Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_028583912.1 G494_RS0106705 phenylacetate--CoA ligase family protein
Query= SwissProt::P76085 (437 letters) >NCBI__GCF_000429965.1:WP_028583912.1 Length = 432 Score = 427 bits (1097), Expect = e-124 Identities = 220/427 (51%), Positives = 297/427 (69%), Gaps = 5/427 (1%) Query: 11 ETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDLRKFPCTTKQD 70 E + ++L+ LQ +RL+ TL +VP YR+KFD + DD R L D+R+ P T KQD Sbjct: 8 ECMAREDLEQLQLERLQSTLYRVGTHVPFYRKKFDELKFNYDDVRSLDDIRRLPFTEKQD 67 Query: 71 LRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARSLRAAGGSPKD 130 LR NYP+ FA+P+ VVR+H+SSGTTG TVVGY++NDI W+N+V R L AAG + D Sbjct: 68 LRSNYPYGLFAIPLRDVVRVHSSSGTTGLATVVGYSRNDIRTWSNLVGRVLTAAGVTNND 127 Query: 131 KIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDMIMVTPSYCLN 190 I +A+GYGLFTGG G HYGAER+GA+VIP+S G T++Q Q+++DF+ ++ TPSY L Sbjct: 128 VIQIAFGYGLFTGGFGLHYGAERIGASVIPISAGNTKRQIQIMQDFKTTALVCTPSYALV 187 Query: 191 LIEELERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGLSEVMGPGVAM 250 + + ++G + +G SLR G+FG EPW++AMR EI +LGITA D YGLSEVMGPGVA Sbjct: 188 MAAAM-MEMGVNPNGLSLRFGLFGGEPWSEAMRTEIHEKLGITATDNYGLSEVMGPGVAG 246 Query: 251 ECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVIRYRTRDLTRL 310 EC + +G I EDHF E+V+P P+A+GE GEL+ TTLTKEA P+IRYRTRDLTR Sbjct: 247 EC-QQCNGLHINEDHFLLEVVDPVTLEPVAEGEVGELVITTLTKEAFPMIRYRTRDLTRF 305 Query: 311 LP---GTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQLEVNRRGH 367 +P RTM+RM R+ GRSDDMLII+GVNVFP Q+E+ + + E PHYQ+ V R H Sbjct: 306 IPEPCACGRTMKRMQRVMGRSDDMLIIKGVNVFPIQIEKVLFEVEGTEPHYQIIVERENH 365 Query: 368 LDSLSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPRSEGKACR 427 D ++V VE+ E+ +++ Q+ ++ R+ + +G+S +V IV SI RS GK+ R Sbjct: 366 TDKVTVLVEVVEAIFFDEMKKQRQIVDHIKARLAAELGVSVEVKIVEEKSIERSMGKSQR 425 Query: 428 VFDLRNI 434 V D R I Sbjct: 426 VIDKRKI 432 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: 573 Number of extensions: 22 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: 437 Length of database: 432 Length adjustment: 32 Effective length of query: 405 Effective length of database: 400 Effective search space: 162000 Effective search space used: 162000 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 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