Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate 7024960 Shewana3_2131 dehydrogenase, E1 component (RefSeq)
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__ANA3:7024960 Length = 392 Score = 177 bits (448), Expect = 6e-49 Identities = 117/324 (36%), Positives = 160/324 (49%), Gaps = 13/324 (4%) Query: 45 MYRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDWLFPTYRESVAL 104 +Y V R + + RQGR++ Y + G+EA VGS A+ D + YRE AL Sbjct: 53 IYDTCVFTRVLDERMLGAQRQGRISFYMTCTGEEAAIVGSVAALDQEDVILAQYREHAAL 112 Query: 105 LTRGIDPVQVLT-LFRGDQHCG--------YDPVTEHTAPQCTPLATQCLHAAGLADAAR 155 RG Q + +F ++ G Y + +PLATQ A G+ + + Sbjct: 113 RYRGFTTEQFMNQMFSNEKDLGKGRQMPIHYGCAALNYQTISSPLATQIPQATGVGYSLK 172 Query: 156 MAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTL 215 M G VA+ Y G+GA SEGDFH LN AAV + PV+F +NN YAIS P +Q A + Sbjct: 173 MQGKRNVAVCYFGEGAASEGDFHAGLNMAAVLKCPVIFFCRNNGYAISTPTEEQFAGNGI 232 Query: 216 ADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTR 275 A + GYGM +R+DGND+L V A A A + P LIEA+TYR+ AH+++DD + Sbjct: 233 ASRGVGYGMHTIRVDGNDMLAVLAATQQARAYAIEHNAPVLIEAMTYRLGAHSSSDDPSG 292 Query: 276 YRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSAPPTGDP 335 YR E W DPV R + L+ G L A AD L+A A P Sbjct: 293 YRSKEEEAKWQQHDPVKRFKLWLINKGWL--AEADDAQRYEKYREEVLAAVKVAEKLPIP 350 Query: 336 M--QMFRHVYHHLPPHLREQSERL 357 M ++ VY P L++Q L Sbjct: 351 MLDEIIEDVYDKPTPALKKQLSEL 374 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: 325 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: 392 Length adjustment: 30 Effective length of query: 338 Effective length of database: 362 Effective search space: 122356 Effective search space used: 122356 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