Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate CCNA_01382 CCNA_01382 long-chain-fatty-acid--CoA ligase
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__Caulo:CCNA_01382 Length = 583 Score = 214 bits (544), Expect = 1e-59 Identities = 153/507 (30%), Positives = 244/507 (48%), Gaps = 35/507 (6%) Query: 58 LAAGLRKSGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTFVARELAYQLQDSG 117 +AA L G+Q+GDRV + N +PV F G + G I T N + EL Y L DSG Sbjct: 87 MAAELESFGVQKGDRVAIVMRNLPEWPVAFYGALSLGAIVTPLNAWWTGPELEYGLVDSG 146 Query: 118 ATYLLCASNSLE-TGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCAYWSDLLASEEEG 176 A + E G L + Y + + +T+P + + G Sbjct: 147 AKVAIVDVERYERMGEHLHNCPDLKR----VYVSRAKEEITHPYV-------IPLESKIG 195 Query: 177 AAFTW---DELSTPALSSTT---LALNYSSGTTGRPKGVEISHRNYVANML--------Q 222 A W DE P ++ T + Y+SGTTG+PKG +HRN +N+ Sbjct: 196 GANDWAKLDEKPLPTVAITADDDATIFYTSGTTGKPKGAIATHRNINSNIFAAAAAGARA 255 Query: 223 YCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIFIAAALYRATPVYIMSKFDFVKMLEY 282 + P + L +P +HA + +L+ + +M K+D + ++ Sbjct: 256 FLRRGEAPPQPDPSAPQKGALLSVPFFHATGCFAVLNPSLFAGAKLAMMRKWDPERAMQV 315 Query: 283 TQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREVCEEVEKLWPPGKI 342 Q ++T VP + + +HP YDLSS+E V G AP E+ +++++WP K Sbjct: 316 IQDEKLTQMGGVPTIAWQIIEHPNRANYDLSSIEAVAYGGAPSAPELVRKIKEIWP--KS 373 Query: 343 NIKQGWGMTEATCSVTGWNPAE--ISTSASVGELNANCEAKIMFDGVEVKER--NSRGEL 398 + GWGMTE + + T N AE + S G + KIM +E GEL Sbjct: 374 SPGNGWGMTETSATATS-NSAEDYENRPDSCGPAVPVTDLKIMTVEAPYRELPIGEVGEL 432 Query: 399 WVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKELIKVKGNQVA 458 W + P V++GYW +AT +T DGW+ TGD+A +D +G ++DR K+++ G + Sbjct: 433 WCKGPQVVRGYWNKPEATAQTFV-DGWVRTGDLARLDAEGFCFIIDRAKDMLIRGGENIY 491 Query: 459 PAELEALLLEHPAISDVAVIGVVINN-DERPRAYVVLRPGQSATANEIAHYLDNKVSAFK 517 E+E L +HPA+ D A++GV E P A V L+PG AT E+ ++ ++++AFK Sbjct: 492 CIEVENCLYDHPAVMDAALVGVPHKTLGEEPAAVVTLKPGAEATEAELRAFVADRLAAFK 551 Query: 518 RITGGVVFLEAIPKNPSGKILRMKLRE 544 V + E +P+N +GKI++ +L++ Sbjct: 552 VPVKVVFWPETLPRNANGKIMKNELKK 578 Lambda K H 0.319 0.134 0.403 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: 765 Number of extensions: 40 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 556 Length of database: 583 Length adjustment: 36 Effective length of query: 520 Effective length of database: 547 Effective search space: 284440 Effective search space used: 284440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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