Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_205630629.1 AU252_RS03450 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >NCBI__GCF_001484605.1:WP_205630629.1 Length = 369 Score = 246 bits (627), Expect = 9e-70 Identities = 139/327 (42%), Positives = 192/327 (58%), Gaps = 2/327 (0%) Query: 40 DRQLL-MYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDWLFPTY 98 D QL +Y + V R + +ATA RQG L ++P GQEA QVGS A+R D++F +Y Sbjct: 32 DEQLCSLYEDLTVIRRIDVEATALQRQGELGLWPPLLGQEAAQVGSGRALRDDDFVFSSY 91 Query: 99 RESVALLTRGIDPVQVLTLFRGDQHCGYDPVTEHTAPQCTPLATQCLHAAGLADAARMAG 158 RE+ RG+D + ++RG G+DP + + A + Q LHA G A + G Sbjct: 92 RENGVAYCRGVDLTDITRVWRGTASSGWDPYSVNMATPQIIIGAQTLHATGYAMGIQNDG 151 Query: 159 DPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTLADK 218 VA+ Y GDGATSEGD +EA+ +AA +APVVF NN +AIS P+ Q+ + +AD+ Sbjct: 152 ADSVAVTYFGDGATSEGDVNEAMVFAASFQAPVVFFCSNNHWAISEPVRLQSHIQ-IADR 210 Query: 219 AAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTRYRP 278 A G+G+P +R+DGNDVL V A A +RAR G GPT IEAVTYR+ HT ADD TRYR Sbjct: 211 ATGFGIPSLRVDGNDVLAVMAATRVALDRARHGGGPTFIEAVTYRMGPHTTADDPTRYRD 270 Query: 279 AGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSAPPTGDPMQM 338 A E + WAA+DP+ R++ L G+L + A++ A E+ + P +PM + Sbjct: 271 ANELEDWAAKDPILRIKALLERKGLLTDQVQQHVHDKAESVAREIRSGCIGMPDPEPMDI 330 Query: 339 FRHVYHHLPPHLREQSERLAAELAADG 365 F+HVY L Q + A LA+ G Sbjct: 331 FKHVYSEPNSWLDRQQDHYARYLASFG 357 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: 316 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: 369 Length adjustment: 30 Effective length of query: 338 Effective length of database: 339 Effective search space: 114582 Effective search space used: 114582 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 Apr 09 2024. 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