Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_009545077.1 CCE_RS17810 thiamine pyrophosphate-binding protein
Query= metacyc::MONOMER-20681 (545 letters) >NCBI__GCF_000017845.1:WP_009545077.1 Length = 544 Score = 302 bits (774), Expect = 2e-86 Identities = 187/509 (36%), Positives = 274/509 (53%), Gaps = 18/509 (3%) Query: 7 LLRALKDRGAQAMFGIPGDFALPFFKVAEETQILPLHTLSHEPAVGFAADAAARYSSTLG 66 L+ L G +FG+PGDF L F K+ E++++ ++T + A GFAADA AR LG Sbjct: 11 LIERLLQLGVNHVFGVPGDFVLGFNKLLEKSELEFINTCDEQGA-GFAADAYARLRG-LG 68 Query: 67 VAAVTYGAGAFNMVNAVAGAYAEKSPVVVISGAPGTTEGNAGLLLHHQGRTLDTQFQVFK 126 V VTY G + N A +AEKSPVVVISG+PG E LLHH+ + DTQ++VF+ Sbjct: 69 VVCVTYCVGGLKIANTTAQCFAEKSPVVVISGSPGVNERTKNPLLHHKVKEFDTQYKVFQ 128 Query: 127 EITVAQARLDDPAKAPAEIARVLGAARALSRPVYLEIPRNMVN----AEVEPVGDDPAWP 182 EITVA LD+P A +EI RVL AA RPVY+EIPR+MVN A+ +P ++ + Sbjct: 129 EITVASTVLDNPDTAYSEIERVLTAALRYKRPVYIEIPRDMVNVTLGADNQPSSNNSS-- 186 Query: 183 VDRDALAACADEVLAAMRSATSPVLMVCVEVRRYGLEAKVAELAQRLGVPVVTTFMGRGL 242 + DAL +E + + A PV++ VE+ R+ L+ + +L ++ +PV T +G+ + Sbjct: 187 SNPDALQEALEEAVNLINQAQHPVILAGVEIHRFKLQESLLKLVEKTNLPVAETLLGKSV 246 Query: 243 LADAPTPPLGTYIGVAGDAEITRLVEESDGLFLLGAILSDTNFAVSQRKIDLRKTIHAFD 302 + + LG Y G G + VEESD + LG LSD N + K++ + I Sbjct: 247 INEMHPNNLGIYEGAMGKEFTRKYVEESDCVIALGTFLSDVNLGIFTAKLNPQSFIDVNS 306 Query: 303 RAVTLGYHTYADIPLAGLVDALLEGLPPSDRTTRGKEPHAYPTGLQA-DGEPIAPMDIAR 361 ++ +H Y DI L ++ LL R PT GE I + Sbjct: 307 EKTSIHFHNYEDISLVDFLNGLLNA-DLKHRQVDLPSRFLLPTNFSVKPGEKITVQRLFE 365 Query: 362 AVNDRVRAGQEPLLIAADMGDCLFTAMDMI---DAGLMAPGYYAGMGFGVPAGIGAQCVS 418 +N + +++ AD+GD LF D++ + ++P YYA +GF VPA IGAQ + Sbjct: 366 RLNLFI---SNDMIVIADVGDALFAGADLVVHQKSRFLSPAYYASLGFAVPASIGAQMAN 422 Query: 419 GGKRILTVVGDGAFQMTGWELGNCRRLGIDPIVILFNNASWEMLRTFQPESAFNDLDDWR 478 R L +VGDGAFQMTG EL R G++PI+I+ NN + R Q + FND+ W Sbjct: 423 STLRPLVLVGDGAFQMTGMELSTIVRYGLNPIIIVLNNLGYGTERPMQ-DGKFNDILLWN 481 Query: 479 FADMAAGM-GGDGVRVRTRAELKAALDKA 506 ++ + G G +RT EL+ L+K+ Sbjct: 482 YSQLPTIFNAGKGFDIRTEDELELGLEKS 510 Lambda K H 0.321 0.137 0.405 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: 648 Number of extensions: 27 Number of successful extensions: 6 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: 545 Length of database: 544 Length adjustment: 35 Effective length of query: 510 Effective length of database: 509 Effective search space: 259590 Effective search space used: 259590 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 (21.9 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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