Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate AO356_28685 AO356_28685 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28685 Length = 496 Score = 485 bits (1249), Expect = e-141 Identities = 246/498 (49%), Positives = 334/498 (67%), Gaps = 11/498 (2%) Query: 5 LPILPATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRA 64 + +LPA FL + ++ IG WQDAA+GR + NPAT L EV DVD AV A Sbjct: 4 IQLLPAVEKFLSQPGRLFIGGTWQDAANGRRFAVENPATEHTLAEVAEGGERDVDAAVAA 63 Query: 65 ARQAFDDSPWSRLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAI 124 AR AF + W++ P +R LL+RLA+L+++ +LA+L L NGK A+ + A Sbjct: 64 ARAAFTGT-WAQQSPAQRGLLLFRLAELLDQHREELAQLITLENGKPIGAARG-EAASAA 121 Query: 125 DFLRYMAGWATKIEGSTVEASMPLMPND--QFHGFVRREAIGVVGAIVAWNFPLLLACWK 182 + +RY AGW TKIEGST +P+ P+ + RE +GV IV WNFPL + WK Sbjct: 122 NIIRYFAGWPTKIEGST----LPVSPSSGAPMLNYTLREPVGVCALIVPWNFPLTMCVWK 177 Query: 183 LGPALATGCTIVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGV 242 LGP LATGC VLKPA++TPL ++L +L++ AG+PAGV N++TG G GA L++HP V Sbjct: 178 LGPVLATGCVAVLKPAEQTPLVAIRLVQLIEAAGFPAGVVNLLTGLGAQTGAPLAQHPDV 237 Query: 243 DKLTFTGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQG 302 DK+ FTGST+VG+LI +AA NM +V+LELGGKSP I++PDA++ AA GAA IF+NQG Sbjct: 238 DKIAFTGSTQVGRLIAQAATGNMKKVSLELGGKSPNIILPDADIVRAAKGAADGIFYNQG 297 Query: 303 QVCCAGSRLYVHRKHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIEL 362 QVC AGSRLYVH D V+ ++ A LG GLDPA MGPL+SA+Q V GY++ Sbjct: 298 QVCTAGSRLYVHASVLDQVLEELQRHAAAHVLGPGLDPASSMGPLVSARQLGTVRGYLQR 357 Query: 363 GRELGATVACGGE---GFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVI 419 G+E GA + CGG+ G+F++P+V +D +R + +EEIFGPVL M + ++DE++ Sbjct: 358 GQEEGAELICGGDRPAHLERGHFIRPSVFLDRAERACVAREEIFGPVLTVMSWTEIDELV 417 Query: 420 GMANDNPYGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREV 479 AND+PYGL A +W+ DL + HR+ ++K+GSVW+NC + +DPA PFGGYK SG GRE+ Sbjct: 418 LRANDSPYGLAAGLWTRDLRSAHRVAAQLKAGSVWINCWNVVDPASPFGGYKQSGWGREM 477 Query: 480 GAAAIEHYTELKSVLIKL 497 G I+ YTE KSV + L Sbjct: 478 GKNVIDAYTETKSVYVDL 495 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: 730 Number of extensions: 31 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: 496 Length adjustment: 34 Effective length of query: 463 Effective length of database: 462 Effective search space: 213906 Effective search space used: 213906 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