Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF3354 PGA1_c34070 long-chain-fatty-acid- CoA ligase IcfB
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Phaeo:GFF3354 Length = 500 Score = 167 bits (422), Expect = 1e-45 Identities = 146/487 (29%), Positives = 231/487 (47%), Gaps = 52/487 (10%) Query: 70 GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLP 129 GD +A S+ + GT+ AG P NP YT E+A+ + ++ + V P Sbjct: 56 GDRVAAQVDKSLAAIQLYLGTVMAGAIFLPLNPAYTEAEVAYFIGDATPRVFVCN----P 111 Query: 130 VAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFLVY 189 V E+ + V + L G+ + A + +G + + P+ D+A ++Y Sbjct: 112 VRHESLRAVAGEATVLTLDGEGQGSLADLA--------AGHAGFEPIERKPS-DLAAILY 162 Query: 190 SSGTTGVPKGVMISHRNIVAN---IRQ--QFIAEGEMLSWNGGPDGKGDRVLAFLPFYHI 244 +SGTTG KG M+SH N+ +N +R QF AE D ++ LP +H Sbjct: 163 TSGTTGRSKGAMLSHENLYSNSLTLRDYWQFTAE--------------DVLIHALPIFHT 208 Query: 245 YGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYD 304 +GL AL G ++++ FD E A + N LL+ D Sbjct: 209 HGLFVATNVALLAGAQVVLLPGFDAEAILAAMPNATALMGVPTFYTRLLVDARLTPDL-- 266 Query: 305 LSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGR 364 +++R+ SG+APL E E +R I + YG++ET+ +T S ++ R A G+VG Sbjct: 267 AANMRLFISGSAPLLVETHEQWEARTGHRILERYGMTETNMST-SNPYDGVRVA-GTVGP 324 Query: 365 LMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQT 424 +P ++A+ + E+ GE+G L ++GPNVF GY + PE T L DGWF T Sbjct: 325 PLPGVEARVTL------DNAEIPLGEIGVLEVRGPNVFQGYWQMPEKTAEELRPDGWFIT 378 Query: 425 GDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSE 484 GD+ D+ G I R K+L+ GF V P E+E + D + + AVIG+ G E Sbjct: 379 GDLAKIDSNGYVTIVGREKDLVISGGFNVYPKEVETLIDDLPGVLESAVIGVPHPDFG-E 437 Query: 485 VPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILR 544 +A VV T E +AA I L +A K+ + + +DE+P+N GK+ + Sbjct: 438 AVVAVVV--------PTEEGTDAASIQAALSEHLAKFKQPK-HIALMDELPRNTMGKVQK 488 Query: 545 RILKQKF 551 + L++ F Sbjct: 489 KALRETF 495 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: 601 Number of extensions: 26 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: 500 Length adjustment: 35 Effective length of query: 527 Effective length of database: 465 Effective search space: 245055 Effective search space used: 245055 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: 52 (24.6 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