Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate Echvi_0363 Echvi_0363 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__Cola:Echvi_0363 Length = 370 Score = 224 bits (571), Expect = 3e-63 Identities = 128/360 (35%), Positives = 205/360 (56%), Gaps = 16/360 (4%) Query: 2 SKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSICT 61 S++ SL ++EV ET DAV+I F+ P + + GQ L + ++G+E RRSYS+CT Sbjct: 17 SQYLSLKVREVVRETPDAVTIYFEQPEPYLE---YKPGQFLTLILDINGKEERRSYSLCT 73 Query: 62 GVN-DGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAA 120 D + +KR+AGG S Y NES+K G+ +EVM P GHF + + +++ +A Sbjct: 74 SPYVDPHPGITVKRIAGGVVSNYLNESIKPGKTIEVMKPMGHFTADFHSKNKNHFIMIAG 133 Query: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSR 180 GSGITPI+ I K+ L EP S+VTL+Y NRS +F + ++ L N +R ++ SR Sbjct: 134 GSGITPIMGIAKSVLINEPESKVTLIYCNRSEEQVIFDQAIQKLVNEQKRRFEVVHTLSR 193 Query: 181 EQQDVDLYNGRIDADKCGQLFSRWIDVKALDAA-----FICGPQAMTETVRDQLKANGMA 235 D GR+D Q+ + ++ K AA ++CGP+ + E + L + Sbjct: 194 PSGDWSGLQGRLDE----QMIEQVLEEKHFAAADKELYYLCGPEGLMEASVEALLKLDVP 249 Query: 236 AERIHFELFAAAGS--AQKREARESAAQDSSVSQITVISDGRELSFELPRNSQSILDAGN 293 E IH E F + S A+K ++A Q + +T+ +G E +FE+P ++IL+AG Sbjct: 250 HENIHRESFYTSSSEEAEKEAETDAADQPALTRSVTIDLEGEEHTFEVP-PGKTILEAGL 308 Query: 294 AQGAELPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLD 353 +G ++PYSC++G+C+ C+ ++ GEV+M+ + L D E GY+L C ++P S V +D Sbjct: 309 DEGYDMPYSCQSGLCTACRGRLSSGEVKMEQDAGLSDGEKKDGYILCCVSYPKSGDVKVD 368 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: 324 Number of extensions: 20 Number of successful extensions: 6 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: 370 Length adjustment: 29 Effective length of query: 328 Effective length of database: 341 Effective search space: 111848 Effective search space used: 111848 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