Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 3609616 Dshi_2999 AMP-dependent synthetase and ligase (RefSeq)
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Dino:3609616 Length = 506 Score = 162 bits (410), Expect = 3e-44 Identities = 148/494 (29%), Positives = 233/494 (47%), Gaps = 46/494 (9%) Query: 70 GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLV----TQA 125 GD LAL S + V G + AG P N YT E+++ + NS AK ++ +A Sbjct: 53 GDRLALQVEKSPEALAVYAGCVQAGIVFLPLNTAYTPAEISYFVGNSGAKLVLCDPRAEA 112 Query: 126 SVLPVAREA-AKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDV 184 + PVA EA A+ + + D G PDA + ++ D+ Sbjct: 113 GLTPVAAEAGAQLLTLAAD-----GTGSFPDAAATAPATFETVARTE----------DDL 157 Query: 185 AFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHI 244 A +Y+SGTTG KG M+S RN+++N AE + W D +L LP +H Sbjct: 158 AAFLYTSGTTGRSKGAMLSQRNLLSN------AEVLVDYWRFTDK---DVLLHALPIFHT 208 Query: 245 YGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYD 304 +GL L G +I + KFD E A++ R + VP L D+ Sbjct: 209 HGLFVGTNITLLAGGSMIFLPKFDAEAVLANLP--RATTMMGVPTFYTRLLAEDRFDRDL 266 Query: 305 LSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGR 364 ++ +R+ SG+APL E +R I + YG++ET+ T S ++ R A G+VG Sbjct: 267 VAHMRLFVSGSAPLLAETHREFEARTGHRILERYGMTETNMNT-SNPYDGARRA-GTVGF 324 Query: 365 LMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQT 424 +P ++ K P+ G+E + +GE+G++ ++GPNVF GY + PE T L DG+F T Sbjct: 325 PLPGVELKVCD-PDTGAE---LPQGEIGQIEVRGPNVFQGYWQMPEKTAAELRADGFFIT 380 Query: 425 GDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSE 484 GD+G D +G I R K+LI G+ + P E+E L + + + AVIG G Sbjct: 381 GDLGLIDDQGYVQIVGRGKDLIISGGYNIYPKEVELALDEAPGVLESAVIGAPHPDFGES 440 Query: 485 VPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILR 544 V V + + + + L ++A K+ R V +D +P+N GK+ + Sbjct: 441 VVGILVPQ--------PGARIDTEAVAARLAGQLARFKQPRKLV-VMDALPRNTMGKVQK 491 Query: 545 RILKQKFKGAAEAP 558 +L+++F A P Sbjct: 492 NVLREQFADAFSEP 505 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: 614 Number of extensions: 28 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: 506 Length adjustment: 35 Effective length of query: 527 Effective length of database: 471 Effective search space: 248217 Effective search space used: 248217 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