Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate PP_0555 PP_0555 Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Putida:PP_0555 Length = 325 Score = 126 bits (316), Expect = 9e-34 Identities = 95/318 (29%), Positives = 144/318 (45%), Gaps = 10/318 (3%) Query: 40 DRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSS-RGQEACQVGSALAVRPTDWLFPTY 98 ++ L Y M RAF + G + + G+EA G +R +D + T+ Sbjct: 8 EQLLHAYEVMRTIRAFEERLHVEFATGEIPGFVHLYAGEEASAAGVMAHLRDSDCIASTH 67 Query: 99 RESVALLTRGIDPVQVLTLFRGDQH--CGYDPVTEHTAPQCTPL--ATQCLHA-----AG 149 R + +G+D ++ G + CG + H A + A + A AG Sbjct: 68 RGHGHCIAKGVDVYGMMAEIYGKKTGVCGGKGGSMHIADLEKGMLGANGIVGAGAPLVAG 127 Query: 150 LADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQ 209 A AA++ G V++A+ GDGA++EG EA+N A++ P +F+ +NN YA + Sbjct: 128 AALAAKLKGRDDVSVAFFGDGASNEGAVFEAMNMASIMNLPCIFVAENNGYAEATASNWS 187 Query: 210 TAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTN 269 A +AD+AAG+GMPGV IDG D VY A A ERAR+G GP+LIE R H Sbjct: 188 VACDHIADRAAGFGMPGVTIDGFDFFAVYEAAGAAIERARSGQGPSLIEVKLSRYYGHFE 247 Query: 270 ADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSA 329 D T P ++ ++D + + AG+L D I A + + R + Sbjct: 248 GDAQTYRAPDEVKNLRESRDCLMQFRNKTTRAGLLTAEQLDAIDARVEDLIEDAVRRAKS 307 Query: 330 PPTGDPMQMFRHVYHHLP 347 P P + VY P Sbjct: 308 DPKPQPADLLTDVYVAYP 325 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: 250 Number of extensions: 8 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: 325 Length adjustment: 29 Effective length of query: 339 Effective length of database: 296 Effective search space: 100344 Effective search space used: 100344 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