Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate 200539 SO1364 iron-sulfur cluster-binding protein (NCBI ptt file)
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__MR1:200539 Length = 325 Score = 137 bits (345), Expect = 4e-37 Identities = 97/328 (29%), Positives = 161/328 (49%), Gaps = 24/328 (7%) Query: 34 FRFTQGQHLVMRTQLDGEEVRRSYSIC-TGVNDGELRVAIKRVAGGRFSAYANESLKAGQ 92 F + GQ + +++GE+ RSY++ T L V IKRV GG S Y + L+ GQ Sbjct: 3 FDYKPGQFITFVLEINGEQACRSYTLSSTPSRPYSLMVTIKRVDGGLVSNYLIDHLQPGQ 62 Query: 93 RLEVMPPSGHFHV-ELDAARHGNYLAVAAGSGITPILSIIKTTLETEPHSRVTLLYGNRS 151 + V+PP+G F++ ++ A + YL ++AG GITP+ S+ + +T+ ++ + +++ R+ Sbjct: 63 TVRVLPPTGQFNLFDIPANK---YLFLSAGCGITPMYSMSRYLTDTQINADIAVVHSART 119 Query: 152 SASTLFREQLEDLKNRYLQRLNLIFLFSREQQDVDL-------YNGRIDADKCGQLFSRW 204 A +F+ LE + R+ L +L D Y GR+ A L + Sbjct: 120 QADIIFKNTLETMAARHAS-FKLCYLVEGVTTDTVWHTEEAFHYVGRLSAQNLLSLVPDF 178 Query: 205 IDVKALDAAFICGPQAMTETVRDQLKANGMAAERIHFELFAAAGSAQKREARESAAQDSS 264 + F+CGP+ + V+ L +++ E FA A + +++ Q + Sbjct: 179 AE----RIVFLCGPELYMQAVKTILTELNFDMNKLYHESFATAVKEAQSHVKQAEIQSET 234 Query: 265 VSQITVISDGRELSF----ELPRNSQSILDAGNAQGAELPYSCKAGVCSTCKCKVVEGEV 320 T S G LS L Q++LD A+G + +C++GVC CKCKV++GE Sbjct: 235 P---TTSSTGFMLSIGDKKHLLTAEQTLLDGIEAEGLPIIAACRSGVCGACKCKVLQGET 291 Query: 321 EMDSNFALEDYEVAAGYVLSCQTFPISD 348 E S L ++ AGYVL+C T SD Sbjct: 292 ESTSYMTLTPTDIEAGYVLACSTRLKSD 319 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: 239 Number of extensions: 13 Number of successful extensions: 5 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: 325 Length adjustment: 28 Effective length of query: 329 Effective length of database: 297 Effective search space: 97713 Effective search space used: 97713 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