Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_028583918.1 G494_RS0106745 phenylacetate--CoA ligase
Query= SwissProt::Q72K16 (445 letters) >NCBI__GCF_000429965.1:WP_028583918.1 Length = 433 Score = 483 bits (1244), Expect = e-141 Identities = 255/445 (57%), Positives = 317/445 (71%), Gaps = 13/445 (2%) Query: 1 MMYQPELETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRI 60 M++ E+E+LPR L ++Q +RL+ V VYE V YR +D AGV P R L DL + Sbjct: 1 MIWVEEVESLPRPGLESIQLKRLQLQVQRVYETVAPYRSKMDAAGVKPADIRSLADLKYL 60 Query: 61 PFTKKTDLRDHYPFGLFAVPREEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARSLAA 120 P+ K DLRD+YPFGLF VP EEV RVHASSGTTG+PTVVGYT+ D+K++A V++R+LA Sbjct: 61 PYNTKDDLRDNYPFGLFTVPMEEVIRVHASSGTTGQPTVVGYTEADIKLWASVMSRALAM 120 Query: 121 AGARPGMMLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRPEVISC 180 AG G M+HNAYGYGLFTGGLG H G EALG TV+PVSGG ++RQ+ +++DF V+ Sbjct: 121 AGVTRGDMVHNAYGYGLFTGGLGAHYGIEALGATVIPVSGGNSKRQITIMRDFGSSVLLS 180 Query: 181 TPSYAQTLAEEFRKRGVSPEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYGLSEII 240 TPSYA LAE GVSPEEL L + GAEPW+E++R++V+ LG+K+ +IYGLSEII Sbjct: 181 TPSYALNLAEAMADVGVSPEELKLRVGIHGAEPWSESMREEVERKLGIKAVDIYGLSEII 240 Query: 241 GPGVSNECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLLRYWT 300 GPGV+ EC+ +G HI EDHFLPE+VDPDT EPLP G+VG LVFTTLTKEA PL+RY T Sbjct: 241 GPGVAMECLHTDRGMHILEDHFLPEIVDPDTLEPLPYGEVGELVFTTLTKEAFPLIRYRT 300 Query: 301 GDLTFLTYEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVPHYQIV 360 D++ L E C CGRT VRM ++GRTDDMLIIRGVNV+P+Q+E VL+ I V PHYQ+ Sbjct: 301 KDISRLIAEPCACGRTLVRMEKVMGRTDDMLIIRGVNVFPSQLEHVLVGIEGVEPHYQLE 360 Query: 361 VRREGTLDEAELKVEVSEPFFREIGQEVLSDEVVEADHRLHALRERIARKIKDNVGVTLK 420 V REG LD + VEVSE F SDE+ L L +RI +KD +GVT K Sbjct: 361 VNREGNLDTMSVLVEVSEHIF--------SDEI----RVLEGLTKRIQSDVKDILGVTCK 408 Query: 421 VTLLPPGQAPRSEGGKLRRVLDLRK 445 V L+ P RSE GK +RV+D RK Sbjct: 409 VKLVEPRSITRSE-GKAQRVIDNRK 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: 579 Number of extensions: 25 Number of successful extensions: 2 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