Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate 208241 DVU2735 phenylacetate-coenzyme A ligase
Query= SwissProt::Q72K16 (445 letters) >MicrobesOnline__882:208241 Length = 432 Score = 391 bits (1004), Expect = e-113 Identities = 212/438 (48%), Positives = 282/438 (64%), Gaps = 15/438 (3%) Query: 8 ETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRIPFTKKTD 67 ET R+++R Q RL+ V R FY L +AG+ P R L+DL RIPFT K D Sbjct: 8 ETWNRDEIRQAQLVRLRNTVEQAM-RSSFYGATLRKAGITPDSIRSLDDLRRIPFTTKDD 66 Query: 68 LRDHYPFGLFAVPREEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARSLAAAGARPGM 127 LR+ YP GL VPR E+ R+HASSGTTG PTVV +T++DL +A+++AR L G R Sbjct: 67 LRNQYPDGLNCVPRTEMVRMHASSGTTGSPTVVYHTQSDLNAWADLMARCLHMVGVRRDD 126 Query: 128 MLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRPEVISCTPSYAQT 187 + N GYGLFTGGLGLH GAE LG +P G T+RQV L++DFR V+ PSYA Sbjct: 127 VFQNMTGYGLFTGGLGLHYGAERLGCLTIPAGPGNTKRQVKLMRDFRTSVVHIIPSYALY 186 Query: 188 LAEEFRKRGVSPEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYGLSEIIGPGVSNE 247 LA + G P L AV+GAEP TE R++++E LG+K+ N YGLSE+ GPGV+ E Sbjct: 187 LAAAVEEGGEDPHALPPRIAVIGAEPHTEEARRRIEEMLGLKAFNSYGLSEMNGPGVAFE 246 Query: 248 CVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLLRYWTGDLTFLT 307 C E+ G H+WED ++ E++DP TGEP+P+G+VG LV TTL + MP+LRY T DLT Sbjct: 247 CTEQ-NGMHVWEDAYIAEIIDPATGEPVPDGEVGELVMTTLCRRGMPVLRYRTRDLTRFL 305 Query: 308 YEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVPHYQIVVRREGTL 367 C CGR H R+ ++GR DDMLII+GVN+YP Q+E VL+A PEV +Y IV+ RE + Sbjct: 306 PGECPCGRVHRRLDRMVGRADDMLIIKGVNIYPMQIEQVLMAFPEVGQNYLIVLEREEFI 365 Query: 368 DEAELKVEVSEPFFREIGQEVLSDEVVEADHRLHALRERIARKIKDNVGVTLKVTLLPPG 427 D+ ++KVE+ + F VE L L++ IAR++KD + VT +V L+ Sbjct: 366 DQIKVKVELRDEAF------------VEDMRVLQGLQKAIARRLKDEILVTPRVELVQNN 413 Query: 428 QAPRSEGGKLRRVLDLRK 445 P++E GK +RVLDLR+ Sbjct: 414 SLPKAE-GKAQRVLDLRE 430 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: 551 Number of extensions: 22 Number of successful extensions: 3 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