Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate 349840 BT0312 2-oxoisovalerate dehydrogenase beta subunit (NCBI ptt file)
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Btheta:349840 Length = 678 Score = 122 bits (306), Expect = 3e-32 Identities = 93/311 (29%), Positives = 150/311 (48%), Gaps = 15/311 (4%) Query: 46 YRAMVVGRAFNRQATAFSRQGRLAVYPSS-RGQEACQ--VGSALAVRPTDWLFPTYRESV 102 Y M +GRA + +A ++ Q Y + G + Q VG + D+LFP YR+ + Sbjct: 19 YHLMTLGRALDEKAPSYQLQSLGWSYHAPYAGHDGIQLAVGQVFTLGE-DFLFPYYRDML 77 Query: 103 ALLTRGIDPVQVLT---LFRGDQHCGYDPVTEHTAPQ-------CTPLATQCLHAAGLAD 152 +L+ G+ +++ D G ++ H A + T LHAAG+A Sbjct: 78 TVLSAGMTAEEIILNGISKATDPGSGGRHMSNHFAKPEWHIENISSATGTHDLHAAGVAR 137 Query: 153 AARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAA 212 A G VA+ G+ ATSEG +EA+N A++ R PV+F++Q+N Y ISVP ++QTA Sbjct: 138 AMVYYGHKGVAITSHGESATSEGFVYEAINGASLERLPVIFVIQDNGYGISVPKSEQTAN 197 Query: 213 RTLADKAAGY-GMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNAD 271 R +A+ +G+ + + +G DV A+ +A E A + P +++A RI +H+N+D Sbjct: 198 RKVAENFSGFKNLKIIYCNGKDVFDSMNAMTEAREYAISTRNPVIVQANCVRIGSHSNSD 257 Query: 272 DDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSAPP 331 T YR E + DP+ + R LL L I A + + + A P Sbjct: 258 KHTLYRDENELEYVKEADPLMKFRRMLLRYKRLTEEELLQIEAESKKELSAANRKALAAP 317 Query: 332 TGDPMQMFRHV 342 DP ++ V Sbjct: 318 EPDPKSIYDFV 328 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: 419 Number of extensions: 21 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: 678 Length adjustment: 34 Effective length of query: 334 Effective length of database: 644 Effective search space: 215096 Effective search space used: 215096 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: 52 (24.6 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