Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_053544053.1 CDES_RS02115 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_001277995.1:WP_053544053.1 Length = 568 Score = 165 bits (417), Expect = 5e-45 Identities = 159/533 (29%), Positives = 241/533 (45%), Gaps = 62/533 (11%) Query: 46 TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105 TY L GL+AL R GD +A+ PN + L G T+ NP YT Sbjct: 53 TYAELDKEVRRTAAGLRALGV-RPGDRVAIILPNCPQHIAAFYAVLKLGATVIEHNPLYT 111 Query: 106 VDELAFQLKNSHAK-------------------GLVTQASV-----LPVAREAAKKVGMP 141 EL K+ A+ L T SV +P + A K+ +P Sbjct: 112 AHELLEPFKDHGARVAIVWDKASPVVEKLRGETNLETIVSVNMINAMPTVQRLALKLPIP 171 Query: 142 ---EDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKD-VAFLVYSSGTTGVP 197 + R L G + ++ G + +T KD VA ++Y+SGTTG P Sbjct: 172 ALRKSREALSGSAPNTVPFETLASAAMGGEGEDIVSEPSVT--KDTVALILYTSGTTGTP 229 Query: 198 KGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYK 257 KG ++H N+ +N+ Q W G K +R+LA LP +H YGLT + T +++ Sbjct: 230 KGAQLTHGNLFSNLLQG-------KHWVPGLGDKPERMLAALPMFHAYGLTMVGTLSVFI 282 Query: 258 GYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYD-----LSSLRMMN 312 G ++++ I+ ++ + ++ +P V L K +VD D + +R Sbjct: 283 GGEMVLLPTPRIDLIMNIMKKHTPTW---LPGVPTLYEK--IVDASDKEGIPIKGVRNAF 337 Query: 313 SGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAK 372 SGA+ L+ VE + + +GYGL+ETSP D R+ G VG P+ + Sbjct: 338 SGASTLSTRTVERWENHTGGRLVEGYGLTETSPIIVGNPMSDHRK-QGYVGIPFPDTIVR 396 Query: 373 YMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDA 432 + PE+ E V +GE GE+ +KGP VF GY EATK + W++TGDVG + Sbjct: 397 -IANPENLDET--VPDGEEGEVLVKGPQVFKGYLNQEEATKNSFHGE-WYRTGDVGVMEE 452 Query: 433 KGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVR 492 G + R+KE+I GF V PAE+E + + ++D AV+GI E GSE +A + Sbjct: 453 DGFIRLVARIKEVIITGGFNVYPAEVEDVITAHPDVEDAAVVGIPRE-DGSENVVAAITL 511 Query: 493 SAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRR 545 + KD A + +K R HF +E+P++ GKI RR Sbjct: 512 VEGAALDPEGLKDFAR-------ENLTRYKVPRTFYHF-EEMPRDQMGKIRRR 556 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: 729 Number of extensions: 32 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