Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate GFF1731 PGA1_c17550 pyruvate dehydrogenase E1 component subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Phaeo:GFF1731 Length = 337 Score = 118 bits (295), Expect = 3e-31 Identities = 88/278 (31%), Positives = 129/278 (46%), Gaps = 15/278 (5%) Query: 37 VPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSR-GQEACQVGSALAVRPTDWLF 95 V D L YR M++ R F +A G + + GQEA VG A D Sbjct: 12 VSADELLEYYREMLLIRRFEEKAGQLYGMGLIGGFCHLYIGQEAVVVGLEAAAEDGDKRV 71 Query: 96 PTYRESVALLTRGIDPVQVLTLFRGDQHCGYDP----------VTEHTAPQCTPLATQCL 145 +YR+ +L G+DP V+ G + GY +H + Q Sbjct: 72 TSYRDHGHMLACGMDPSGVMAELTGREG-GYSKGKGGSMHMFSKEKHFYGGHGIVGAQVP 130 Query: 146 HAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVP 205 AGLA + + G+ V AY GDGA ++G +E N A + PVVF+++NNQYA+ Sbjct: 131 LGAGLAFSDKYKGNDRVTFAYFGDGAANQGQVYETYNMAQLWDLPVVFVIENNQYAMGTS 190 Query: 206 LAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRID 265 + + T + L + YG+ G +DG DVL V A A RAG GP ++E TYR Sbjct: 191 VQRSTKSPALWKRGEAYGIKGEEVDGMDVLAVKEAGERAVAHCRAGKGPYILEVKTYRYR 250 Query: 266 AHTNADDDTRYRPAGEAD-VWAAQDPVDRLERDLLAAG 302 H + D +YR E + +DP++++ RD+L G Sbjct: 251 GH-SMSDPAKYRTREEVQKMREERDPIEQV-RDMLLTG 286 Lambda K H 0.319 0.132 0.395 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: 271 Number of extensions: 10 Number of successful extensions: 2 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: 368 Length of database: 337 Length adjustment: 29 Effective length of query: 339 Effective length of database: 308 Effective search space: 104412 Effective search space used: 104412 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 (21.8 bits) S2: 49 (23.5 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