Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate BPHYT_RS21775 BPHYT_RS21775 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__BFirm:BPHYT_RS21775 Length = 553 Score = 213 bits (542), Expect = 2e-59 Identities = 160/530 (30%), Positives = 256/530 (48%), Gaps = 57/530 (10%) Query: 46 TYKSLRDASLDFGKGLKALYE---WRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANP 102 T++ LRD + L+A + + G+V+++F N I T ++ +++G +P N Sbjct: 44 TFRELRDDC----RALEARFREAGLQPGEVISVFMGNGIQTARLLLAAMYSGLVANPLNL 99 Query: 103 GYTVDELAFQLKNSHAKGLVTQA---SVLPVAREAAKKVGMPEDRIILIG---DQRDPDA 156 ++ + + +S + + + +V+ A + G+ + I LI D +P + Sbjct: 100 LCQPSQVRYIVDHSDTRMIFAASDTHAVIGAAVAELRAAGLTRE-IALIQTEPDDAEPPS 158 Query: 157 RVKHFTSV-----RNISGATR----YRKQKITP-------------AKDVAFLVYSSGTT 194 KH ++ SGAT K+ + P A DVA L+Y+SGTT Sbjct: 159 LAKHEPALVEAAAHGASGATAPAPALAKRSVAPRPVTSRATAYEPTADDVALLMYTSGTT 218 Query: 195 GVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQA 254 G PKGV+++HRN+VAN R AE + S DRVLA LP YHI GL + Sbjct: 219 GTPKGVLLTHRNLVANARN-ISAEHRLAS--------DDRVLASLPLYHINGLVVTLLAP 269 Query: 255 LYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSG 314 L+ G ++ S+F + V + C++ +VP +V L YDLS+L+ S Sbjct: 270 LFHGGSAVMTSRFSARTFWRDVALHACTWINVVPTIVAYLLNADEACTYDLSALKFCRSA 329 Query: 315 AAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYM 374 +A L + A +R +G+ + G++ET+ S +E R +GS+G L +AK + Sbjct: 330 SAALPADHHRAFEARFGIGVIETMGMTETAAPVFSNPYEMERRRVGSIG-LPSGGEAKVI 388 Query: 375 TMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKG 434 E +E E GEL L+G V GY++ PE T + DGW +TGD+GY+DA G Sbjct: 389 DR-----EGRECAANECGELVLRGEQVMGGYYKRPEETAAAFTSDGWLRTGDLGYRDADG 443 Query: 435 NFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSA 494 FYI R KELI G + P E++ L+ + + D A +G+ +G ++ +A VV Sbjct: 444 YFYINGRAKELIIKGGENIAPREIDEALLRHPDVLDAAAVGVPDPAYGQDI-VAFVVPRM 502 Query: 495 KSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILR 544 D ++ L + + K R FVDE+P+ PSGK+ R Sbjct: 503 SDGRGAPDPADLREHCLREL-GRYKTPKEFR----FVDELPRGPSGKVQR 547 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: 687 Number of extensions: 26 Number of successful extensions: 5 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: 553 Length adjustment: 36 Effective length of query: 526 Effective length of database: 517 Effective search space: 271942 Effective search space used: 271942 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 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