Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate SMc04397 SMc04397 L-sorbosone dehydrogenase, NADP dependent protein
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__Smeli:SMc04397 Length = 504 Score = 358 bits (918), Expect = e-103 Identities = 196/479 (40%), Positives = 278/479 (58%), Gaps = 8/479 (1%) Query: 17 RKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSR 76 R+ +M I W D A GRT+ P G V+ AA D +RA+ AAR+AFD+ PW R Sbjct: 18 REFRMLIDGQWVDGAEGRTIERVAPGHGVVVSRYQAAAKADAERAIAAARRAFDEGPWPR 77 Query: 77 LRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATK 136 + ER +L R AD++ A +LA L+ + +GK + A+ ++ A D RY A A + Sbjct: 78 MTASERSLILLRAADMIAARADELAFLDAVESGKPISQAKG-ELAGAADIWRYAAALARE 136 Query: 137 IEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLK 196 + G + + G V RE IGVV I WNFP L+ KL ALA GCT V+K Sbjct: 137 LSGESYNTL-----GEGTLGVVLREPIGVVSIITPWNFPFLIVSQKLPFALAAGCTTVVK 191 Query: 197 PADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKL 256 P++ T S L L E+++ AG P GV N++ GTG AGA L+ HP VD ++FTGST +G+L Sbjct: 192 PSELTSASTLVLGEILEAAGVPQGVVNIIVGTGPEAGAPLTTHPHVDMVSFTGSTGIGQL 251 Query: 257 IGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRK 316 A + +V+LELGGK+P IV PDANL E A +FN G+ C AGSRL +HR Sbjct: 252 TMANAAQTLKKVSLELGGKNPQIVFPDANLDEFIDAAVFGAYFNAGECCNAGSRLILHRD 311 Query: 317 HFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGGE- 375 + V A IA ++ +K+G+ LDP Q+G +I+ + ++ GY+ GA +A GG Sbjct: 312 IAEEVTARIASLSAKVKVGDPLDPETQVGAIITPQHLQKIAGYVSSASNEGARIAHGGTT 371 Query: 376 -GFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIW 434 G G F+ PT++ V + +EE+FGPVL + F+ +E I +AN YGL A +W Sbjct: 372 LDLGMGQFMAPTILSAVRPEMAVAREEVFGPVLSVLTFEKTEEAIRIANSIDYGLSAGVW 431 Query: 435 SNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSV 493 S D + R+++G+VW+N LPFGGY+ SG+GRE+G A+E YTE K++ Sbjct: 432 SRDFDTCLTIGRRVRAGTVWMNTFMDGASELPFGGYRQSGLGRELGRHAVEDYTETKTL 490 Lambda K H 0.320 0.137 0.413 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: 574 Number of extensions: 23 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: 497 Length of database: 504 Length adjustment: 34 Effective length of query: 463 Effective length of database: 470 Effective search space: 217610 Effective search space used: 217610 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: 52 (24.6 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