_3283 1,2-epoxyphenylacetyl-CoA isomerase
Query= uniprot:Q92VJ6 (261 letters) >FitnessBrowser__Putida:PP_3283 Length = 263 Score = 105 bits (261), Expect = 1e-27 Identities = 85/266 (31%), Positives = 131/266 (49%), Gaps = 11/266 (4%) Query: 1 MTFDTIRCAIDQRGVARVTLARSEKHNALSATMIGELTAVVGRLATDASIRAVILDAEGK 60 MTF I +I+ GVA ++L R E+ N+ + M E+ + ++ + R ++L AEG+ Sbjct: 1 MTFQHILFSIED-GVAFLSLNRPEQLNSFNTAMHLEVREALRQVRQSSDARVLLLTAEGR 59 Query: 61 SFCAGGDLDWMRQQFSADRPTRIAEATRLAM-MLKALNDLPKPLIARVHGNAFGGGVGLI 119 FCAG DL A+ P + +++ L DLP P+I V+G A G G + Sbjct: 60 GFCAGQDLSDRNVAPGAEMPDLGQSIDKFYNPLVRTLRDLPLPVICAVNGVAAGAGANIP 119 Query: 120 SVCDTVIAASGAQFGLTETRLGLIPATISPYVIAR-TGEARARPLFMSARVFGAEEAKVA 178 CD V+AA A F ++GL+P + +++ R G ARA+ L M GAE+A+ Sbjct: 120 LACDLVLAARSASFIQAFCKIGLVPDSGGTWLLPRLVGMARAKALAMLGERLGAEQAEQW 179 Query: 179 GFVTTVVDGTMLDGAVEAAVTAYLVAAPGAAGRAKRLARSLGLPITDAVIAATIEQLAD- 237 G + VVD L EA A +AA G + RSL D A +E D Sbjct: 180 GLIYRVVDDAALRD--EALTLARHLAAQPTYG-LTLIKRSLNASF-DNGFEAQLELERDL 235 Query: 238 ---TWETDEAREGVSAFFERRNPSWR 260 +++ REGV+AF +R P+++ Sbjct: 236 QRLAGRSEDYREGVNAFMNKRTPAFK 261 Lambda K H 0.321 0.133 0.383 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: 6 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: 261 Length of database: 263 Length adjustment: 25 Effective length of query: 236 Effective length of database: 238 Effective search space: 56168 Effective search space used: 56168 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