Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate GFF3388 Psest_3453 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__psRCH2:GFF3388 Length = 518 Score = 191 bits (484), Expect = 5e-53 Identities = 124/354 (35%), Positives = 190/354 (53%), Gaps = 25/354 (7%) Query: 4 FHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSICTGV 63 F +LT+ + ET DA S + VPAEL + F GQ + +R + RSYS+ + Sbjct: 187 FAALTVIARQAETADAASFSLQVPAELRERFAAQPGQFVTLRVPCSEPPLLRSYSLSKPL 246 Query: 64 -NDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHV-ELDAARHGNYLAVAAG 121 +DG LR++++RV GGR S + ++L+ GQR++V+PP+G +LD G+ L + AG Sbjct: 247 GSDGVLRISVRRVPGGRASNWLLDNLQVGQRIDVLPPAGRLVPHDLD----GDLLLLGAG 302 Query: 122 SGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSRE 181 SGITP+ +I++ LE + RV L Y +R +AS +F E+L D RY +RL L E Sbjct: 303 SGITPLRAILQAALE-QGRGRVFLFYASRDAASLIFAEELADFAARYPERLQLRIWLDAE 361 Query: 182 QQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIHF 241 Q G A W +A F+CGPQ + L ++++ IH Sbjct: 362 Q-------GIPSAPAIAAKIGDWPQGEA----FVCGPQPFMDGASVALAELDVSSDAIHV 410 Query: 242 ELF-AAAGSAQKREARESAAQDSSVSQITVISDGRELSFELPRNSQSILDAGNAQGAELP 300 E F AA A E R+ S++ V DGR + ++ + + +LDA G + P Sbjct: 411 ERFNTAAPVAPLSELRQPLH-----SRLQVALDGRRHALDV-QQGEVLLDAMEQAGLQPP 464 Query: 301 YSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDF 354 +C+AGVC+ C+C+VVEG V M SN L D +V G+ L+CQ P S ++ +++ Sbjct: 465 SACRAGVCAACRCRVVEGSVSMRSNQVLSDQQVRQGWTLACQAVPTSTRLAVEY 518 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: 376 Number of extensions: 18 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: 518 Length adjustment: 32 Effective length of query: 325 Effective length of database: 486 Effective search space: 157950 Effective search space used: 157950 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: 51 (24.3 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