Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate RR42_RS21725 RR42_RS21725 ABC transporter substrate-binding protein
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Cup4G11:RR42_RS21725 Length = 334 Score = 126 bits (317), Expect = 7e-34 Identities = 102/328 (31%), Positives = 149/328 (45%), Gaps = 14/328 (4%) Query: 29 AAAPAAAGVPPDRQ--LLMYRAMVVGRAFN-RQATAFSRQGRLAVYPSSRGQEACQVGSA 85 A+ A +P D+Q L +YR M R F R F R G+EA VG Sbjct: 5 ASGTAGNTLPLDKQELLAVYRRMRTIRDFEERLHVDFGRGDIPGFVHLYAGEEAAGVGIL 64 Query: 86 LAVRPTDWLFPTYRESVALLTRGIDPVQVLTLFRGDQ--HCGYDPVTEHTAPQCTPL--A 141 + D + T+R + +G+DPV ++ G + C + H A + A Sbjct: 65 HHLGDGDRIASTHRGHGHCIAKGVDPVAMMKEIYGRKGGSCNGKGGSMHIADLSKGMMGA 124 Query: 142 TQCLHAA-----GLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQ 196 L A G A AA+ G + + + GDGA+++G F E+LN AAV PV+F+++ Sbjct: 125 NGILGAGAPLVCGAALAAKFRGKGEIGITFAGDGASNQGTFLESLNLAAVWNLPVIFVIE 184 Query: 197 NNQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTL 256 NN YA S TA + D+AAG+G+PGV +DG D V+ A + +RAR G GP L Sbjct: 185 NNGYAESTARDYGTAVDSYVDRAAGFGIPGVTVDGTDFFAVHEAAGEVIKRAREGGGPAL 244 Query: 257 IEAVTYRIDAHTNADDDTRYRPAGEA-DVWAAQDPVDRLERDLLAAGVLDRAAADGIAAA 315 +E R H D T YR +GE D+ A +D + + + AGV+ I Sbjct: 245 LECKMVRFYGHFEGDAQT-YRASGELDDIRANKDCLKKFTATVTQAGVIALDELKAIDEQ 303 Query: 316 ADAFAGELSARFSAPPTGDPMQMFRHVY 343 A + + A P P + VY Sbjct: 304 VAALIEDAVQQAKAAPFPTPADLLTDVY 331 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: 297 Number of extensions: 15 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: 334 Length adjustment: 29 Effective length of query: 339 Effective length of database: 305 Effective search space: 103395 Effective search space used: 103395 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