Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate WP_038202624.1 Q392_RS05600 oxidoreductase
Query= metacyc::MONOMER-15950 (357 letters) >NCBI__GCF_000745855.1:WP_038202624.1 Length = 326 Score = 107 bits (267), Expect = 4e-28 Identities = 99/327 (30%), Positives = 143/327 (43%), Gaps = 44/327 (13%) Query: 36 FTQGQHLVMRTQL-DGEEVRRSYSIC-------TGVNDGELRVAIKRVAGGRFSAYANES 87 FT G H+ ++ +L DG R YS+ TG +A++R GR + + Sbjct: 34 FTAGAHVRVQVELPDGASDWRHYSLVNTHAGADTGAPQPHYTIAVRREDEGRGGSRWMHA 93 Query: 88 LKAGQRLEVMPPSGHFHVELDAARHGNYLAVAAGSGITPILSIIKTTLETEPHSRVTLLY 147 L+AGQR+E+ PP F + A G + VA G GITP+ S+ V +LY Sbjct: 94 LQAGQRIEIEPPKNDFPL---GAHAGCAVLVAGGIGITPLASM--AAARRAAGLPVRMLY 148 Query: 148 GNRSSASTLFREQLEDLKNRYLQRLNLIFLFSREQQDVDLYNGRIDADKCGQLFSRWIDV 207 RS A F +L+ L +L E+Q L + D C Sbjct: 149 AGRSRALMAFLPELQALLGE-----SLAVHADEERQGAPLDVAAL-LDGCA--------- 193 Query: 208 KALDAAFICGPQAMTETVRDQLKANGMAAERIHFELFAAAGSAQKREARESAAQDSSVSQ 267 A D ++CGP+AM + V A ER+HFELF A +AA D + + Sbjct: 194 -AEDQLYVCGPRAMLDAVLAAADARAWPRERVHFELFTAP---------VAAAGDQPI-E 242 Query: 268 ITVISDGRELSFELPRNSQSILDAGNAQGAELPYSCKAGVCSTCKCKVVEGEVEMDSNFA 327 + + G++L+ QSILD G + + CK G C C VVEGE E ++ Sbjct: 243 LVLAQSGQQLTVPA---GQSILDCLIEHGCDPLFDCKRGECGVCSAAVVEGEPE-HRDYF 298 Query: 328 LEDYEVAAGYVLS-CQTFPISDKVVLD 353 L D E A G V+ C + ++VLD Sbjct: 299 LSDAEKAGGKVMQICVSRAKGRRLVLD 325 Lambda K H 0.319 0.133 0.377 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: 273 Number of extensions: 13 Number of successful extensions: 3 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: 357 Length of database: 326 Length adjustment: 29 Effective length of query: 328 Effective length of database: 297 Effective search space: 97416 Effective search space used: 97416 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 24 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