Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate 8500984 DvMF_1721 Phenylacetate--CoA ligase (RefSeq)
Query= SwissProt::P76085 (437 letters) >FitnessBrowser__Miya:8500984 Length = 431 Score = 328 bits (840), Expect = 3e-94 Identities = 178/421 (42%), Positives = 258/421 (61%), Gaps = 10/421 (2%) Query: 16 DELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDLRKFPCTTKQDLRDNY 75 + L +QT+ L+WT++HAY N P Y+ KFDAAGVHPDD R L D+ + P + +DLR+ Y Sbjct: 13 ETLHRVQTEGLRWTVRHAYANSPAYKAKFDAAGVHPDDIRTLDDIVRLPTASVEDLREGY 72 Query: 76 PFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARSLRAAGGSPKDKIHVA 135 P +VP VVRIHASSGTTGK ++ YTQND+D +A +AR AG + +D++ +A Sbjct: 73 PLPLLSVPESDVVRIHASSGTTGKRKILAYTQNDVDTFALQMARCYELAGLTREDRVQIA 132 Query: 136 YGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDMIMVTPSYCLNLIEEL 195 GYGL+T G G G+E+ GA +P+ G E Q QL+ D + T S L + EE+ Sbjct: 133 VGYGLWTAGAGFQLGSEKFGALTVPVGPGNLEMQLQLLVDMGVTCLGSTASMALLMAEEV 192 Query: 196 ERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGIT-ALDIYGLSEVMGPGVAMECLE 254 ER G LR +FGAE + MR E++LG+T + DI G++E+ GPG +EC + Sbjct: 193 ER--NGLLDKVKLRKVIFGAETHSPRMRATFEQKLGLTGSYDIAGMTEMYGPGTGLEC-D 249 Query: 255 TTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVIRYRTRDLTRLLPG- 313 +G W D F EI++P P+A GE GE++ T+L KEA P++RYRTRDLTR+LPG Sbjct: 250 AREGLHYWADLFIIEILDPATLQPVAPGEVGEMVVTSLRKEASPLVRYRTRDLTRMLPGQ 309 Query: 314 --TARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQLEVNRRGHLDSL 371 R + R D I GRSDDM+I RGVN++P Q+ + + +F L Y +++ R D++ Sbjct: 310 CSCGRCIPRHDHILGRSDDMIIFRGVNIYPGQIADVLHEFPVLGSEYHIQLTRTDGRDAM 369 Query: 372 SVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPRSEGKACRVFDL 431 ++VE +E + T + + ++ R+ + V +V+ G +PRS GK+ RV DL Sbjct: 370 LLQVERQEGT---TADADAGLAREVGDRLHKKLMARVAVQMVDPGVLPRSFGKSKRVTDL 426 Query: 432 R 432 R Sbjct: 427 R 427 Lambda K H 0.320 0.137 0.411 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: 502 Number of extensions: 27 Number of successful extensions: 6 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: 437 Length of database: 431 Length adjustment: 32 Effective length of query: 405 Effective length of database: 399 Effective search space: 161595 Effective search space used: 161595 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 (21.8 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