Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate AO353_03310 AO353_03310 long-chain fatty acid--CoA ligase
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03310 Length = 566 Score = 194 bits (492), Expect = 1e-53 Identities = 160/526 (30%), Positives = 252/526 (47%), Gaps = 37/526 (7%) Query: 46 LTTHDLRLWSQRLAAGLRK-SGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104 LT +L S AA L++ + LQ GDR+ + N L +P+ G I AG I NP + Sbjct: 50 LTYGELYELSGAFAAYLQQHTDLQPGDRIAVQLPNLLQYPIAVFGAIRAGLIVVNTNPLY 109 Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTS---------IYDG 155 ARE+ +Q DSGA L+C +N L A K H+ + + + + Sbjct: 110 TAREMEHQFNDSGAKALVCLANMAH--LAEAVVPKTGVKHVIVTEVADLLPPLKRLLINS 167 Query: 156 VTNPQKGC--AY-------WSDLLASEEEGAAFTWDELSTPALSSTTLALNYSSGTTGRP 206 V K AY ++D+L S+ G T + PA SS L Y+ GTTG Sbjct: 168 VIKYVKKMVPAYHLPKAVKFNDVL-SKGHGQPVTE---ANPA-SSDVAVLQYTGGTTGVA 222 Query: 207 KGVEISHRNYVANMLQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIF-IAAALYRA 265 KG ++HRN VANM+Q + + + + LP+YH A +A L Sbjct: 223 KGAMLTHRNLVANMMQCRALMGSNLNEGCEI----LITPLPLYHIYAFTFHCMAMMLIGN 278 Query: 266 TPVYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPL 325 + I + D M++ +++ + F+ + + VAL + A + D S +++ SG L Sbjct: 279 HNILISNPRDLPAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSGLKITLSGGMAL 338 Query: 326 GREVCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKIMFD 385 E + + I +G+GMTE T V NP + ++G + K++ D Sbjct: 339 QLAAAERWKAVTGCA---ICEGYGMTE-TSPVATVNPNQNIQIGTIGIPVPSTLCKVIDD 394 Query: 386 GVEVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDR 445 + GEL V+ P VMKGYW+ ++AT E +GWL TGDIA + DG +VDR Sbjct: 395 AGVEQPLGEIGELCVKGPQVMKGYWQRQEATDEILDSEGWLKTGDIALIQPDGYMRIVDR 454 Query: 446 MKELIKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANE 504 K++I V G V P ELE +L P + A IGV + E + ++V +PG + T + Sbjct: 455 KKDMILVSGFNVYPNELEDVLATLPGVLQCAAIGVPDEKSGEAIKIFIVAKPGVTLTKEQ 514 Query: 505 IAHYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAKEEL 550 + ++ V+ +K + + F +A+P GKILR +LR++ ++L Sbjct: 515 VMTHMRANVTGYK-VPRAIEFRDALPTTNVGKILRRELRDEELKKL 559 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: 688 Number of extensions: 31 Number of successful extensions: 4 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: 566 Length adjustment: 36 Effective length of query: 520 Effective length of database: 530 Effective search space: 275600 Effective search space used: 275600 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