Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_011842537.1 RSPH17029_RS18475 AMP-binding protein
Query= SwissProt::Q72K16 (445 letters) >NCBI__GCF_000015985.1:WP_011842537.1 Length = 481 Score = 227 bits (578), Expect = 7e-64 Identities = 151/449 (33%), Positives = 230/449 (51%), Gaps = 26/449 (5%) Query: 8 ETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLP-RIPFTKKT 66 ET+P+ + A RL+ + AY ++ PFYRR DEAG P + LED ++P +K Sbjct: 32 ETMPQAEREAAILARLQAICAYAWDHAPFYRRKWDEAGFHPSHLKSLEDFEDKVPVIRKA 91 Query: 67 DLRD----HYPFGLF-AVPREEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARSLAAA 121 DLR H PFG + VP EV VH +SGTTG+PT ++ D + A AR + A Sbjct: 92 DLRAAQAAHPPFGDYLCVPDAEVFHVHGTSGTTGRPTAFAVSQGDWRAIANAHARIMWAM 151 Query: 122 GARPGMMLHNAYGYGLFTGGLGLHGGAEALGMTVVPV---SGGMTERQVMLIQDFRPEVI 178 G RPG + A + L+ G G GAE LG P + GM+ R + +P Sbjct: 152 GMRPGDTICVAAIFSLYMGSWGALAGAERLGAKAFPFGAGAAGMSSRCAQWLDILKPAGF 211 Query: 179 SCTPSYAQTLAEEFRKRGVSPEELSLEYAVLGAEPWTE--AIRKQVDEGLGVKSTNIYGL 236 TP+YA LAE K G+ P L+Y EP +IR+++++ + + + Sbjct: 212 YGTPTYAIHLAETAIKDGLDPRRFGLKYMFFSGEPGASIPSIRERIEDLYAARVYDSGSM 271 Query: 237 SEIIGPGVSNECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLL 296 E+ P + E G W+D EV DP T +P G+ G V+T L + + P++ Sbjct: 272 GEMT-PWMHVGGSRETPGMLCWQDIVYTEVCDPQTHRRVPYGQRGTPVYTHLERMSQPMI 330 Query: 297 RYWTGDLTFLTYEACTCGRTHVRMG-PILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVP 355 R +GDLT T + CGRT+ ++ I+GR DDM+ IRG NVYP+++EA L +P Sbjct: 331 RLESGDLTVWTNDPTPCGRTYPQLPMGIIGRVDDMITIRGENVYPSEIEAALCQLPGYGG 390 Query: 356 HYQIVVRREGTLDEAELKVEVSEPFFREIGQEVLSDEVVEADHRLHALRERIARKIKDNV 415 ++I + REGT+DE + VE++ P E G++V A ++A + + Sbjct: 391 EHRIFITREGTMDEMMISVELA-PERWERGEDV-----------RRAFHAQVAAHLHSML 438 Query: 416 GVTLKVTLLPPGQAPRSEGGKLRRVLDLR 444 G+ + ++ P PR++ K +RV+D R Sbjct: 439 GLRSVIEIVAPNTHPRTD-FKAKRVIDDR 466 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: 552 Number of extensions: 28 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: 481 Length adjustment: 33 Effective length of query: 412 Effective length of database: 448 Effective search space: 184576 Effective search space used: 184576 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 Apr 10 2024. 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