Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_011767163.1 AZO_RS17285 phenylacetate--CoA ligase family protein
Query= SwissProt::Q72K16 (445 letters) >NCBI__GCF_000061505.1:WP_011767163.1 Length = 410 Score = 148 bits (373), Expect = 4e-40 Identities = 122/392 (31%), Positives = 186/392 (47%), Gaps = 31/392 (7%) Query: 22 RLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRIPFTKKTDLRDHY----PFGLF 77 RL +A+ P + RLL A +DP G E L R+P +K++L + PFG F Sbjct: 22 RLPAQIAHARTHAPAFARLL--ADIDPGAVTGREALARLPVIRKSELLEAQKAARPFGGF 79 Query: 78 AVPR--EEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARSLAAAGARPGMMLHNAYGY 135 A RV AS G +P G + ++ AR+ AAG R G ++HN + Y Sbjct: 80 AAVGWGASCRRVFASPGPLYEPE--GSRADYYRM-----ARAFHAAGFRAGDLVHNTFSY 132 Query: 136 GLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRPEVISCTPSYAQTLAEEFRKR 195 G + A ALG TV P G TE+QV I D P + TPS+ + L ++ + Sbjct: 133 HFTPAGSMMETAAHALGCTVFPAGVGQTEQQVAAIADLAPNAYAGTPSFLRILLDKAAEL 192 Query: 196 GVSPEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYGLSEIIGPGVSNECVEERQGS 255 GV P + A + E + ++R GV + Y ++I G+ E R+G Sbjct: 193 GVKP---AFTKAFVSGEAFPPSLR-DAFAARGVAAFQAYATADI---GLIAYETEAREGM 245 Query: 256 HIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLLRYWTGDLTFLTYEACTCGR 315 + ED L E+V P TG+P+ G+VG +V TT + PL+R+ TGDL+ L A CGR Sbjct: 246 VVDEDIIL-EIVRPGTGDPVAPGEVGEVVVTTFNPD-YPLIRFGTGDLSALLPGASPCGR 303 Query: 316 THVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVPHYQIVVRREGTLDEAELKVE 375 T++R+ +GR D ++G+ V+P Q+ V+ P+ + ++VV D L E Sbjct: 304 TNLRIKGWMGRADQTAKVKGMFVHPGQIADVVRRHPQ-LGRARLVVENPDLTDRMTLHCE 362 Query: 376 VSEPFFREIGQEVLSDEVVEADHRLHALRERI 407 + G + L+ V + L LR + Sbjct: 363 T------QAGSDALAAAVATSIRELTKLRGEV 388 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: 435 Number of extensions: 23 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: 410 Length adjustment: 32 Effective length of query: 413 Effective length of database: 378 Effective search space: 156114 Effective search space used: 156114 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