Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase
Query= metacyc::MONOMER-15732 (497 letters) >NCBI__GCF_001484605.1:WP_058929223.1 Length = 508 Score = 400 bits (1029), Expect = e-116 Identities = 218/488 (44%), Positives = 289/488 (59%), Gaps = 12/488 (2%) Query: 16 ERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWS 75 +R M I W ++SG T + +P G VPAA EDVDRAVRAAR+AFD+ W Sbjct: 18 DRSYSMLIDGAWVQSSSGETFACVDPYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWP 77 Query: 76 RLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWAT 135 + P +R LL R ADL+ +A +LA + NGK +Q+ Y+AG A Sbjct: 78 QTLPSQRAALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQMG-QHAHYVAGLAE 136 Query: 136 KIEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVL 195 I+G T+E++ P F RE IGVV I WN PL+L WKL ALA G T+V+ Sbjct: 137 TIQGRTIESNWP-----NTAAFTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVI 191 Query: 196 KPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGK 255 KP++ TP S L++AEL EAG+P GV NVVTG G G+AL H GVDK+ FTGST G+ Sbjct: 192 KPSEATPTSTLRMAELAMEAGFPPGVINVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGR 251 Query: 256 LIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHR 315 I K A + RVTLELGGKSP I+ DA++ A GA IF GQ C GSR+ V Sbjct: 252 AINKQAAERFARVTLELGGKSPNIIFSDADIDNAVHGAMAGIFGATGQTCMGGSRVLVQD 311 Query: 316 KHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGG- 374 +D+ V +A + LG+ LDP V MGP+ + Q +V Y++LG+ GA V GG Sbjct: 312 SIYDDFVDRMARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGA 371 Query: 375 -----EGFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGL 429 G F +PTV +V RL QEEIFGPV + F D DE + +AN + +GL Sbjct: 372 RCMTTSELSKGLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFGL 431 Query: 430 GASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTE 489 A +W+ND++ HRMI R++SG+VWVN + + ++PFGG+K SG+GRE+G A++ YTE Sbjct: 432 AAGVWTNDVSRAHRMIRRVRSGTVWVNTYRLTNYSVPFGGFKQSGIGRELGPDALDAYTE 491 Query: 490 LKSVLIKL 497 +KS I L Sbjct: 492 VKSAWIDL 499 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: 628 Number of extensions: 33 Number of successful extensions: 4 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: 508 Length adjustment: 34 Effective length of query: 463 Effective length of database: 474 Effective search space: 219462 Effective search space used: 219462 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 Apr 09 2024. 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