Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_004302898.1 C665_RS06075 indolepyruvate/phenylpyruvate decarboxylase
Query= metacyc::MONOMER-20681 (545 letters) >NCBI__GCF_000310185.1:WP_004302898.1 Length = 542 Score = 708 bits (1828), Expect = 0.0 Identities = 368/542 (67%), Positives = 428/542 (78%), Gaps = 3/542 (0%) Query: 1 MKLAEALLRALKDRGAQAMFGIPGDFALPFFKVAEETQILPLHTLSHEPAVGFAADAAAR 60 M L E+LL AL D GA+ +FGIPGDFALP+F++ E+T ILPLHTLSHEP VGFAADAAAR Sbjct: 1 MNLTESLLHALVDHGARQIFGIPGDFALPYFRIIEQTGILPLHTLSHEPGVGFAADAAAR 60 Query: 61 YSSTLGVAAVTYGAGAFNMVNAVAGAYAEKSPVVVISGAPGTTEGNAGLLLHHQGRTLDT 120 +GVAAVTYGAGA NMVNAVA AYAEKSP+VVISG PG E +GLLLHHQ +TLD+ Sbjct: 61 VQGGIGVAAVTYGAGALNMVNAVAAAYAEKSPLVVISGGPGLGESQSGLLLHHQAKTLDS 120 Query: 121 QFQVFKEITVAQARLDDPAKAPAEIARVLGAARALSRPVYLEIPRNMVNAEVEPVGDDPA 180 Q ++F+EIT Q RLDD A+APA+IARVLG S PVY+EIPR+MV PV + Sbjct: 121 QLRIFQEITCDQVRLDDAARAPADIARVLGNCVRNSLPVYIEIPRDMVARPCAPVVREAP 180 Query: 181 WPVDRDALAACADEVLAAMRSATSPVLMVCVEVRRYGLEAKVAELAQRLGVPVVTTFMGR 240 VD DALAAC +E+LA +R+A +PVLM VEVRR+GLE KVAEL++RLG+PVVT+FMGR Sbjct: 181 RAVDADALAACVEEILARLRAARAPVLMAGVEVRRFGLEDKVAELSRRLGIPVVTSFMGR 240 Query: 241 GLLADAPTPPLGTYIGVAGDAEITRLVEESDGLFLLGAILSDTNFAVSQRKIDLRKTIHA 300 GLLAD P +GTY+G+AG E++ LVE+SDGLFL+G I+SDTNFAVS + IDLR TI A Sbjct: 241 GLLADQDAPLMGTYMGLAGLPEVSALVEDSDGLFLVGVIISDTNFAVSGKHIDLRHTIQA 300 Query: 301 FDRAVTLGYHTYADIPLAGLVDALLEGLPPSDRTTRGKEPHAYPTGLQADGEPIAPMDIA 360 + VT+GYHTYADIPL L+D LL +P +D P A+P GLQAD IAP DIA Sbjct: 301 LEARVTMGYHTYADIPLDALIDGLLARVPHADAHFTVDRP-AFPHGLQADEATIAPADIA 359 Query: 361 RAVNDRVRAGQEPLLIAADMGDCLFTAMDMIDAGLMAPGYYAGMGFGVPAGIGAQCVSGG 420 AVND + A L IA+DMGDCLFTAMD+ L+APGYYA MGFGVPAG+G Q + G Sbjct: 360 CAVND-LMAAHGKLPIASDMGDCLFTAMDIEHTALVAPGYYATMGFGVPAGLGVQAAT-G 417 Query: 421 KRILTVVGDGAFQMTGWELGNCRRLGIDPIVILFNNASWEMLRTFQPESAFNDLDDWRFA 480 +R L +VGDGAFQMTGWELGNCRR G DPIV+LFNNASWEMLRTFQPES FNDLDDW FA Sbjct: 418 QRPLILVGDGAFQMTGWELGNCRRYGWDPIVLLFNNASWEMLRTFQPESGFNDLDDWGFA 477 Query: 481 DMAAGMGGDGVRVRTRAELKAALDKAFATRGRFQLIEAMIPRGVLSDTLARFVQGQKRLH 540 MAAG+GGDGVRV TRA+LKAALDKA ATRGRFQLIE MIPRGVLS++L+RFV KRL+ Sbjct: 478 QMAAGLGGDGVRVHTRAQLKAALDKAIATRGRFQLIEVMIPRGVLSESLSRFVNAVKRLN 537 Query: 541 AA 542 AA Sbjct: 538 AA 539 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: 931 Number of extensions: 28 Number of successful extensions: 4 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: 542 Length adjustment: 35 Effective length of query: 510 Effective length of database: 507 Effective search space: 258570 Effective search space used: 258570 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 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