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 RR42_RS10060 RR42_RS10060 ferredoxin:oxidoreductase FAD/NAD(P)-binding protein
Query= SwissProt::P76081 (356 letters) >FitnessBrowser__Cup4G11:RR42_RS10060 Length = 339 Score = 181 bits (458), Expect = 3e-50 Identities = 126/353 (35%), Positives = 175/353 (49%), Gaps = 22/353 (6%) Query: 4 FHSLTVAKVESETRDAVTITFAVPQPLQEAYRFRPGQHLTLKASFDGEELRRCYSICRSY 63 FH+LTVA++ ET DA + VP LQ+++ +R GQHLT + + DG+ L R YS+ S Sbjct: 3 FHNLTVAQITWETEDARSYALLVPDALQQSFVYRAGQHLTFRVNVDGKTLLRSYSLSSSP 62 Query: 64 LPGEISVA-VKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAI-AAG 121 G + V VK I GGR S + H+ G LEV P G F E G L AAG Sbjct: 63 EAGGLPVVTVKRIPGGRASGWFHAHVDAGTRLEVSAPTGRF----VCEDMGAPLFFCAAG 118 Query: 122 SGITPMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIFSQE 181 SGITP+L++I + L + S TL Y NR + S +F +A L + RL + Sbjct: 119 SGITPVLSMIRSALAST-SSAMTLYYANRDAASTIFAAQIAKLSRDHSDRLAV------- 170 Query: 182 TLDSDLLHGRIDGEKLQSLGASLINFRLYDEAFICGPAAMMDDAETALKALGMPDKTIHL 241 L H DG + A+L++ + + ++CGP M A + GM +HL Sbjct: 171 ----HLHHDDTDGFPERGKIAALLSAVPHCQLYLCGPGPFMQTVLEAAEVAGMGPGCVHL 226 Query: 242 ERFNTPGTR--VKRSVNVQSDGQKVTVRQDGRDREIVLNADDESILDAALRQGADLPYAC 299 ERF+ V + + + TV G +V A +S+L AAL G D PYAC Sbjct: 227 ERFDAAAQEPEVASAAPMPAQACDATVTLGGA-LHVVRVASGQSLLQAALACGVDAPYAC 285 Query: 300 KGGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLTS-DVVVDFD 351 + G C +C K + G V N DELAAG++L+CQA P V + FD Sbjct: 286 EEGYCGSCAAKCVDGAVVHARNDVFSADELAAGWILTCQARPRQERPVAITFD 338 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: 304 Number of extensions: 15 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: 339 Length adjustment: 29 Effective length of query: 327 Effective length of database: 310 Effective search space: 101370 Effective search space used: 101370 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