Align ring 1,2-phenylacetyl-CoA epoxidase PaaC subunit (EC 1.14.13.149) (characterized)
to candidate WP_012402210.1 BPHY_RS14570 phenylacetate-CoA oxygenase subunit PaaI
Query= metacyc::MONOMER-15949 (253 letters) >NCBI__GCF_000020045.1:WP_012402210.1 Length = 267 Score = 210 bits (534), Expect = 3e-59 Identities = 117/261 (44%), Positives = 151/261 (57%), Gaps = 16/261 (6%) Query: 8 IEYLLRLGDSALIQGQRLCEWCGRAPALEEELALMNVGLDLVGQARNWLDYAAEL----L 63 + Y+LRL D+ALI GQR EWCG P LEE++AL N+ LDL+GQAR +AA+L Sbjct: 8 LAYVLRLADTALILGQRNAEWCGHGPILEEDIALSNMSLDLIGQARLLYTHAADLEKTLT 67 Query: 64 ADGRDADHLAFRRDERAYRNLLLVEQPN-----------GDFAVTMAKQFLYDAWHFQVL 112 R D AF R ER + N L E P+ D+AVT+ + FLY V Sbjct: 68 GKSRTEDDYAFFRAEREFANYTLAELPHVGPLAGTAHADKDYAVTIVRNFLYSTLMLHVW 127 Query: 113 DGLSRSGDARVAGIAAKALKEVTYHLRRSGEWVQRLGDGTEESHRRMQAAIPQLWRFTVE 172 L+ S DA++A IAAK++KE YH+ S EW+ R GDGT+ESH R QAA+ L +T E Sbjct: 128 SALTGSSDAQLAAIAAKSIKETQYHVHHSREWLVRFGDGTDESHGRAQAALDYLMPYTRE 187 Query: 173 MSDGDEVEQRLCEAGIAPDPAQIAGAWQAKVAEVFAAATLPLPEPAVNFYLSGRRGLHSE 232 D E+ + AGI P+ + + AW V ATL LPE AV +G+ G HSE Sbjct: 188 FFSADATEKAIAAAGIGPNTSDLEAAWLEDVRAALDEATLTLPE-AVKHTTTGKHGEHSE 246 Query: 233 HLGLLLAEMQFLQRAYPDATW 253 H+G LLAEMQ L R +P A+W Sbjct: 247 HMGFLLAEMQSLARQHPGASW 267 Lambda K H 0.321 0.136 0.421 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: 186 Number of extensions: 6 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: 253 Length of database: 267 Length adjustment: 24 Effective length of query: 229 Effective length of database: 243 Effective search space: 55647 Effective search space used: 55647 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 (21.9 bits) S2: 47 (22.7 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