Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate WP_086509215.1 BZY95_RS06865 phenylacetate-CoA oxygenase/reductase subunit PaaK
Query= metacyc::MONOMER-15950 (357 letters) >NCBI__GCF_002151265.1:WP_086509215.1 Length = 359 Score = 463 bits (1191), Expect = e-135 Identities = 223/359 (62%), Positives = 288/359 (80%), Gaps = 2/359 (0%) Query: 1 MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60 MS+FH LT++++R ET ++VSIAF+VP L ++FRFTQGQ+L +R ++ GEEVRRSYSIC Sbjct: 1 MSRFHDLTVRDIRKETSESVSIAFEVPESLHEAFRFTQGQYLTLRREIAGEEVRRSYSIC 60 Query: 61 TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAA 120 TGV++GE+RVA+K V GG FS +AN L G L+VMPP G F V LD +R G+YLAVAA Sbjct: 61 TGVHEGEIRVAVKLVPGGAFSTFANHELAVGDTLQVMPPQGKFFVPLDPSRKGHYLAVAA 120 Query: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSR 180 GSGITPILSII TTLETEP SR TL+YGN S+++T+FRE+L+DLKNR+++RLNLI +F+R Sbjct: 121 GSGITPILSIISTTLETEPMSRFTLVYGNFSTSTTMFRERLQDLKNRHMERLNLIHIFNR 180 Query: 181 EQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIH 240 E+QD++LYNG IDA+KC LF RW+DV+ L+AAF+CGPQ M+ TVR+ L+ GM ERIH Sbjct: 181 EEQDIELYNGIIDAEKCRTLFDRWLDVRGLEAAFLCGPQEMSTTVREVLQEYGMPVERIH 240 Query: 241 FELFAAA--GSAQKREARESAAQDSSVSQITVISDGRELSFELPRNSQSILDAGNAQGAE 298 ELF + SA+++ + S I VI DGR L F+LPRN++SIL+AGN GA+ Sbjct: 241 LELFGSRPNASARRQTTPGGGQATAGSSHIKVIIDGRTLEFDLPRNTRSILEAGNKHGAD 300 Query: 299 LPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQI 357 LP+SCKAGVCSTC KV EGEVEMD+NFALEDYE+AAG VLSCQ +P+S+KVVL++D++ Sbjct: 301 LPFSCKAGVCSTCLAKVEEGEVEMDANFALEDYEIAAGMVLSCQCYPVSEKVVLNYDEV 359 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: 417 Number of extensions: 13 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: 359 Length adjustment: 29 Effective length of query: 328 Effective length of database: 330 Effective search space: 108240 Effective search space used: 108240 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