Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate 350099 BT0571 phenylacetate-coenzyme A ligase (NCBI ptt file)
Query= SwissProt::Q72K16 (445 letters) >FitnessBrowser__Btheta:350099 Length = 432 Score = 447 bits (1149), Expect = e-130 Identities = 225/445 (50%), Positives = 307/445 (68%), Gaps = 14/445 (3%) Query: 1 MMYQPELETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRI 60 M++ +E + RE LR +Q RLK++V YVY PFYR+ + E G+ P ++D+ ++ Sbjct: 1 MIWNETIECMDRESLRKIQSIRLKKIVDYVYHNTPFYRKKMQEMGITPDDINTIDDIVKL 60 Query: 61 PFTKKTDLRDHYPFGLFAVPREEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARSLAA 120 PFT K DLRD+YPFGL AVP ++ R+HASSGTTGKPTVVGYT+ DL +AE ++R+ A Sbjct: 61 PFTTKHDLRDNYPFGLCAVPMSQIVRIHASSGTTGKPTVVGYTRKDLSSWAECISRAFTA 120 Query: 121 AGARPGMMLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRPEVISC 180 GA + +YGYGLFTGGLG H GAE +G +V+P+S G TE+Q+ L+ DF V+ C Sbjct: 121 YGAGRSDIFQVSYGYGLFTGGLGAHAGAENIGASVIPMSSGNTEKQITLMHDFGSTVLCC 180 Query: 181 TPSYAQTLAEEFRKRGVSPEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYGLSEII 240 TPSYA LA+ + G EE L+ LGAEPWTE +R +++E LG+K+ +IYGLSEI Sbjct: 181 TPSYALYLADAIKDSGYPREEFQLKVGALGAEPWTENMRHEIEEKLGIKAYDIYGLSEIA 240 Query: 241 GPGVSNECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLLRYWT 300 GPGV EC E + G+H+ EDH+ PE++DP+T +P+ G+ G LVFT LTKE MPLLRY T Sbjct: 241 GPGVGYEC-ECQHGTHLNEDHYFPEIIDPNTLQPVEPGQTGELVFTHLTKEGMPLLRYRT 299 Query: 301 GDLTFLTYEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVPHYQIV 360 DLT L Y+ C+CGRT VRM ILGR+DDMLIIRGVNV+PTQ+E+V+L + E PHY ++ Sbjct: 300 RDLTALHYDKCSCGRTLVRMDRILGRSDDMLIIRGVNVFPTQIESVILEMEEFEPHYLLI 359 Query: 361 VRREGTLDEAELKVEVSEPFFREIGQEVLSDEVVEADHRLHALRERIARKIKDNVGVTLK 420 V RE D EL+VEV F+ SDE+ +R+ AL++++A +++ +G+ + Sbjct: 360 VGRENNTDTMELQVEVRPDFY--------SDEI----NRMLALKKKLASRLQSVLGLGVN 407 Query: 421 VTLLPPGQAPRSEGGKLRRVLDLRK 445 V L+ P RS GK +RV+D RK Sbjct: 408 VKLVEPRSIERSV-GKAKRVIDNRK 431 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: 525 Number of extensions: 13 Number of successful extensions: 2 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: 432 Length adjustment: 32 Effective length of query: 413 Effective length of database: 400 Effective search space: 165200 Effective search space used: 165200 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