Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate WP_086509699.1 BZY95_RS09490 aldehyde dehydrogenase
Query= SwissProt::O06837 (502 letters) >NCBI__GCF_002151265.1:WP_086509699.1 Length = 481 Score = 325 bits (834), Expect = 2e-93 Identities = 196/486 (40%), Positives = 275/486 (56%), Gaps = 14/486 (2%) Query: 18 RLPHQMLIGGQWVNAQSDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWR 77 +L HQ I W ++ ++ L V NP + + +V G +DV+ AV +A L AWR Sbjct: 3 QLDHQF-IDNCWTPSRGERCLPVMNPYREEAIAEVCAGHPDDVDDAVAAAQRALP--AWR 59 Query: 78 RMPPSARERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWAT 137 + + R L R AD L DEL RL + NNGK+L + + ++ + RY AG A Sbjct: 60 ALGGAERAHYLERFADALARRRDELIRLSSTNNGKVLAEAGI-DLDDAIACYRYYAGQAR 118 Query: 138 KLT---GSTLDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNT 194 L G +++ + A PVGVV I PWNFPL+ + WK+APALA G T Sbjct: 119 DLDRRQGRLVEVGME-----GVEARCYHDPVGVVGLITPWNFPLVTSAWKLAPALAAGCT 173 Query: 195 VVLKPAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTE 254 VVLKP+E TPL LAE+A+E GLP G LN++ G G G L HP V KV+FTGS Sbjct: 174 VVLKPSEVTPLPERALAEIALEIGLPPGVLNLLFGDGAGIGAPLAAHPGVDKVSFTGSNR 233 Query: 255 VGRIIGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLY 314 VG + A VSLELGGKSP++V+ D D ++AA+ A I+FN GQ+C+A SRL Sbjct: 234 VGEAVMRAAAERTADVSLELGGKSPILVMEDADAEQAADWVMAGIYFNAGQICSATSRLL 293 Query: 315 VHESIYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLIC 374 VHE+I E + LAV +++V+G L +G MGP+ S + E+VL ++ ++G + Sbjct: 294 VHEAIAEPLYAALAVRIDALVLGDPLAEGSDMGPLTSARQRESVLAYLAIAEQEGLLAVR 353 Query: 375 GGTEAPC-AQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYG 433 AQG+FV PT+F + RL +E+FGPVL A + E ++ AN S +G Sbjct: 354 DARHRQLPAQGYFVAPTLFRDVPTMS-RLWREEIFGPVLCARSVNSEQEAIDLANASEFG 412 Query: 434 LGASIWTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYT 493 L A++ D A+RI +L+AG+VW+N +V P +GGFK SG+GRE G + Y Sbjct: 413 LAATVVCADRQRAIRIGRQLQAGSVWINGEQLVLPETGWGGFKRSGIGRELGPWGLSAYL 472 Query: 494 TTRSLV 499 + LV Sbjct: 473 AVKHLV 478 Lambda K H 0.317 0.134 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: 550 Number of extensions: 27 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: 502 Length of database: 481 Length adjustment: 34 Effective length of query: 468 Effective length of database: 447 Effective search space: 209196 Effective search space used: 209196 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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