Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_053937789.1 WG78_RS10575 long-chain-fatty-acid--CoA ligase FadD
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_001294205.1:WP_053937789.1 Length = 554 Score = 196 bits (499), Expect = 2e-54 Identities = 159/527 (30%), Positives = 241/527 (45%), Gaps = 49/527 (9%) Query: 46 TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105 TY+ L S F L+ +G + + PN + PV ++G L AG + NP YT Sbjct: 50 TYQELDQLSTAFAAYLQQTLRLSRGARVGIMMPNLLQYPVALFGILKAGMVVVNINPLYT 109 Query: 106 VDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDAR-------- 157 EL QLK+S A+ +V A+ + K + + IGD D R Sbjct: 110 PRELEHQLKDSGAEAIVIVANFAHTLDKCIGKTAVKHVIVSQIGDMLDFPKRQLVNAVIK 169 Query: 158 -VKHFTSVRNISGATRY-------RKQKITPAK----DVAFLVYSSGTTGVPKGVMISHR 205 +K N+ GA + R Q + P D+AFL Y+ GTTGV KG M++HR Sbjct: 170 YIKKMVPAYNLPGAVSFNHALADGRAQTLAPVNLTLDDLAFLQYTGGTTGVAKGAMLTHR 229 Query: 206 NIVANIRQQFIAEGEMLSWNGGPDGKG-DRVLAFLPFYHIYGLTC---LITQALYKGYHL 261 NIVAN++Q +W GG G + ++ LP YHI+ LT + T+ +L Sbjct: 230 NIVANMQQAH-------AWIGGVVADGRELIVTALPLYHIFSLTANGMIFTKI--GATNL 280 Query: 262 IVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQE 321 ++ + DI + + Y + V + L HP K D SS ++ G + Q Sbjct: 281 LITNPRDIPGFIKELGKYPVTAITGVNTLFNALVNHPDFLKLDFSSWKLTLGGGMAVQQP 340 Query: 322 LVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGS 381 + + V + + YGL+ETSP RE G +G +P+ A+ EDGS Sbjct: 341 VADKWKKVTGVTLVEAYGLTETSPAAMINPMT-LREYNGMIGLPVPSTDAQIRG--EDGS 397 Query: 382 EPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDR 441 G GEL++KGP V GY + + T + DG+ TGDV G F I DR Sbjct: 398 VQPP---GSAGELFIKGPQVMKGYWQRADETAKVIGADGYLATGDVAIMSPTGFFRIADR 454 Query: 442 VKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGT 501 K+++ GF V P E+E + + + +VA +G+ + G V + VVR + + Sbjct: 455 KKDMVLVSGFNVYPNEVEDVVARHPGVLEVACVGVPDDKSGEAVKI-FVVRKDPTLTE-- 511 Query: 502 SEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILK 548 A +I + ++ ++K R V F D +PK+ GKILRR L+ Sbjct: 512 ------AALIAYCREQLTNYKVPR-KVEFRDALPKSNVGKILRRELR 551 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: 674 Number of extensions: 34 Number of successful extensions: 6 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: 562 Length of database: 554 Length adjustment: 36 Effective length of query: 526 Effective length of database: 518 Effective search space: 272468 Effective search space used: 272468 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