Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate SM_b21636 SM_b21636 ferredoxin reductase electron transfer protein
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__Smeli:SM_b21636 Length = 358 Score = 354 bits (909), Expect = e-102 Identities = 181/360 (50%), Positives = 248/360 (68%), Gaps = 6/360 (1%) Query: 1 MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60 M++F+ L + EVR +TRDAV + + E +F FTQGQ+L R GEE+RRSYSIC Sbjct: 1 MARFYPLQVTEVRRDTRDAVVVTLEPREEDRAAFDFTQGQYLTFRRLFGGEELRRSYSIC 60 Query: 61 TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFH--VELDAARHGNYLAV 118 G+++G L+V IKRV G FS++ANE L+ G LE MPP G F +E +AA+H YL Sbjct: 61 AGLDEGALKVGIKRVDDGCFSSWANEELEPGDTLEAMPPMGAFFTPIEPEAAKH--YLGF 118 Query: 119 AAGSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLF 178 A GSGITP+LS++KT L EP S TL+Y NR +S +FRE+L+DLKN YL RL+++ + Sbjct: 119 AGGSGITPVLSLVKTVLAREPRSAFTLVYANRHFSSIMFREELDDLKNLYLGRLSVLHVL 178 Query: 179 SREQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAER 238 E Q++DL++GR+D +KC LF WIDV++ D AFICGP+ M V L+A+G+ +R Sbjct: 179 ESEAQEIDLFSGRLDREKCTALFRSWIDVRSADTAFICGPEPMMLGVAAALRAHGLGDDR 238 Query: 239 IHFELFAAAGSAQKREARESAAQDSSVS--QITVISDGRELSFELPRNSQSILDAGNAQG 296 I FELFAA+ + R ESAA S + + TV DG SF P+ S+L+A Sbjct: 239 IKFELFAASQPGRARRKVESAAGADSRARCEATVTLDGATRSFTFPKEGLSLLEAALENR 298 Query: 297 AELPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQ 356 + P++CKAGVCS+C+ KV+EGEVEM+SN ALEDYEV GYVL+CQ++P+SD++V+ +DQ Sbjct: 299 MDAPFACKAGVCSSCRAKVLEGEVEMESNNALEDYEVEQGYVLTCQSYPLSDRIVVSYDQ 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: 357 Number of extensions: 16 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 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