Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_011605406.1 FRAAL_RS18710 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >NCBI__GCF_000058485.1:WP_011605406.1 Length = 365 Score = 241 bits (615), Expect = 2e-68 Identities = 145/322 (45%), Positives = 185/322 (57%), Gaps = 11/322 (3%) Query: 46 YRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDWLFPTYRESVALL 105 Y +MV+ R + +ATA RQG L ++ RGQEA QVGSA AVRP D++FP+YRE Sbjct: 41 YSSMVLARRLDEEATALQRQGELVLWIPLRGQEAAQVGSAAAVRPRDFIFPSYREHAVAW 100 Query: 106 TRGIDPVQVLTLFRGDQHCGYDPVTEHTAPQCTPLATQCLHAAG-----LADAARMAGDP 160 RG+ +V+ L RG H G+D + A LA+Q LHA G + D A GDP Sbjct: 101 HRGVPAAEVIRLLRGVSHDGWDTAEHNMANYTIVLASQTLHAVGYGMGMVLDGAVGTGDP 160 Query: 161 I---VALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTLAD 217 L Y+GDGA S+GD +EA +AA APVVFL QNNQ+AIS P +Q+ + LA Sbjct: 161 DRDGAVLVYLGDGAMSQGDANEAFVWAASFGAPVVFLCQNNQWAISTPTRRQSTMQ-LAR 219 Query: 218 KAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTRYR 277 +A G+G PGVR+DGNDVL ++ A E AR G GP LIEA TYR+ HT +DD TRY+ Sbjct: 220 RADGFGFPGVRVDGNDVLAMHAVTTWALEHARGGGGPVLIEANTYRMAPHTTSDDATRYQ 279 Query: 278 PAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAADAFAGELSARFSAPPTGDPMQ 337 PA E VW A+DP++RL LL A + D + AD AG+L A P+ Sbjct: 280 PAEELAVWRARDPIERLR--LLLAAEVSAGWFDEVREHADDAAGDLRRACLAMDPPAPVT 337 Query: 338 MFRHVYHHLPPHLREQSERLAA 359 MF +V R Q E A Sbjct: 338 MFGNVSADETADQRAQREWFTA 359 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: 361 Number of extensions: 17 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: 365 Length adjustment: 30 Effective length of query: 338 Effective length of database: 335 Effective search space: 113230 Effective search space used: 113230 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 24 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