Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate SMc01030 SMc01030 pyruvate dehydrogenase alpha2 subunit protein
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Smeli:SMc01030 Length = 348 Score = 129 bits (324), Expect = 1e-34 Identities = 98/329 (29%), Positives = 157/329 (47%), Gaps = 23/329 (6%) Query: 11 APAPAGPVTAGPVTAAPAA---AAPAAAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGR 67 AP + V++ A PA A A + L YR M++ R F +A G Sbjct: 2 APRKSASVSSRKTAAKPAKKDFAGGTIAEFSKEDDLKAYREMLLIRRFEEKAGQLYGMGF 61 Query: 68 LAVYPSSR-GQEACQVGSALAVRPTDWLFPTYRESVALLTRGIDPVQV---LTLFRGDQH 123 + + GQEA VG LA++ D + YR+ +L G+ V LT RG Sbjct: 62 IGGFCHLYIGQEAVVVGMQLALKEGDQVITGYRDHGHMLACGMSARGVMAELTGRRGGLS 121 Query: 124 CGYD------PVTEHTAPQCTPLATQCLHAAGLADAARMAGDPIVALAYIGDGATSEGDF 177 G +H + Q GLA A R G+ V+LAY GDGA ++G Sbjct: 122 KGKGGSMHMFSKEKHFYGGHGIVGAQVSLGTGLAFANRYRGNDNVSLAYFGDGAANQGQV 181 Query: 178 HEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQV 237 +E+ N AA+ + PV+++V+NN+YA+ +++ +A + + A +G+PG ++DG DV V Sbjct: 182 YESFNMAALWKLPVIYIVENNRYAMGTSVSRASAQTDFSQRGASFGIPGYQVDGMDVRAV 241 Query: 238 YRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTRYRPAGEADVWAAQ-DPVDRLER 296 A +A E R+G GP ++E +TYR H + D +YR E ++ DP+++++ Sbjct: 242 KAAADEAVEHCRSGKGPIILEMLTYRYRGH-SMSDPAKYRSKDEVQKMRSEHDPIEQVKA 300 Query: 297 DLLAAG--------VLDRAAADGIAAAAD 317 L G +D+ D +A +AD Sbjct: 301 RLTDKGWATEDELKQIDKEVRDIVADSAD 329 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: 270 Number of extensions: 7 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: 348 Length adjustment: 29 Effective length of query: 339 Effective length of database: 319 Effective search space: 108141 Effective search space used: 108141 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