Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF2964 PS417_15170 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__WCS417:GFF2964 Length = 567 Score = 186 bits (472), Expect = 2e-51 Identities = 154/509 (30%), Positives = 239/509 (46%), Gaps = 50/509 (9%) Query: 68 RKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASV 127 RKG+ +AL PN + P+ + GT+ AG + NP YT EL LK+S A+ +V + Sbjct: 81 RKGERVALMMPNCLQYPICLLGTILAGAVVVNVNPLYTSHELKHLLKDSGAETVVIFENF 140 Query: 128 LPVAREAAKKVGMPEDRIILIGDQRDPDA---------RVKHFTSVRNISGATRY----- 173 + + I IGD RV+ N+ G+ R+ Sbjct: 141 AHTLEKVITGSSVKRVVIAAIGDLLGTFKGAAMNFILRRVQKQVPAFNLPGSVRFNQVLK 200 Query: 174 --RKQKITPAK----DVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGG 227 R P + +AFL Y+ GTTG KGVM+SHRNI+AN+ Q G+ L + Sbjct: 201 QGRALNHFPVEMHLDALAFLQYTGGTTGDAKGVMLSHRNIIANLLQAKAWVGDQLDQD-- 258 Query: 228 PDGKGDRVLAFLPFYHIYGLT--CLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSY 285 K + + LP YHI+ LT CL+ L G ++++ + D+++ ++ R + Sbjct: 259 ---KQETNVTLLPLYHIFSLTVNCLMFMCL-GGRNILIANPRDVKRVQMILRKERFNGIA 314 Query: 286 IVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSP 345 V + L ++ D S LRM+ +G + + + I +GYGL+E SP Sbjct: 315 GVNTLFNGLLENEAFCARDFSDLRMVIAGGMATHTAVAKRWKEVTGLPIIEGYGLTECSP 374 Query: 346 TTHSQRWEDWR----EAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGE-GEVGELYLKGPN 400 + R E GS+G +P+ +++ EDG E+ E GE GEL ++GP Sbjct: 375 VVSISPIDIARMREMEFTGSIGVPLPSTWVRFVR--EDG----ELAEIGEQGELQVRGPQ 428 Query: 401 VFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEG 460 V GY + PEAT L +GW TGD+G DA+G + DR K++I GF V P E+E Sbjct: 429 VMQGYWQRPEATAEVLDAEGWLSTGDIGVMDARGYIRLVDRKKDMILVSGFNVYPNEIED 488 Query: 461 YLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDS-KVA 519 + + A+ +VA IG+E G +V + V K +++ A ++L K+ Sbjct: 489 VVALHPAVAEVAAIGVEDGVTGEKVKIIVV-----RKDPNLTQEQILAHCREYLTGYKMP 543 Query: 520 SHKRLRGGVHFVDEIPKNPSGKILRRILK 548 + R E+PK GK+LRR L+ Sbjct: 544 KYVEFR-----TTELPKTTVGKVLRRALR 567 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: 677 Number of extensions: 30 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: 567 Length adjustment: 36 Effective length of query: 526 Effective length of database: 531 Effective search space: 279306 Effective search space used: 279306 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