Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate SMc00981 SMc00981 ferredoxin protein
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__Smeli:SMc00981 Length = 364 Score = 137 bits (344), Expect = 6e-37 Identities = 107/355 (30%), Positives = 169/355 (47%), Gaps = 27/355 (7%) Query: 5 HSLTIKEVRPETRDAVSIAF--DVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSICTG 62 H L ET D ++ F D PA FR+ GQ + + + + V R+Y++ + Sbjct: 21 HMLECMSAVAETADVMTFTFRSDKPAW----FRYLPGQFVTLELPVAAKPVMRTYTLSSS 76 Query: 63 VNDG-ELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGN--YLAVA 119 + + V +K G + + ++LK G L+ P G F RH YL ++ Sbjct: 77 PSRPLSVAVTVKAQPGSIGTRWMFDNLKPGMMLKAFGPLGDFSF----VRHPGEKYLFIS 132 Query: 120 AGSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFS 179 AGSG+TP++S+ + + P + VT + R LFR +LE L R + LNL FL Sbjct: 133 AGSGVTPMMSMTRWMADCAPETDVTFISCARRPDDLLFRSELEVLA-RQMPGLNLGFLVE 191 Query: 180 REQQDVDLYN--GRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAE 237 + + GRIDA K L +++ F CGP+ VR L+A G Sbjct: 192 GHEARHGWHGLRGRIDAAKLPMLAPDFLE----RTVFCCGPEPFMGNVRAMLEAAGFDMA 247 Query: 238 RIHFELF--AAAGSAQKREARESAAQDSSV--SQITVISDGRELSFELPRNSQSILDAGN 293 R H E F AAA +A++ R D+ +++T G+E + +P Q+IL Sbjct: 248 RYHQESFQPAAAPAAEELAIRAGPTADAGAGAARVTFTMSGKEAT-AVP--GQTILQTAR 304 Query: 294 AQGAELPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISD 348 A G + +C+ G+C TC+ + G+VEM+ N + D E+ GY+L+C + P SD Sbjct: 305 ANGVRIGAACEGGICGTCRVLKIAGDVEMNHNGGILDDEIEEGYILACCSRPTSD 359 Lambda K H 0.319 0.133 0.377 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: 269 Number of extensions: 10 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: 357 Length of database: 364 Length adjustment: 29 Effective length of query: 328 Effective length of database: 335 Effective search space: 109880 Effective search space used: 109880 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 (21.8 bits) S2: 49 (23.5 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