Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Pf1N1B4_572 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_572 Length = 341 Score = 151 bits (381), Expect = 4e-41 Identities = 106/344 (30%), Positives = 175/344 (50%), Gaps = 11/344 (3%) Query: 211 ISHRNYVANMLQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIF-IAAALYRATPVY 269 ++HRN VANMLQ + + + + LP+YH A +A L + Sbjct: 2 LTHRNLVANMLQCKALMGSNLNEGCEI----LITPLPLYHIYAFTFHCMAMMLIGNHNIL 57 Query: 270 IMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREV 329 I + D M++ +++ + F+ + + VAL + A + D SS+++ SG L Sbjct: 58 ISNPRDLTAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSSLKITLSGGMALQLAA 117 Query: 330 CEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKIMFDGVEV 389 E +++ I +G+GMTE T V NP++ ++G + K++ D Sbjct: 118 AERWKEV---AGCPICEGYGMTE-TSPVATVNPSQNIQIGTIGIPVPSTLCKVIDDAGVE 173 Query: 390 KERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKEL 449 + + GEL V+ P VMKGYW+ + AT E +GWL TGDIA + DG +VDR K++ Sbjct: 174 QPLGAIGELCVKGPQVMKGYWQRQDATDEILDSEGWLKTGDIALIQPDGYMRIVDRKKDM 233 Query: 450 IKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANEIAHY 508 I V G V P ELE +L P + A IGV + E + ++V +PG + T +++ + Sbjct: 234 ILVSGFNVYPNELEDVLATLPGVLQCAAIGVPDEKSGEAIKIFIVAKPGVTLTKDQVMEH 293 Query: 509 LDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAKEELRV 552 + V+ +K + V F +A+P GKILR +LR++ ++L V Sbjct: 294 MRANVTGYK-VPKAVEFRDALPTTNVGKILRRELRDEELKKLGV 336 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: 394 Number of extensions: 21 Number of successful extensions: 3 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: 556 Length of database: 341 Length adjustment: 32 Effective length of query: 524 Effective length of database: 309 Effective search space: 161916 Effective search space used: 161916 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: 51 (24.3 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