Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate YP_002827125.1 NGR_c26150 phenylacetate-CoA oxygenase/reductase PaaK
Query= metacyc::MONOMER-15950 (357 letters) >NCBI__GCF_000018545.1:YP_002827125.1 Length = 358 Score = 367 bits (941), Expect = e-106 Identities = 182/358 (50%), Positives = 244/358 (68%), Gaps = 2/358 (0%) Query: 1 MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60 M++FH L + EVR ETRDAV I E +F FTQGQ+L R + DGEE+RRSYSIC Sbjct: 1 MARFHPLQVTEVRRETRDAVVITLQPREEDRAAFDFTQGQYLTFRRRFDGEELRRSYSIC 60 Query: 61 TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAA 120 G ++G L+V IKRV GG FS + NE LK G+ LE MPP G F ++ +YL A Sbjct: 61 AGKDEGVLKVGIKRVDGGCFSTWINEELKPGETLEAMPPMGAFFTPIEPEVAKHYLGFAG 120 Query: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSR 180 GSGITPILSIIKTTL EP ++ TL+Y NR +S +FRE+LEDLKN +L R +++ Sbjct: 121 GSGITPILSIIKTTLAREPRAQFTLVYANRHVSSIMFREELEDLKNLHLGRFAALYVLES 180 Query: 181 EQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIH 240 E QD+DL+ GRIDA+KC LF WID+K++D FICGP+ M + L+A+G+ E+I Sbjct: 181 EAQDIDLFTGRIDAEKCEALFRSWIDLKSVDTVFICGPEPMMLAIAAALRAHGLRDEQIK 240 Query: 241 FELFAAA--GSAQKREARESAAQDSSVSQITVISDGRELSFELPRNSQSILDAGNAQGAE 298 FELFA++ G A+++ +A + + TV DG +F P+ QS+L+A + Sbjct: 241 FELFASSQPGLARRKVVSADSADRRATCEATVTLDGTTRNFSFPKEGQSLLEAALENRMD 300 Query: 299 LPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQ 356 PY+CKAGVCSTC+ KV+EGEVEM++N ALEDYEV GYVL+CQ +P+SD++V+ +DQ Sbjct: 301 APYACKAGVCSTCRAKVIEGEVEMETNHALEDYEVEQGYVLTCQCYPLSDRIVVSYDQ 358 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: 374 Number of extensions: 18 Number of successful extensions: 2 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: 358 Length adjustment: 29 Effective length of query: 328 Effective length of database: 329 Effective search space: 107912 Effective search space used: 107912 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 24 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