Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate GFF1675 HP15_1634 branched-chain alpha-keto acid dehydrogenase complex E1 alpha subunit
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Marino:GFF1675 Length = 382 Score = 201 bits (512), Expect = 2e-56 Identities = 125/339 (36%), Positives = 176/339 (51%), Gaps = 13/339 (3%) Query: 34 AAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDW 93 A + D+ L +YRAMV R + + A RQGRL+ Y G+EA +GSA A+ D Sbjct: 28 APDLDKDKALRIYRAMVTTRILDERMLAAQRQGRLSFYMQCTGEEAAVIGSAAALDDGDM 87 Query: 94 LFPTYRESVALLTRGIDPVQVLTLFRGDQ-----------HCGYDPVTEHTAPQCTPLAT 142 + YRE AL RG + + G++ H G + T +PLAT Sbjct: 88 IMAQYREQGALAYRGFTIDEFMNQLFGNEMDYGKGRQMPVHYGSKKLNYMTIS--SPLAT 145 Query: 143 QCLHAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAI 202 Q AAG A ++ G+ + + Y G+GA SEGDFH ALN AAV R PV+FL +NN YAI Sbjct: 146 QIPQAAGYAYGQKLRGEGLCTITYFGEGAASEGDFHAALNMAAVHRVPVIFLCRNNGYAI 205 Query: 203 SVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTY 262 S P A+Q AA +A +A GY M +R+DGND+L +Y+A +A + A + P LIEA++Y Sbjct: 206 STPAAEQFAADGVAPRAYGYKMDVIRVDGNDILAMYQATQEARKLAVEHNRPVLIEAMSY 265 Query: 263 RIDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGE 322 R+ AH+++DD + YR E VW +DP+ R+ L + + E Sbjct: 266 RLAAHSSSDDPSGYRSKDEEAVWREKDPILRMRLWLESKKWWSEDDEKQLQENMRREVLE 325 Query: 323 LSARFSAPPTGDPMQMFRHVYHHLPPHLREQSERLAAEL 361 R P + VY +PP L EQ E+L A + Sbjct: 326 TMKRAQKRPPPPLESLVSDVYDEVPPALAEQFEKLKAHI 364 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: 345 Number of extensions: 15 Number of successful extensions: 3 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: 382 Length adjustment: 30 Effective length of query: 338 Effective length of database: 352 Effective search space: 118976 Effective search space used: 118976 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