Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate WP_057506719.1 ABB28_RS00370 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15732 (497 letters) >NCBI__GCF_001431535.1:WP_057506719.1 Length = 510 Score = 186 bits (472), Expect = 2e-51 Identities = 145/476 (30%), Positives = 221/476 (46%), Gaps = 27/476 (5%) Query: 26 DWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRLRPRERQNL 85 +W A G ++ NP TGE + +V A A++ + + A++AF W R P R+ Sbjct: 24 EWSTATGGELITPVNPTTGEAIAQVRATTADEYETVIARAQEAF--KIW-RTTPAPRRGE 80 Query: 86 LWRLA-DLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEGSTVEA 144 RL + + + L L L GKS +VQ ID + G + + G T+ + Sbjct: 81 AVRLCGEALRANKDALGSLVALEMGKSKPEGDG-EVQEMIDIADFAVGQSRMLYGYTMHS 139 Query: 145 SMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKPADETPLS 204 P + + + +G+VG I A+NFP+ + W A G + KP+++TPL+ Sbjct: 140 ERP-----GHRMYEQYQPLGLVGIISAFNFPVAVWAWNAFLATVCGDICLWKPSNKTPLT 194 Query: 205 VLKLAELVDEAGYPAG---VFNVVTGTGLNAGAALSRHPGVDK----LTFTGSTEVGKLI 257 + + +EA AG +F ++ +AG ALS DK ++FTGST+VG+ + Sbjct: 195 AIASMRICNEALRDAGFPDLFFLIN----DAGTALSETMVADKRVPLISFTGSTQVGRTV 250 Query: 258 GKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKH 317 + + R LELGG + I+ A+L+ A G GQ C RL VH Sbjct: 251 AEKVAHRLGRCLLELGGNNAIILDETADLKLAIPGIVFGAVGTAGQRCTTTRRLIVHESI 310 Query: 318 FDNVVADIAGIANGM--KLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGGE 375 D+V+A + + K+G+ DPA MGPL S + IE + G TV GG Sbjct: 311 HDDVLATLVKAYKQVEGKIGDPTDPANLMGPLNSDGAVQQFLASIEKAKASGGTVQTGGT 370 Query: 376 GFG-PGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIW 434 G FV P ++ + +VQ E F P+L M + LDE I M N P GL +SI+ Sbjct: 371 RIDRAGNFVLPAIVTGLKNSDEVVQHETFAPILYVMKYSTLDEAIDMQNGVPQGLSSSIF 430 Query: 435 SNDLAAVHRMIPRIKSGSVWVNCH---SALDPALPFGGYKMSGVGREVGAAAIEHY 487 + +L R + S N + S + FGG K +G GRE G+ A + Y Sbjct: 431 TTNLKTAERFLSAAGSDCGIANVNIGTSGAEIGGAFGGEKDTGGGRESGSDAWKVY 486 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: 596 Number of extensions: 32 Number of successful extensions: 6 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: 510 Length adjustment: 34 Effective length of query: 463 Effective length of database: 476 Effective search space: 220388 Effective search space used: 220388 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 24 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