Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_067075175.1 MCUHO_RS05965 phenylacetate--CoA ligase
Query= SwissProt::Q72K16 (445 letters) >NCBI__GCF_001602375.1:WP_067075175.1 Length = 433 Score = 383 bits (983), Expect = e-111 Identities = 206/439 (46%), Positives = 286/439 (65%), Gaps = 16/439 (3%) Query: 7 LETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRIPFTKKT 66 +E +P ++LR LQ + +K LV +Y FYRR + E V P R LED+ ++PF K+ Sbjct: 8 MEEVPFDELRRLQFKLVKSLVYRLYSFNDFYRRRMKEQQVHPDDIRTLEDVAKLPFMYKS 67 Query: 67 DLRDHYPFGLFAVPREEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARSLAAAGARPG 126 DLRD YP +F+ + E+ R H SSGTTGKPTVVGYT+ D++ ++E +AR ++ G G Sbjct: 68 DLRDGYPDRIFSAEQNELVRYHVSSGTTGKPTVVGYTERDIENWSESLARGFSSCGLGRG 127 Query: 127 MMLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRPEVISCTPSYAQ 186 ++ +YGYGLFTGGLG H GAE +G TV+P S G TERQ+ L+QD R I+CTPSY Sbjct: 128 DVMQVSYGYGLFTGGLGAHYGAERVGATVLPTSVGNTERQIELMQDLRVTAIACTPSYLL 187 Query: 187 TLAEEFRKRGVS-PEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYGLSEIIGPGVS 245 + E K GVS + L LGAEPW+E +R ++++ LG+++ +IYG SE+ GP + Sbjct: 188 HIGEVAEKMGVSIKNDTDLRMGFLGAEPWSEQMRTRIEDWLGIRAYDIYGTSELSGP-MF 246 Query: 246 NECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLLRYWTGDLTF 305 EC E+ QG HIW D L E+VDP TGE L G+ G L T L KEA+P++RY GDLT Sbjct: 247 TECAEQ-QGIHIWGDLALVEIVDPATGEVLEAGEQGELTITMLQKEALPMVRYRIGDLTA 305 Query: 306 LTYEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVPHYQIVVRREG 365 + C CGRTH R+G I GR DDMLI+RG+NV+P+QVE LL IP+V H+QIVV R+G Sbjct: 306 IEEGPCACGRTHPRIGRIRGRVDDMLIVRGINVFPSQVEHALLEIPQVGRHFQIVVDRKG 365 Query: 366 TLDEAELKVEVSEPFFREIGQEVLSDEVVEADHRLHALRERIARKIKDNVGVTLKVTLLP 425 LD ++VEVSE E SD++ E L +++ + +++ ++ V++ V L+ Sbjct: 366 ALDSMLVRVEVSE--------EAFSDKITE----LMVIKKAVEHRLRSSLNVSVDVELVE 413 Query: 426 PGQAPRSEGGKLRRVLDLR 444 PG PR E GK ++V+D R Sbjct: 414 PGTLPRFE-GKSKKVVDRR 431 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: 480 Number of extensions: 16 Number of successful extensions: 4 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: 433 Length adjustment: 32 Effective length of query: 413 Effective length of database: 401 Effective search space: 165613 Effective search space used: 165613 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 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