Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate 349956 BT0428 phenylacetate-coenzyme A ligase (NCBI ptt file)
Query= SwissProt::Q72K16 (445 letters) >FitnessBrowser__Btheta:349956 Length = 435 Score = 365 bits (938), Expect = e-105 Identities = 192/443 (43%), Positives = 286/443 (64%), Gaps = 17/443 (3%) Query: 3 YQPELETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRIPF 62 ++ E+E + REKL+ LQ +RLK+ + + P+Y+ + + G+ + L+D+ +IPF Sbjct: 6 WEEEIEIMSREKLQELQLQRLKKTIN-IAANSPYYKEVFSKNGITGDSIQSLDDIRKIPF 64 Query: 63 TKKTDLRDHYPFGLFAVP-REEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARSLAAA 121 T K+D+R +YPFGL A + + R+H+SSGTTG PTV+ ++++DL +A +VAR L Sbjct: 65 TTKSDMRANYPFGLVAGDMKRDGVRIHSSSGTTGNPTVIVHSQHDLDSWANLVARCLYMV 124 Query: 122 GARPGMMLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRPEVISCT 181 G R + N+ GYG+FTGGLG GAE LG VP + G ++RQ+ I DF+ + Sbjct: 125 GIRKTDVFQNSSGYGMFTGGLGFQYGAERLGCLTVPAAAGNSKRQIKFISDFKTTALHAI 184 Query: 182 PSYAQTLAEEFRKRGVSPEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYGLSEIIG 241 PSYA LAE F++ G+ P E +L+ V+GAEP T+ R++++ L VK+ N +G++E+ G Sbjct: 185 PSYAIRLAEVFQEEGIDPRETTLKTLVIGAEPHTDEQRRKIERMLNVKAYNSFGMTEMNG 244 Query: 242 PGVSNECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLLRYWTG 301 PGV+ EC +E+ G H WED +L E++DP+TGEP+PEG++G LV TTL +E MPL+RY T Sbjct: 245 PGVAFEC-QEQNGMHFWEDCYLVEIIDPETGEPVPEGEIGELVLTTLDREMMPLIRYRTR 303 Query: 302 DLTFLTYEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVPHYQIVV 361 DLT + C CGRTH+R+ I GR+DDM II+GVN++P QVE +L+ PE+ +Y I + Sbjct: 304 DLTRILPGKCPCGRTHLRIDRIKGRSDDMFIIKGVNIFPMQVEKILVQFPELGSNYLITL 363 Query: 362 RREGTLDEAELKVEVSEPFFREIGQEVLSDEVVEADHRLHALRERIARKIKDNVGVTLKV 421 DE ++VE+S ++ +D +E L +R I R++KD + VT KV Sbjct: 364 ETVNNQDEMIVEVELS---------DLSTDNYIE----LEKIRRDIIRQLKDEILVTPKV 410 Query: 422 TLLPPGQAPRSEGGKLRRVLDLR 444 L+ G P+SE GK RV DLR Sbjct: 411 KLVKKGSLPQSE-GKAVRVKDLR 432 Lambda K H 0.319 0.139 0.409 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: 493 Number of extensions: 24 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: 445 Length of database: 435 Length adjustment: 32 Effective length of query: 413 Effective length of database: 403 Effective search space: 166439 Effective search space used: 166439 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 (21.7 bits) S2: 51 (24.3 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