Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate 8499247 DvMF_0027 indolepyruvate/phenylpyruvate decarboxylase (RefSeq)
Query= metacyc::MONOMER-20681 (545 letters) >FitnessBrowser__Miya:8499247 Length = 572 Score = 588 bits (1515), Expect = e-172 Identities = 327/576 (56%), Positives = 393/576 (68%), Gaps = 45/576 (7%) Query: 1 MKLAEALLRALKDRGAQAMFGIPGDFALPFFKVAEETQILPLHTLSHEPAVGFAADAAAR 60 M + EALL ALK+RGA+ ++GIPGDFALP+FK+ E+T ILPL TL+HEP +GFAADAAAR Sbjct: 1 MNITEALLHALKERGAREVWGIPGDFALPYFKIIEQTGILPLVTLTHEPGLGFAADAAAR 60 Query: 61 YSSTLGVAAVTYGAGAFNMVNAVAGAYAEKSPVVVISGAPGTTEGNAGLLLHHQGRTLDT 120 L VAAVTYGAGA NM+NAVA A+AEKSP+VV+SGAPGT E GLLLHHQ +T+ + Sbjct: 61 IRRGLSVAAVTYGAGAINMLNAVAQAFAEKSPLVVVSGAPGTAERARGLLLHHQVKTVGS 120 Query: 121 QFQVFKEITVAQARLDDPAKAPAEIARVLGAARALSRPVYLEIPRNMVNAEVEPVGDDPA 180 QF++++E+T Q LDDPA APA I RVL SRPVYLEIPR+M PV Sbjct: 121 QFRMYQEVTCDQGILDDPATAPAIIERVLRNCLEHSRPVYLEIPRDMPAVACGPVAPHMP 180 Query: 181 WPVDRDALAACADEVLAAMRSATSPVLMVCVEVRRYGLEAKVAELAQRLGVPVVTTFMGR 240 P D +A+AACA EVLA +R+A+ PVLMV VEVRRYGLE +VAELA RLGVPVVT+FMGR Sbjct: 181 TPCDAEAVAACAAEVLARLRAASRPVLMVGVEVRRYGLEDRVAELADRLGVPVVTSFMGR 240 Query: 241 GLLADAPTPPLGTYIGVAGDAEITRLVEESDGLFLLGAILSDTNFAVSQRKIDLRKTIHA 300 GLLA GTY+GVAGDA IT+ VE SDGL LLG I+SDTNF VS ID R+ +HA Sbjct: 241 GLLAGKACLQ-GTYMGVAGDAAITQAVEGSDGLLLLGVIMSDTNFGVSASHIDRRRLMHA 299 Query: 301 FDRAVTLGYHTYADIPLAGLVDALLEGLPPSDRTTRGKEPHAYPTGLQADG--------- 351 DR V +G+HTY DIPL LVDALL LP G + A P GL DG Sbjct: 300 EDRQVRMGFHTYHDIPLESLVDALLAALP------EGGQACAVPAGLDGDGGALGRNVVY 353 Query: 352 --------EPIAPMDIARAVND---------RVRAGQEPL-----------LIAADMGDC 383 P+ P DIA +ND V A +P +A D+GDC Sbjct: 354 RRGFVADDAPVTPDDIAVLLNDFYDGVLNGPAVSAEPDPFPWPFGGRPLPWPLACDIGDC 413 Query: 384 LFTAMDMIDAGLMAPGYYAGMGFGVPAGIGAQCVSGGKRILTVVGDGAFQMTGWELGNCR 443 LFTA+ + ++ PGYYA MGFGVPAG+G Q V+ G+R LT+VGDGAFQMTG ELGNC Sbjct: 414 LFTALSVRPVPMVGPGYYASMGFGVPAGMGLQ-VTTGQRSLTLVGDGAFQMTGMELGNCA 472 Query: 444 RLGIDPIVILFNNASWEMLRTFQPESAFNDLDDWRFADMAAGMGGDGVRVRTRAELKAAL 503 RLGIDP+V++FNNASWEMLR FQPE++++ ++ FA A +GG G RV TR EL AA Sbjct: 473 RLGIDPVVVVFNNASWEMLRVFQPETSYSAINTLDFAAFADALGGHGYRVTTRRELAAAF 532 Query: 504 DKAFATRGRFQLIEAMIPRGVLSDTLARFVQGQKRL 539 A RGRFQLI+ + +G +SDTLA FV G KR+ Sbjct: 533 ASATTERGRFQLIDVRLEKGAISDTLANFVAGVKRV 568 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: 935 Number of extensions: 54 Number of successful extensions: 5 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: 572 Length adjustment: 36 Effective length of query: 509 Effective length of database: 536 Effective search space: 272824 Effective search space used: 272824 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: 53 (25.0 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