Align 1,2-phenylacetyl-CoA epoxidase, subunit E; 1,2-phenylacetyl-CoA epoxidase, reductase subunit; 1,2-phenylacetyl-CoA monooxygenase, subunit E; EC 1.-.-.- (characterized)
to candidate PfGW456L13_2523 Probable phenylacetic acid degradation NADH oxidoreductase paaE (EC 1.-.-.-)
Query= SwissProt::P76081 (356 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2523 Length = 360 Score = 185 bits (469), Expect = 2e-51 Identities = 118/354 (33%), Positives = 180/354 (50%), Gaps = 23/354 (6%) Query: 6 SLTVAKVESETRDAVTITFAVPQPLQEAYRFRPGQHLTLKASFDGEELRRCYSICRSYLP 65 SL V V ET DA ++ VP L+E +R++PGQ L+ + F G+ L RCYS+ S L Sbjct: 19 SLQVCAVIDETLDARSLVLDVPPALRERFRYKPGQFLSFRVPFAGKLLTRCYSMASSPLA 78 Query: 66 GEI-SVAVKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAIAAGSGI 124 + V VK ++GGR S + E ++ G LEV+ P GHF PQA+ + + GSGI Sbjct: 79 DALPKVTVKRVDGGRVSNWMNE-VQVGDWLEVLPPAGHFCLDPQADTEKPLVLFGGGSGI 137 Query: 125 TPMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIFSQETLD 184 TP+ +I+ + L + LIY NR S++F+ L L +P +L ++ + Sbjct: 138 TPVFSILKSVLHSS-RRPIKLIYANRDEASVIFKDELCQLIKAHPDQLHVVHVL------ 190 Query: 185 SDLLHGRIDGEKLQSLGASLINFRLYDEAFICGPAAMMDDAETALKALGMPDKTIHLERF 244 D + G + +++ L + + FICGP MD E L A+G + IH+ERF Sbjct: 191 -DSVQGFLTDHQVRHL----LRGSAGGDYFICGPGPFMDTVERTLLAVGEAAERIHVERF 245 Query: 245 NTPGT--------RVKRSVNVQSDGQKVTVRQDGRDREIVLNADDESILDAALRQGADLP 296 +P V R+ + S + + V DG+ EI D ++L + G D+P Sbjct: 246 VSPPDPDELLAEEAVARAAAMDSQCEALIVELDGQQHEIACKPGD-TLLQSCKAAGLDVP 304 Query: 297 YACKGGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLTSDVVVDF 350 +C+ G C C C V G+V + N L P ELA G+ L+CQ+ P + V + F Sbjct: 305 SSCEEGFCGACMCVVREGEVQLARNDVLTPKELADGWTLACQSRPTGARVRLKF 358 Lambda K H 0.320 0.135 0.390 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: 340 Number of extensions: 12 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: 356 Length of database: 360 Length adjustment: 29 Effective length of query: 327 Effective length of database: 331 Effective search space: 108237 Effective search space used: 108237 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