Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_034410719.1 H566_RS0103055 long-chain fatty acid--CoA ligase
Query= BRENDA::D3GE78 (556 letters) >NCBI__GCF_000482785.1:WP_034410719.1 Length = 561 Score = 194 bits (492), Expect = 1e-53 Identities = 170/517 (32%), Positives = 246/517 (47%), Gaps = 30/517 (5%) Query: 50 DLRLWSQRLAAGLRKSGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTFVAREL 109 D+ + ++ AA L+ GL RG RV + N FPV G++ AG NP + REL Sbjct: 55 DVDVAARHFAAWLQSLGLARGARVAVMLPNLPQFPVALFGILRAGYTVVNVNPLYTPREL 114 Query: 110 AYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDT---SIYDGVTN-----PQK 161 YQL+DSGA ++ N T + + L + A ++ GV N +K Sbjct: 115 EYQLKDSGAEAIVILENFAHTLEQVIARTALRHVAVTAVGDMLGALKGGVVNLVLRRVKK 174 Query: 162 GCAYWSDLLASEEEGAAFTWDE---LSTPALSSTTLA-LNYSSGTTGRPKGVEISHRNYV 217 W L A E + + +A L Y+ GTTG KG I+H N + Sbjct: 175 VVPAWK-LPGHVRFMRALAIGERLPFARAKVGRDDIAFLQYTGGTTGVAKGAVITHANML 233 Query: 218 ANMLQYCHTASLHPDYKARL---ERSRWLCFLPMYHAMAQN-IFIAAALYRATPVYIMSK 273 AN+LQ +A+ + R+ E+ R L LP+YH A N + + A + I + Sbjct: 234 ANVLQ---SAAWYEPALRRIPVGEQVRQLGALPLYHIFALNTVCLLGMCVGAEVLLIPNA 290 Query: 274 FDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVEL-VGSGAAPLGREVCEE 332 DF +L ++ + F V + AL HPA G D S ++L VG G A Sbjct: 291 RDFGALLGALKKHPVHVFPAVNTLFNALMDHPAFGGIDWSKLKLSVGGGMAVQSGVAARW 350 Query: 333 VEKLWPPGKINIKQGWGMTEATCSVTGWNPAEIST-SASVGELNANCEAKIMFDGVEVKE 391 +EK +I +G+G++E T V NP S + S+G + I D Sbjct: 351 LEKTG----CSIVEGYGLSE-TSPVVCCNPTTASGWNGSIGMPLPGTDISIRNDDGNPVA 405 Query: 392 RNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKELIK 451 GEL V+ P VM+GYW T++ T DG+L+TGDIA +D+ G +VDR K++I Sbjct: 406 IGVPGELCVKGPQVMRGYWNRPDETRKVMTPDGYLMTGDIAVLDERGFVKIVDRKKDMIL 465 Query: 452 VKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANEIAHYLD 510 V G V P E+E +L P + +VA IGV ++ E R YVV R G A A D Sbjct: 466 VSGFNVYPNEVEDVLGACPGVKEVAAIGVPDQHSGEAVRVYVVRRDGSLDEATLRAWAKD 525 Query: 511 NKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAK 547 N ++ +KR +VF + +PK P GKILR LR++AK Sbjct: 526 N-LTGYKR-PKEIVFRDELPKTPVGKILRRVLRDEAK 560 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: 717 Number of extensions: 32 Number of successful extensions: 5 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: 556 Length of database: 561 Length adjustment: 36 Effective length of query: 520 Effective length of database: 525 Effective search space: 273000 Effective search space used: 273000 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 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