Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate 5209454 Shew_1925 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (RefSeq)
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__PV4:5209454 Length = 392 Score = 178 bits (451), Expect = 3e-49 Identities = 118/335 (35%), Positives = 164/335 (48%), Gaps = 19/335 (5%) Query: 37 VPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDWLFP 96 + D +Y V R + + A RQGR++ Y + G+EA VGS A+ D + Sbjct: 45 IDQDLAAKIYDTCVFTRVLDERMLAAQRQGRISFYMTCTGEEAAVVGSVAALDQDDVILA 104 Query: 97 TYRESVALLTRGIDPVQVLT--------LFRGDQ---HCGYDPVTEHTAPQCTPLATQCL 145 YRE A+ RG Q + L +G Q H G + + T +PLATQ Sbjct: 105 QYREHAAIRYRGFTTEQFMNQMFSNEKDLGKGRQMPIHYGCEALNYQTIS--SPLATQIP 162 Query: 146 HAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVP 205 A G+ + +M G VA+ Y G+GA SEGDFH LN AAV +PV+F +NN YAIS P Sbjct: 163 QATGVGYSLKMQGKRNVAICYFGEGAASEGDFHAGLNMAAVLNSPVIFFCRNNGYAISTP 222 Query: 206 LAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRID 265 +Q A +A + GYGM +R+DGND+L V A A A + P LIEA+TYR+ Sbjct: 223 TNEQFAGNGIASRGVGYGMHTIRVDGNDMLAVMAATQQARAYALEHNKPVLIEAMTYRLG 282 Query: 266 AHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSA 325 AH+++DD + YR E W DPV R + L+ G L A AA + + E+ A Sbjct: 283 AHSSSDDPSGYRSKDEEAKWQQHDPVKRFKLWLINKGWL---AESDDAALYEKYREEVLA 339 Query: 326 RFSAP---PTGDPMQMFRHVYHHLPPHLREQSERL 357 P ++ V P L++Q L Sbjct: 340 AVKVAEKLPAPKIDEIIEDVLDEPTPRLKQQLTEL 374 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: 321 Number of extensions: 11 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: 392 Length adjustment: 30 Effective length of query: 338 Effective length of database: 362 Effective search space: 122356 Effective search space used: 122356 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: 50 (23.9 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