Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate Dsui_1114 Dsui_1114 coenzyme F390 synthetase
Query= SwissProt::Q72K16 (445 letters) >FitnessBrowser__PS:Dsui_1114 Length = 410 Score = 166 bits (420), Expect = 1e-45 Identities = 139/413 (33%), Positives = 204/413 (49%), Gaps = 31/413 (7%) Query: 1 MMYQPELETL-PREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPR 59 M Y LET P E+ R+L E RL R VA+ P++ RLL E V+P L R Sbjct: 1 MKYYDSLETRDPEERERSLME-RLPRQVAHAKLHSPYFARLLAE--VNPNDIHNRAALAR 57 Query: 60 IPFTKKTDL----RDHYPFG-LFAVPREEVARVHASSGTTGKPTVVGYTKNDLKVFAEVV 114 +P T+K+DL R+ PFG + A P ++RV+AS G P G D FA Sbjct: 58 LPVTRKSDLVHLQREQAPFGGINATPLSGLSRVYASPGPIYDPEGRG---QDWWRFA--- 111 Query: 115 ARSLAAAGARPGMMLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFR 174 R+L AG R G ++HN + Y G L G A LG V P G TE QV I D + Sbjct: 112 -RALHGAGFRAGELIHNTFSYHFTPAGFMLEGAAHKLGCPVFPAGIGQTEMQVQAINDLK 170 Query: 175 PEVISCTPSYAQTLAEEFRKRGVSPEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIY 234 P TPS+ + + E+ + + + SL A++ E ++R+ ++ G+ Y Sbjct: 171 PAAYVGTPSFLKIILEKADE--LKADATSLTKALVSGEALPPSLRQALN-ARGITVRQCY 227 Query: 235 GLSEIIGPGVSNECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMP 294 +++ G+ E +QG + ED L E+V P TG+P+ +G+VG ++ TT + P Sbjct: 228 ATADL---GMIAYESEAQQGLTLDED-VLMEIVRPGTGDPVADGEVGEVLITTFNLD-YP 282 Query: 295 LLRYWTGDLTFLTYEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVV 354 LLR+ TGDL+ + CGRT+VR+ LGR D ++G+ V+P QV AV+ PE + Sbjct: 283 LLRFATGDLSAVLPGISPCGRTNVRIKGWLGRADQTTKVKGMFVHPHQVAAVVKRHPE-I 341 Query: 355 PHYQIVVRREGTLDEAELKVEVSEPFFREIGQEVLSDEVVEADHRLHALRERI 407 ++VV D L E G +VL D VV + + LR + Sbjct: 342 GKARLVVDNALGQDRMVLHCESGR------GDDVLGDAVVASIRDVTKLRGEV 388 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: 423 Number of extensions: 24 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: 410 Length adjustment: 32 Effective length of query: 413 Effective length of database: 378 Effective search space: 156114 Effective search space used: 156114 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