Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate PfGW456L13_2690 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2690 Length = 502 Score = 516 bits (1330), Expect = e-151 Identities = 252/489 (51%), Positives = 343/489 (70%), Gaps = 5/489 (1%) Query: 10 ATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAF 69 AT+ FL + KM IG W +A+ G+T P+T ++ +P +D+DRAV+AAR F Sbjct: 17 ATQTFLGKVQKMFIGGAWVEASDGQTSDVVEPSTEGLITRIPMGTTDDLDRAVQAARAQF 76 Query: 70 DDSPWSRLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRY 129 D W + +P ER+ ++ RLADL+E++A +LA++E ++ GKS A A+ +D+Q +D LRY Sbjct: 77 DGGAWRQAKPAERERMMQRLADLIEQNAAELAQIESIDMGKSVAFAKDVDIQGTVDTLRY 136 Query: 130 MAGWATKIEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALAT 189 AGWATK+ G TVE S+P + + R+EA+GVVGAIV WNFPL WKLG ALAT Sbjct: 137 FAGWATKLHGRTVEPSLP----GNYLAYTRKEAVGVVGAIVPWNFPLQTMAWKLGAALAT 192 Query: 190 GCTIVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTG 249 GCT+V+KPA+ T LS L+ AELV EAG P GV N+VTG G GAA++ HPG+DKLTFTG Sbjct: 193 GCTVVVKPAELTSLSALRFAELVQEAGIPDGVINIVTGRGSVVGAAMATHPGIDKLTFTG 252 Query: 250 STEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGS 309 ST VG+ +G+AA+D+M R+TLELGGKSP IV DA++ AA A +FFN GQVC AG+ Sbjct: 253 STPVGQTVGRAALDDMKRLTLELGGKSPVIVCADADIPAAAQAVANGVFFNSGQVCDAGT 312 Query: 310 RLYVHRKHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGAT 369 R Y+H +D + ++ +K+ GLDP +GPL+SA Q+ RVT YIE G+ GA Sbjct: 313 RAYIHSSVYDEFLRELITYTRTLKMAPGLDPDCFIGPLVSALQKQRVTEYIETGKAEGAE 372 Query: 370 VACGGEGF-GPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYG 428 + GG+ GPG+FV+PT+ + R+VQEEIFGPVLV PFDD +E + +AND+PYG Sbjct: 373 LVYGGQPVDGPGFFVEPTIFANCRNDMRIVQEEIFGPVLVTAPFDDEEEALALANDSPYG 432 Query: 429 LGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYT 488 L A+++SNDL VH +IPR+K+GSV+VN H LDP++PFGGYK SG G+++GA +++ Sbjct: 433 LAAALYSNDLGKVHSLIPRLKAGSVYVNAHGTLDPSMPFGGYKQSGFGKDLGAEQLDYLL 492 Query: 489 ELKSVLIKL 497 E K+V I L Sbjct: 493 ETKAVWITL 501 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: 694 Number of extensions: 31 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: 502 Length adjustment: 34 Effective length of query: 463 Effective length of database: 468 Effective search space: 216684 Effective search space used: 216684 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