Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_043745126.1 AMB_RS18190 phenylacetate--CoA ligase family protein
Query= SwissProt::Q72K16 (445 letters) >NCBI__GCF_000009985.1:WP_043745126.1 Length = 407 Score = 172 bits (435), Expect = 2e-47 Identities = 125/380 (32%), Positives = 195/380 (51%), Gaps = 23/380 (6%) Query: 3 YQPELETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRIPF 62 + LET ++ A Q E L +A P + R+L E VDP G L R+P Sbjct: 4 FYDSLETRSTDEREAAQFEALPEQIALAKADSPAFARVLAE--VDPASVTGRAALARLPV 61 Query: 63 TKKTDLRDHY----PFG-LFAVPREEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARS 117 T+K++L D PF L A P+ E+ RV AS G P G+ + ++ AR+ Sbjct: 62 TRKSELIDAQQADPPFASLIATPKSELRRVFASPGPIYDPE--GWDNDWWRI-----ARA 114 Query: 118 LAAAGARPGMMLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRPEV 177 L AAG R G ++HN + Y GG+ GA ALG V P G T++Q + D +P Sbjct: 115 LYAAGFRRGDLMHNCFSYHFTPGGVMFETGAHALGCPVFPAGIGNTDQQAKAVADLKPAG 174 Query: 178 ISCTPSYAQTLAEEFRKRGVSPEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYGLS 237 TPS+ + + E + G+ + SL A + E +R+ + + LGV T Y + Sbjct: 175 YGGTPSFLKIILERAEEMGL--DHSSLTKACVSGEALLPPLRQSLKD-LGVDVTQCYATA 231 Query: 238 EIIGPGVSNECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLLR 297 ++ G+ + R+G I ++ + E+V P TG+P+PEG+VG +V T+ ++ PL+R Sbjct: 232 DL---GLIAYETKAREGL-IVDEGVIVEIVRPGTGDPVPEGEVGEVVVTSFNQD-YPLIR 286 Query: 298 YWTGDLTFLTYEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVPHY 357 + TGDL+ + CGRT++R+ +GR D I+G+ V+P Q+ V PEV+ Sbjct: 287 FATGDLSAILTGRSPCGRTNMRLKGWMGRADQTTKIKGMFVHPRQIAEVAKRHPEVI-RA 345 Query: 358 QIVVRREGTLDEAELKVEVS 377 ++VV ++G D L VE S Sbjct: 346 RLVVEKDGENDRLTLNVETS 365 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: 454 Number of extensions: 35 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: 407 Length adjustment: 32 Effective length of query: 413 Effective length of database: 375 Effective search space: 154875 Effective search space used: 154875 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