Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate Ga0059261_0016 Ga0059261_0016 pyruvate dehydrogenase E1 component, alpha subunit
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Korea:Ga0059261_0016 Length = 349 Score = 112 bits (279), Expect = 2e-29 Identities = 95/346 (27%), Positives = 154/346 (44%), Gaps = 17/346 (4%) Query: 11 APAPAGPVTAGP-VTAAPAAAAPAAAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLA 69 A APA P VT P + L YR M++ R F +A G + Sbjct: 2 AKAPAKSRKIEPAVTNRERPNEPDRYKASKEELLEFYRQMLLIRRFEEKAGQLYGLGFIG 61 Query: 70 VYPSSR-GQEACQVGSALAVR-PTDWLFPTYRESVALLTRGIDPVQVLTLFRGDQHCGYD 127 + GQEA VG A+ D + YR+ +L GIDP +++ G + G Sbjct: 62 GFCHLYIGQEAVAVGLQSALDGEKDSVITGYRDHGHMLAYGIDPKEIMAELTG-RAAGIS 120 Query: 128 PVTEHTAPQCTP----------LATQCLHAAGLADAARMAGDPIVALAYIGDGATSEGDF 177 + + + Q GLA + D VA+AY GDGA+++G Sbjct: 121 RGKGGSMHMFSTEKKFYGGHGIVGAQVSLGTGLAFTHKYNEDGGVAMAYFGDGASNQGQV 180 Query: 178 HEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQV 237 +E+ N A + + P++++++NNQYA+ + + ++ L + + +PG+++DG DVL Sbjct: 181 YESFNMAELWKLPIIYVIENNQYAMGTSVNRSSSEDQLYRRGESFRIPGIQVDGMDVLAC 240 Query: 238 YRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTRYRPAGEA-DVWAAQDPVDRLER 296 A +A RAG GP ++E TYR H + D +YR E V DP++ +++ Sbjct: 241 RGAAEEALAWVRAGKGPIILEMKTYRYRGH-SMSDPAKYRSRDEVQSVRDNSDPIEGVKK 299 Query: 297 DLLAAGVLDRAAADGIAAAADAFAGELSARFSAPPTGDPMQMFRHV 342 +L AAGV + I A E + P DP +++ V Sbjct: 300 ELEAAGVKE-DELKAIEAEIRKAVNESADFAEQTPEPDPAELYTDV 344 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: 269 Number of extensions: 10 Number of successful extensions: 3 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: 368 Length of database: 349 Length adjustment: 29 Effective length of query: 339 Effective length of database: 320 Effective search space: 108480 Effective search space used: 108480 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