Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate GFF2074 PGA1_c21070 betaine aldehyde dehydrogenase BetB
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__Phaeo:GFF2074 Length = 488 Score = 325 bits (832), Expect = 3e-93 Identities = 187/483 (38%), Positives = 270/483 (55%), Gaps = 12/483 (2%) Query: 17 RKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSR 76 ++ + IG + D ++ R+PA+GEV +P A A DV+ AV AAR AF W+ Sbjct: 2 QQFQQYIGGVFSDGSA--RFESRDPASGEVWAMMPEARASDVEAAVAAARAAFHAPDWAG 59 Query: 77 LRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATK 136 + R LL+RLADL+ +A LA+LE + GK +A D+ RY AG A K Sbjct: 60 MTATGRGKLLYRLADLIAENAETLAQLETRDTGKIIRETSAQIAYVA-DYYRYYAGLADK 118 Query: 137 IEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLK 196 IEG+ + P M ++RRE +GVV A+V WN L LA K+GPALA GCT+VLK Sbjct: 119 IEGAHLPIDKPDM-----EVWLRREPLGVVAAVVPWNSQLFLAAVKIGPALAAGCTVVLK 173 Query: 197 PADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKL 256 ++E P +L+ A + D+AG+P GV NV+TG G + GA L+ HPG+D + FTG + + Sbjct: 174 ASEEAPAPLLEFARIFDQAGFPRGVLNVITGFGADCGAVLTAHPGIDHIAFTGGPDTARH 233 Query: 257 IGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRK 316 + + + +N+ +LELGGKSP IV D ++ A +AIF GQ C AGSRL + + Sbjct: 234 VVRNSAENLASTSLELGGKSPFIVFEDVDIDSAVNAQVSAIFAATGQSCVAGSRLIISNQ 293 Query: 317 HFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGGEG 376 + + A +++G P ++GPL + Q R + GA + GG+ Sbjct: 294 IKAQFLHRLKEKAENIRIGAPELPETEVGPLCTDAQMRRAVELVAASLAAGARIVTGGQP 353 Query: 377 F-GPGYFVKPTVIVDVDQRHR--LVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASI 433 G G F PT I+D + ++EE FGPVL FD E + +AND +GL + + Sbjct: 354 LEGEGNFFPPT-ILDCSEAPEAPCLREEFFGPVLSVCGFDTEAEALALANDTAHGLASGV 412 Query: 434 WSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSV 493 ++ DL HRMI I++G VWVN + A+ P PFGG +SG GRE G A YT +K+V Sbjct: 413 FTRDLTRAHRMIRGIRAGIVWVNTYRAVSPIAPFGGQGLSGHGREGGLQAALDYTRVKTV 472 Query: 494 LIK 496 ++ Sbjct: 473 WLR 475 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: 579 Number of extensions: 24 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: 497 Length of database: 488 Length adjustment: 34 Effective length of query: 463 Effective length of database: 454 Effective search space: 210202 Effective search space used: 210202 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