Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_067077069.1 MCUHO_RS08885 phenylacetate--CoA ligase family protein
Query= SwissProt::Q9L9C1 (440 letters) >NCBI__GCF_001602375.1:WP_067077069.1 Length = 475 Score = 105 bits (262), Expect = 3e-27 Identities = 97/335 (28%), Positives = 149/335 (44%), Gaps = 14/335 (4%) Query: 11 LEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADLAKFPFT 70 L+ ++ S++EL A Q L + HAYENVP+YR+ F +G+ P+D++S DL PF Sbjct: 35 LQESQRWSREELAAYQARALSRLLDHAYENVPYYRRVFRERGLVPEDIQSPEDLGLLPFL 94 Query: 71 AKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYT--LKDIDTWATVVARSIRAS 128 + DL+ N P + + G+TG P Y + WA + + R Sbjct: 95 TREDLQTNLPDLKARNYPDSAFEYVTTGGSTGIPVGFYYEKGVSRAREWAFMKTQWDRV- 153 Query: 129 GGRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEK----QIQLIQDFKPDI 184 G R D + GY + + G ++ G ++ S TE+ I I+ FKP Sbjct: 154 GYRFTDRCVVLRGYTIESARDGVYWKKTLCGRWLLMSSHHMTEETLPAYIDRIKRFKPRF 213 Query: 185 IMVTPSYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLS 244 I PS + + M GI+P T +K + G+E R + G YG S Sbjct: 214 IQGYPSTAVILARYMREHGIEPFPT-VKAILCGSENLYPWQRDLLTGVFGCRVFSWYGNS 272 Query: 245 EVMGPGVANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIR 304 E +A EC E+ I+ ++ E+I + V G+ GE+V T LT P+IR Sbjct: 273 E--QTVLAGECEESTHYH-IFPEYGIVELIGRNGQPVQGTGAMGEVVATNLTNFICPLIR 329 Query: 305 YRTRDLTRLLP---PTARSMRRMAKITGRSDDMLI 336 YRT DL RS + ++ GR D ++ Sbjct: 330 YRTMDLATAAGGPCSCGRSYPILERVEGRVQDFIV 364 Lambda K H 0.318 0.137 0.406 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: 494 Number of extensions: 22 Number of successful extensions: 3 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: 440 Length of database: 475 Length adjustment: 33 Effective length of query: 407 Effective length of database: 442 Effective search space: 179894 Effective search space used: 179894 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