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 BWI76_RS13110 BWI76_RS13110 phenylacetic acid degradation protein
Query= SwissProt::P76081 (356 letters) >FitnessBrowser__Koxy:BWI76_RS13110 Length = 356 Score = 545 bits (1403), Expect = e-160 Identities = 265/356 (74%), Positives = 308/356 (86%) Query: 1 MTTFHSLTVAKVESETRDAVTITFAVPQPLQEAYRFRPGQHLTLKASFDGEELRRCYSIC 60 MTTFHSLTVAKVE ETRDAVTITFA+P L++AY FRPGQHLTLKA GEELRRCYSIC Sbjct: 1 MTTFHSLTVAKVEPETRDAVTITFAIPDALRDAYAFRPGQHLTLKARLGGEELRRCYSIC 60 Query: 61 RSYLPGEISVAVKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAIAA 120 RS PGEISVAVKAI+GGRFSRYA+ I+ GM LEVMVPQGHFGYQP+A R+ YLAIAA Sbjct: 61 RSRAPGEISVAVKAIDGGRFSRYAQSDIQPGMALEVMVPQGHFGYQPRAGRRADYLAIAA 120 Query: 121 GSGITPMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIFSQ 180 GSGITPM+AI+ TL E +S+FTLIYGNR+S SMMFRQALADLKD+YPQRLQ++ +FSQ Sbjct: 121 GSGITPMMAIVDATLACETDSRFTLIYGNRSSHSMMFRQALADLKDRYPQRLQVVHLFSQ 180 Query: 181 ETLDSDLLHGRIDGEKLQSLGASLINFRLYDEAFICGPAAMMDDAETALKALGMPDKTIH 240 E +DSDLL GRIDG+KL+ L L++F +D AFICGPAAMMD+AE L+ LG+P+K IH Sbjct: 181 EAMDSDLLQGRIDGDKLRELAGHLLDFSRFDHAFICGPAAMMDEAEMTLRELGVPEKAIH 240 Query: 241 LERFNTPGTRVKRSVNVQSDGQKVTVRQDGRDREIVLNADDESILDAALRQGADLPYACK 300 LERFNTPG+ +R+ VQ++G+ VT+RQDGRDR I L+A+D+SILDAALRQGADLP+ACK Sbjct: 241 LERFNTPGSGARRAAGVQAEGRSVTIRQDGRDRTIALSAEDDSILDAALRQGADLPFACK 300 Query: 301 GGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLTSDVVVDFDAKGMA 356 GGVCATCKCKVLRG+VAM NYSLE DE+AAGYVLSCQALP + DV+VDFDA+GMA Sbjct: 301 GGVCATCKCKVLRGEVAMAANYSLEADEVAAGYVLSCQALPTSGDVIVDFDARGMA 356 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: 500 Number of extensions: 16 Number of successful extensions: 1 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: 356 Length adjustment: 29 Effective length of query: 327 Effective length of database: 327 Effective search space: 106929 Effective search space used: 106929 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