Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate 3608766 Dshi_2158 Pyruvate dehydrogenase (acetyl-transferring) (RefSeq)
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Dino:3608766 Length = 331 Score = 121 bits (304), Expect = 2e-32 Identities = 89/280 (31%), Positives = 131/280 (46%), Gaps = 15/280 (5%) Query: 46 YRAMVVGRAFNRQATAFSRQGRLAVYPSSR-GQEACQVGSALAVRPTDWLFPTYRESVAL 104 YR M++ R F +A G + + GQEA VG A D +YR+ + Sbjct: 21 YREMLLIRRFEEKAGQLYGMGLIGGFCHLYIGQEAVVVGLEAAAEDGDKRVTSYRDHGHM 80 Query: 105 LTRGIDPVQVLTLFRGDQHCGYDP----------VTEHTAPQCTPLATQCLHAAGLADAA 154 L G+DP V+ G + GY +H + Q AGLA + Sbjct: 81 LACGMDPKGVMAELTGREG-GYSKGKGGSMHMFSKEKHFYGGHGIVGAQVPIGAGLAFSD 139 Query: 155 RMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAART 214 + G+ V AY GDGA ++G +E N A + PVVF+++NNQYA+ +A+ T + + Sbjct: 140 KYRGNDRVTFAYFGDGAANQGQVYETYNMAELWMLPVVFVIENNQYAMGTSVARSTKSPS 199 Query: 215 LADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDT 274 L ++ A YG+PG +DG DVL V A A RAG GP ++E TYR H + D Sbjct: 200 LWERGAAYGIPGEEVDGMDVLAVKAAGEKAVAHCRAGKGPYILEVKTYRYRGH-SMSDPA 258 Query: 275 RYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAA 314 +YR E Q R++L +G + A+ D + A Sbjct: 259 KYRTREEVQKVREQRDAIEHVREMLLSG--NHASEDELKA 296 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: 267 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: 331 Length adjustment: 29 Effective length of query: 339 Effective length of database: 302 Effective search space: 102378 Effective search space used: 102378 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