Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__Korea:Ga0059261_3374 Length = 474 Score = 290 bits (741), Expect = 1e-82 Identities = 177/481 (36%), Positives = 255/481 (53%), Gaps = 20/481 (4%) Query: 19 LKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRLR 78 LK IG +W ++ G NPAT + E+ D D+AV AA+ AFD +SR Sbjct: 5 LKHYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDS--FSRTS 62 Query: 79 PRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIE 138 ER LL + + A LA+ G ++A+ V I L Sbjct: 63 VDERIALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLM---------- 112 Query: 139 GSTVEASMPLMPNDQF-HGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKP 197 ST+ A ++Q V E IGVV I WN+PL K+ PALA G T+VLKP Sbjct: 113 -STINALKAFEFSEQIGQSLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKP 171 Query: 198 ADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLI 257 ++E P S AE++D+AG PAGVFN+V G G G ALSRH VD ++FTGST G + Sbjct: 172 SEEAPGSAAIFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQV 231 Query: 258 GKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKH 317 K A + + RV ELGGKSP +++P A+L A ++ N GQ C A +R+ VH Sbjct: 232 AKNAAETVKRVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQ 291 Query: 318 FDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGG--- 374 +G+ ++ G+ +GP+++ Q +++ G I G E GA + GG Sbjct: 292 AAEAAQIASGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGR 351 Query: 375 -EGFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASI 433 +G GYFVKPT+ V + +EEIFGPV+ +P+ D +E + +AND YGL A + Sbjct: 352 PDGIETGYFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLSAVL 411 Query: 434 WSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSV 493 + + V R+ PR+++G V++N DP+LPFGGYK SG GRE G + + E+K++ Sbjct: 412 FGSP-EEVKRVAPRLRAGMVYIN-GGQPDPSLPFGGYKQSGNGREHGKFGLAEFMEVKAM 469 Query: 494 L 494 + Sbjct: 470 V 470 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: 567 Number of extensions: 25 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: 474 Length adjustment: 34 Effective length of query: 463 Effective length of database: 440 Effective search space: 203720 Effective search space used: 203720 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