Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate PfGW456L13_4938 Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase) (EC 1.14.12.17)
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4938 Length = 393 Score = 100 bits (249), Expect = 7e-26 Identities = 70/237 (29%), Positives = 122/237 (51%), Gaps = 9/237 (3%) Query: 15 ETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSICTGVNDGELRVAIKR 74 E+ + S F+ PA+ GQ++ M+ LDGEE+RR+YS+ N G+ R+++KR Sbjct: 166 ESAEITSFYFE-PADKGPILLAEPGQYIGMKLILDGEEIRRNYSLSALANKGQYRISVKR 224 Query: 75 VAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAAGSGITPILSIIKTT 134 AGGR S + ++ L G +++ PPSG F + A + ++ G GITP L++++ Sbjct: 225 EAGGRASNFLHDQLHVGASIQLFPPSGEFVL---TASDKPLVLISGGVGITPTLAMLEAA 281 Query: 135 LETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSREQQDVDLYNGRIDA 194 LET+ V ++ R+ + FR+ ++ L R+ Q L + +S E V ++ Sbjct: 282 LETQ--RPVHFIHCARNGSVHAFRDWIDGLAERHPQ-LKRFYCYS-EDDGVSPAAHKMGL 337 Query: 195 DKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIHFELFAAAGSAQ 251 QL + LDA F+ GP+ ++ LKA G+ ++ +E F A + + Sbjct: 338 LSQQQLHQWLPQERDLDAYFL-GPKGFMVAIKRHLKALGVPEKQSRYEFFGPAAALE 393 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: 257 Number of extensions: 13 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: 357 Length of database: 393 Length adjustment: 30 Effective length of query: 327 Effective length of database: 363 Effective search space: 118701 Effective search space used: 118701 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: 50 (23.9 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