Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate H281DRAFT_05858 H281DRAFT_05858 ring-1,2-phenylacetyl-CoA epoxidase subunit PaaA
Query= metacyc::MONOMER-15947 (330 letters) >FitnessBrowser__Burk376:H281DRAFT_05858 Length = 332 Score = 449 bits (1154), Expect = e-131 Identities = 208/307 (67%), Positives = 254/307 (82%), Gaps = 1/307 (0%) Query: 20 APEERAFQERIDAEIKIEAKNWMPDAYRQTLIRQISQHAHSEIVGMLPEGNWVTRAPTLK 79 +PE+ F + A+ KIE ++WMP+AYR+TL+RQISQHAHSEIVGMLPEGNW+TRAP+LK Sbjct: 21 SPEQTQFDAVMAADGKIEPQDWMPEAYRKTLVRQISQHAHSEIVGMLPEGNWITRAPSLK 80 Query: 80 RKLQLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKLHSGKAKYSSIFNYPTLNWADMGA 139 RK L+AK+QDEAGHGLYLYSA ETLG RD+ +A LHSGKAKYSSIFNYPT WAD+G Sbjct: 81 RKAILLAKVQDEAGHGLYLYSAAETLGVSRDQLVAALHSGKAKYSSIFNYPTPTWADVGV 140 Query: 140 VGWLVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESFHQRQGYEILLTMMRHGTQAQKDM 199 +GWLVDGAAI+NQ+ L R +YGPY+RAMIRICKEESFHQRQG++ L+ MM GT+AQ+++ Sbjct: 141 IGWLVDGAAIMNQIPLCRCTYGPYARAMIRICKEESFHQRQGFDALMAMM-SGTEAQREL 199 Query: 200 VQDAINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQSNDELRQRFIDQTVPQLELLGCT 259 VQ A+NR WWP LMMFGPSD+ S +S QS W IKR SND+LRQ+F+D TV Q ++LG T Sbjct: 200 VQQAVNRWWWPVLMMFGPSDKDSIHSNQSSKWGIKRISNDDLRQKFVDATVDQAKVLGVT 259 Query: 260 APDPELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNAERIATRRNAIDNGAWVREAAVAH 319 PDP+LKWNE RGHYD+G IDW EF+ V+ G+GPCN ER+ TR A + GAWVREAA+AH Sbjct: 260 LPDPDLKWNEARGHYDYGDIDWEEFWRVVNGDGPCNRERLGTRVKAHNEGAWVREAALAH 319 Query: 320 ARKQQHK 326 A KQ+ + Sbjct: 320 AEKQRQR 326 Lambda K H 0.318 0.131 0.402 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: 433 Number of extensions: 15 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: 330 Length of database: 332 Length adjustment: 28 Effective length of query: 302 Effective length of database: 304 Effective search space: 91808 Effective search space used: 91808 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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