Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF1301 Psest_1334 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__psRCH2:GFF1301 Length = 562 Score = 185 bits (469), Expect = 5e-51 Identities = 153/522 (29%), Positives = 234/522 (44%), Gaps = 30/522 (5%) Query: 46 LTTHDLRLWSQRLAAGLRK-SGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104 L+ DL S A L+ + LQ GDR+ + N L +P+ G + AG I NP + Sbjct: 50 LSYSDLERHSAAFTAWLQHHTDLQPGDRIAIQMPNLLQYPIAVFGALRAGLIVVNTNPLY 109 Query: 105 VARELAYQLQDSGA---TYLLCASNSLE-----TGLEAAKQAKLPQSHIFAYDTSIYDGV 156 +RE+ +Q QDSGA YL ++++ T +E + ++ + V Sbjct: 110 TSREMRHQFQDSGARALVYLNTFGHNVQEVLPDTAIEHLIEVRIGDMLPPLKGVLVNAAV 169 Query: 157 TNPQKGCAYWS--------DLLASEEEGAAFTWDELSTPALSSTTLALNYSSGTTGRPKG 208 + +K +S D+L +GA + P L Y+ GTTG KG Sbjct: 170 KHLKKMVPDYSLPQAISFKDVL---RDGARH--NHKPAPLELDHVAVLQYTGGTTGVAKG 224 Query: 209 VEISHRNYVANMLQY---CHTASLHPDYKARLERSRWLCFLPMYHAMAQNIFIAAALYRA 265 ++H N VANM Q H R + + LP+YH A + + Sbjct: 225 AMLTHGNLVANMQQVRANMQQLDEHGHPIIREGQEVMIAPLPLYHIYAFTVNCMCMVVTG 284 Query: 266 TP-VYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAP 324 V I + D ++ QR++ + F+ + + VAL HP + D S ++ SG Sbjct: 285 NHNVLITNPRDINGFVKELQRWQFSAFLGLNTLFVALMAHPQFKKIDFSRLKGTNSGGTA 344 Query: 325 LGREVCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKIMF 384 L V E + + + +G+G+TE + V E S +VG K++ Sbjct: 345 LVSAVAERWKSMTG---CTVVEGYGLTETSPVVCANPHGEHSRLGTVGLPVPGTTVKVID 401 Query: 385 DGVEVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVD 444 D RGEL V+ P VMKGYW+ AT E E+GWL TGDIA +D+DG +VD Sbjct: 402 DEGNALPLGERGELCVKGPQVMKGYWQRPDATAEVLDEEGWLKTGDIAVIDEDGFVSIVD 461 Query: 445 RMKELIKVKGNQVAPAELEALLLEHPAISDVAVIGVVINNDERPRAYVVLRPGQSATANE 504 R K+LI V G V P E+E +++ HP ++ A IGV V+ + +E Sbjct: 462 RKKDLIIVSGFNVYPNEIEDVVMAHPKVAACAAIGVADEKSGEAVKLFVVPSDPTLDQDE 521 Query: 505 IAHYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQA 546 + Y + +K + VF +A+P P GKILR +LR+ A Sbjct: 522 LHAYCRENFTGYK-MPRHYVFRDALPMTPVGKILRRELRDIA 562 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: 725 Number of extensions: 37 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: 562 Length adjustment: 36 Effective length of query: 520 Effective length of database: 526 Effective search space: 273520 Effective search space used: 273520 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