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 CA265_RS25075 CA265_RS25075 phenylacetic acid degradation protein
Query= SwissProt::P76081 (356 letters) >FitnessBrowser__Pedo557:CA265_RS25075 Length = 348 Score = 154 bits (390), Expect = 3e-42 Identities = 112/355 (31%), Positives = 164/355 (46%), Gaps = 25/355 (7%) Query: 7 LTVAKVESETRDAVTITFAVPQPLQEAY-RFRPGQHLTLKASFDGEELRRCYSICRSYLP 65 L + K+ ++ D +T F + + E Y ++ GQ ++L +E+RR YS S Sbjct: 4 LRINKIINQPGDNITFQF---EEVDEPYPKYLAGQFISLIFQGKHKEIRRSYSFNSSPDV 60 Query: 66 GE-ISVAVKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAIAAGSGI 124 E +S+ VK +E G SR+ L PQG F Y P + AAG GI Sbjct: 61 DEPLSITVKRVENGEISRFLHHKTSVNDILLAQEPQGMFSYLPDENLERDLFLFAAGVGI 120 Query: 125 TPMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIFSQETLD 184 TP+ +I+ T L E +S TL+Y NR+ + +F L++ + KYP+RL+++ +FS Sbjct: 121 TPLFSILKTALVREKKSLVTLVYSNRSMEDALFYDELSEWQKKYPERLKIVWVFSN---S 177 Query: 185 SDLLHGRIDGEKLQSLGASLINFRLYDEAFI-CGPAAMMDDAETALKALGMPDKTIHLER 243 +L+ R++ ++ L ++F D F CGP MD L +G K I E Sbjct: 178 KNLMTARLNKFYIEKLLKEHLHFDRNDALFYSCGPIIYMDLCRITLLGVGFDIKQIKRET 237 Query: 244 FNTPGTRVKRSVNVQSDGQKVTVRQDGRDREIVLNADDE----------SILDAALRQGA 293 F P V + DG V D +VLN E ILD AL Sbjct: 238 FVLPEDEVD-----EDDGSAEKV-VDKNTYSVVLNFKGEIYHLDVPWPKRILDVALENKI 291 Query: 294 DLPYACKGGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLTSDVVV 348 LPY+C+GGVC+TC +G V M+ N L DEL G VL C P + + Sbjct: 292 KLPYSCRGGVCSTCVANCTKGGVRMDYNEVLTDDELERGRVLVCTGHPTENGTTI 346 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: 289 Number of extensions: 11 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: 356 Length of database: 348 Length adjustment: 29 Effective length of query: 327 Effective length of database: 319 Effective search space: 104313 Effective search space used: 104313 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