Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 15923 b1805 acyl-CoA synthase (NCBI)
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__Keio:15923 Length = 561 Score = 191 bits (484), Expect = 8e-53 Identities = 163/523 (31%), Positives = 251/523 (47%), Gaps = 38/523 (7%) Query: 46 LTTHDLRLWSQRLAAGLRKS-GLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104 +T L S+ AA L++ GL++GDRV L N L +PV G++ AG I NP + Sbjct: 49 MTFRKLEERSRAFAAYLQQGLGLKKGDRVALMMPNLLQYPVALFGILRAGMIVVNVNPLY 108 Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCA 164 REL +QL DSGA+ ++ SN T LE Q I T + D ++ KG Sbjct: 109 TPRELEHQLNDSGASAIVIVSNFAHT-LEKVVDKTAVQHVIL---TRMGDQLSTA-KGTV 163 Query: 165 ------YWSDLLASEEEGAAFTWD---------ELSTPALSSTTLA-LNYSSGTTGRPKG 208 Y L+ A ++ + P L LA L Y+ GTTG KG Sbjct: 164 VNFVVKYIKRLVPKYHLPDAISFRSALHNGYRMQYVKPELVPEDLAFLQYTGGTTGVAKG 223 Query: 209 VEISHRNYVANMLQYCHTAS--LHPDYKARLERSRWLCFLPMYHAMAQNIFIAAAL-YRA 265 ++HRN +AN+ Q T LHP + + LP+YH A I + Sbjct: 224 AMLTHRNMLANLEQVNATYGPLLHPG------KELVVTALPLYHIFALTINCLLFIELGG 277 Query: 266 TPVYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPL 325 + I + D +++ ++ T V + AL + Q D SS+ L G P+ Sbjct: 278 QNLLITNPRDIPGLVKELAKYPFTAITGVNTLFNALLNNKEFQQLDFSSLHLSAGGGMPV 337 Query: 326 GREVCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEIST-SASVGELNANCEAKIMF 384 + V E KL G+ + +G+G+TE V+ NP +I S S+G + EAK++ Sbjct: 338 QQVVAERWVKL--TGQY-LLEGYGLTECAPLVSV-NPYDIDYHSGSIGLPVPSTEAKLVD 393 Query: 385 DGVEVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVD 444 D GEL V+ P VM GYW+ AT E ++GWL TGDIA +D++G +VD Sbjct: 394 DDDNEVPPGQPGELCVKGPQVMLGYWQRPDATDEI-IKNGWLHTGDIAVMDEEGFLRIVD 452 Query: 445 RMKELIKVKGNQVAPAELEALLLEHPAISDVAVIGVVINNDERPRAYVVLRPGQSATANE 504 R K++I V G V P E+E ++++HP + +VA +GV + V++ S T Sbjct: 453 RKKDMILVSGFNVYPNEIEDVVMQHPGVQEVAAVGVPSGSSGEAVKIFVVKKDPSLTEES 512 Query: 505 IAHYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAK 547 + + +++ +K + V F + +PK+ GKILR +LR++A+ Sbjct: 513 LVTFCRRQLTGYK-VPKLVEFRDELPKSNVGKILRRELRDEAR 554 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: 662 Number of extensions: 35 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 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