Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate Ac3H11_4625 Phenylacetate-coenzyme A ligase (EC 6.2.1.30)
Query= SwissProt::Q72K16 (445 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4625 Length = 415 Score = 146 bits (369), Expect = 1e-39 Identities = 118/383 (30%), Positives = 189/383 (49%), Gaps = 31/383 (8%) Query: 7 LETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRIPFTKKT 66 LET + A L VA+ + P + +L AGVD L R+P T+K Sbjct: 8 LETRNPSEREAALLAALPAQVAHAQKASPAFASIL--AGVDASSVTSRAALARLPVTRKY 65 Query: 67 DLRDHYP-------FGLFAVPR--EEVARVHASSGTTGKP--TVVGYTKNDLKVFAEVVA 115 +L + FG F+ + RV AS GT +P T Y + +A Sbjct: 66 ELLERQQAGRATNVFGGFSALGFGPGMTRVFASPGTIYEPEGTRPDYWR---------MA 116 Query: 116 RSLAAAGARPGMMLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRP 175 R++ AAG R G ++HN++ Y G + GA ALG TV P G TE+QV + + +P Sbjct: 117 RAIHAAGFRGGELIHNSFSYHFVPAGSMMETGAHALGCTVFPGGTGQTEQQVQAMAELKP 176 Query: 176 EVISCTPSYAQTLAEEFRKRGVSPEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYG 235 TPS+ + + E+ + GV+ S+ A++ E + ++R E G+ Y Sbjct: 177 AGYIGTPSFLKIIVEKAAELGVALP--SVTKAMVSGEAFPPSLRDWFAE-RGIAGYQCYA 233 Query: 236 LSEIIGPGVSNECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPL 295 +++ G+ R+G + ++ + E+V P TG+P+PEG+VG LV TTL + PL Sbjct: 234 TADL---GLIAYETSAREGL-VLDEGVIVEIVRPGTGDPVPEGEVGELVVTTLNPD-YPL 288 Query: 296 LRYWTGDLTFLTYEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVP 355 +R+ TGDL+ + C GRT+ R+ +GR D +RG+ V+P Q+ + P+V+ Sbjct: 289 IRFGTGDLSAVLPGPCPTGRTNTRIKGWMGRADQTTKVRGMFVHPGQIATIARRFPQVL- 347 Query: 356 HYQIVVRREGTLDEAELKVEVSE 378 ++VV E D+ L+VE +E Sbjct: 348 RARLVVSGEMANDQMVLQVETTE 370 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: 451 Number of extensions: 27 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: 445 Length of database: 415 Length adjustment: 32 Effective length of query: 413 Effective length of database: 383 Effective search space: 158179 Effective search space used: 158179 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