Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_058857116.1 AS188_RS00055 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_001482365.1:WP_058857116.1 Length = 568 Score = 168 bits (426), Expect = 5e-46 Identities = 149/513 (29%), Positives = 233/513 (45%), Gaps = 62/513 (12%) Query: 70 GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLP 129 GD +A+ PN V + L G + NP YT EL Q ++ A+ V Sbjct: 82 GDRVAIVLPNCPQHIVAFYAVLRLGAVVVEHNPLYTAPELRHQFEDHGAR-------VAI 134 Query: 130 VAREAAKKV-GMPED----RIILIGDQRDPDARVKHFTSVRNISGATRYRKQKIT----- 179 V AA ++ +PED ++ + + R + ++R A R + ++T Sbjct: 135 VWDRAADRIRSLPEDLRLDAVVAVDVTQAMPRRTR--AALRLPLPAARASRAQLTGPAPG 192 Query: 180 --------------------PAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEG 219 A D+A L Y+SGTTG+PKG M++HRN+ +N Sbjct: 193 TIPWRRLVAAEPLAADHPRPTAHDLALLQYTSGTTGLPKGAMLTHRNLESNA-------- 244 Query: 220 EMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNY 279 ++ + G+ + V LP +H +GLT +T A+ G L++ + ++ Sbjct: 245 -LMGQHWLHSGEDEVVHGVLPLFHAFGLTLGVTFAMSLGARLVLFPTVRADLVLKALRRS 303 Query: 280 RCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYG 339 R + VPPV L DL + + SGA L LVE + +GYG Sbjct: 304 RPTVLPAVPPVYEKLLDAAEERGADLRGIAVAVSGAMTLPVPLVERWERATGGMLVEGYG 363 Query: 340 LSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGP 399 L+E SP D R A GS+G P+ + + + D ++V G GEL+++GP Sbjct: 364 LTECSPLVACNPLNDSRRA-GSIGVPFPSTEIRLV----DPETLEDVPRGHEGELWVRGP 418 Query: 400 NVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELE 459 VF GY + PE T L EDGW +TGDV D G + DR+KE+I GF V P E+E Sbjct: 419 QVFRGYWKRPEETARVLVEDGWLRTGDVVTVDDDGFLRVVDRIKEVIITGGFNVAPTEVE 478 Query: 460 GYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVA 519 L +D + D AV+G++ + G E +A VV + G ++A R + KV Sbjct: 479 TALKLHDDVADAAVVGLD-DGRGGEAVVAAVV-----LAPGAVLDEQALR--EHCYGKVT 530 Query: 520 SHKRLRGGVHFVDEIPKNPSGKILRRILKQKFK 552 +K R + V+++P+ GK LRR ++ + + Sbjct: 531 RYKVPR-RIVAVEDLPRTMLGKTLRREVRARLE 562 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: 647 Number of extensions: 31 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: 568 Length adjustment: 36 Effective length of query: 526 Effective length of database: 532 Effective search space: 279832 Effective search space used: 279832 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