Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate PP_4401 PP_4401 branched-chain alpha-keto acid dehydrogenase complex, alpha subunit
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Putida:PP_4401 Length = 410 Score = 192 bits (488), Expect = 1e-53 Identities = 128/350 (36%), Positives = 180/350 (51%), Gaps = 26/350 (7%) Query: 29 AAAPAAAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAV 88 A P A + P RAM+ R F+ + RQ +++ Y S G+EA G ALA+ Sbjct: 64 AQGPWAEDIDPQILRQGMRAMLKTRIFDSRMVVAQRQKKMSFYMQSLGEEAIGSGQALAL 123 Query: 89 RPTDWLFPTYRESVALLTRGIDPVQVLTLFRGDQHCGYDPVTEHTAPQCTP--------- 139 TD FPTYR+ L+ R + V+++ ++ DP+ P Sbjct: 124 NRTDMCFPTYRQQSILMARDVSLVEMICQLLSNER---DPLKGRQLPIMYSVREAGFFTI 180 Query: 140 ---LATQCLHAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQ 196 LATQ + A G A A+ + GD +A A+IGDGAT+E DFH AL +A V RAPV+ V Sbjct: 181 SGNLATQFVQAVGWAMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNVV 240 Query: 197 NNQYAISVPLAKQTA-ARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPT 255 NNQ+AIS A + T A + G G+ +R+DGND + VY A AAERAR G GP+ Sbjct: 241 NNQWAISTFQAIAGGESTTFAGRGVGCGIASLRVDGNDFVAVYAASRWAAERARRGLGPS 300 Query: 256 LIEAVTYRIDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAA 315 LIE VTYR H+ +DD ++YRPA + + DP+ RL++ L+ G + + A Sbjct: 301 LIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLIKIG--HWSEEEHQAVT 358 Query: 316 ADAFAGELSARFSAPPTG--------DPMQMFRHVYHHLPPHLREQSERL 357 A+ A ++A+ A G MF VY +P HLR Q + L Sbjct: 359 AELEAAVIAAQKEAEQYGTLANGHIPSAASMFEDVYKEMPDHLRRQRQEL 408 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: 355 Number of extensions: 15 Number of successful extensions: 4 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: 410 Length adjustment: 30 Effective length of query: 338 Effective length of database: 380 Effective search space: 128440 Effective search space used: 128440 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