Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_090443437.1 BLS63_RS09785 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_900100495.1:WP_090443437.1 Length = 562 Score = 181 bits (459), Expect = 7e-50 Identities = 157/556 (28%), Positives = 246/556 (44%), Gaps = 53/556 (9%) Query: 21 LFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNS 80 +FER + + D T TY L S F L+ + G+ +A+ PN Sbjct: 29 VFERSCKKFADRPAFSNMGVT---LTYAELDRLSGAFAAYLQKHTDLAPGERIAVQMPNV 85 Query: 81 IDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGM 140 + P+ ++G + AG + NP YT E+ Q K++ + LV + ++ + Sbjct: 86 LQYPIAVFGAMRAGLIVVNTNPLYTAREMRHQFKDAGVRALVYLNMFGKLVQDV-----L 140 Query: 141 PEDRIILIGDQRDPDA--------------RVKHFTSVRNISGATRYR-----------K 175 P+ I + + R D +VK + A ++ K Sbjct: 141 PDTEIDYLIEARMGDLQPSLKGWLVNTLVKKVKKLVPDYQLPQAVPFKAALKQGQGHALK 200 Query: 176 QKITPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDR- 234 + VA L Y+ GTTGV KG M++H N+VAN+ Q + L +G P K + Sbjct: 201 PVTVGHQHVAVLQYTGGTTGVAKGAMLTHGNLVANMLQVDACLSQ-LGEDGSPLMKQGQE 259 Query: 235 -VLAFLPFYHIYGLTCLITQALYKGYHLIVMSK-FDIEKWCAHVQNYRCSFSYIVPPVVL 292 ++A LP YHIY T + G H +++S DI + + ++ S + + + Sbjct: 260 IMIAPLPLYHIYAFTANCMCMMVNGNHNVLISNPRDIAGFVKELGKWQFSALLGLNTLFV 319 Query: 293 LLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRW 352 L HP D S L++ NSG L + E S + +GYGL+ET+P + + Sbjct: 320 ALMDHPEFKNLDFSKLKVTNSGGTALVKATAERWQSMTGCTVVEGYGLTETAPVASTNPY 379 Query: 353 EDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEAT 412 + +G+VG +P K + +DG+E GE GEL +KGP V GY + EAT Sbjct: 380 GA-KARLGTVGIPVPGTAFK--VIDDDGNEQ---ALGERGELCIKGPQVMKGYWQREEAT 433 Query: 413 KGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVA 472 L +GWF+TGD+ D G I DR K++I GF V P E+E ++ + + A Sbjct: 434 AEVLDAEGWFKTGDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVASCA 493 Query: 473 VIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVD 532 IG+ E G V + V R ++E+ +A + KV H + F D Sbjct: 494 AIGVPDEKSGEVVKLFVVARD----GGLSAEELKAYCKENFTGYKVPKH------IVFRD 543 Query: 533 EIPKNPSGKILRRILK 548 +P P GKILRR L+ Sbjct: 544 SLPMTPVGKILRRELR 559 Lambda K H 0.317 0.136 0.410 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: 714 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 562 Length of database: 562 Length adjustment: 36 Effective length of query: 526 Effective length of database: 526 Effective search space: 276676 Effective search space used: 276676 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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