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_RS31980 RR42_RS31980 3-ketosteroid-9-alpha-hydroxylase
Query= SwissProt::P76081 (356 letters) >FitnessBrowser__Cup4G11:RR42_RS31980 Length = 342 Score = 191 bits (484), Expect = 3e-53 Identities = 120/351 (34%), Positives = 184/351 (52%), Gaps = 20/351 (5%) Query: 4 FHSLTVAKVESETRDAVTITFAVPQPLQEAYRFRPGQHLTLKASFDGEELRRCYSICRS- 62 FH L +A+V +ET +A ++ F +P L++ + +RPGQ LTLK +G +RCYS+ S Sbjct: 6 FHPLRIAQVVAETDEASSLVFELPDGLRDTFAYRPGQFLTLKVPLEGAAQQRCYSLSSSP 65 Query: 63 YLPGEISVAVKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAIAAGS 122 + + V +K + GGR S + + + G T+EVM P G F G L A GS Sbjct: 66 QVDSALRVTIKRVRGGRVSNWICDRLGAGDTVEVMPPAGVF---TPRSLDGDLLLFAGGS 122 Query: 123 GITPMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIFSQET 182 GITP+L+I L+ TLIY NR +S++FR AL +L ++ RL+++ Sbjct: 123 GITPVLSIAKAALR-HGGGNVTLIYANRDERSVIFRDALCELAARHADRLRVI-----HW 176 Query: 183 LDSDLLHGRIDGEKLQSLGASLINFRLYDEAFICGPAAMMDDAETALKALGMPDKTIHLE 242 LDS + G +L++L A + + FICGP MD A+ AL+ LG+ + IH+E Sbjct: 177 LDS--VQGPPSQAQLEALAAPWG----HADCFICGPGPFMDGAQAALQTLGVARERIHVE 230 Query: 243 RFNTP---GTRVKRSVNVQSDGQKVTVRQDGRDREIVLNADDESILDAALRQGADLPYAC 299 RF P K + V DG + +A E++LDA LR G P +C Sbjct: 231 RFGAPPPAAVPAKEQTPAACAPAALEVELDGVRHRLDAHAG-ETVLDAMLRAGVAAPNSC 289 Query: 300 KGGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLTSDVVVDF 350 + G+C C C+V G+ + N+ L+ + AG+ L+CQA S++ + F Sbjct: 290 RSGLCGACMCQVTHGEATLGENHVLDAADREAGWTLACQARAAGSELHLKF 340 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: 309 Number of extensions: 20 Number of successful extensions: 6 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: 342 Length adjustment: 29 Effective length of query: 327 Effective length of database: 313 Effective search space: 102351 Effective search space used: 102351 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