Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate CCNA_00424 CCNA_00424 aldehyde dehydrogenase
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__Caulo:CCNA_00424 Length = 479 Score = 299 bits (766), Expect = 1e-85 Identities = 183/479 (38%), Positives = 261/479 (54%), Gaps = 18/479 (3%) Query: 20 KMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRLRP 79 K I W D A+ TL NPAT EV G + DVD+AVRAAR+AF + +S+ Sbjct: 6 KFYIDGAWVDPAAPNTLDVINPATEEVCGVISMGSEADVDKAVRAARKAF--ASFSQTSR 63 Query: 80 RERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEG 139 ER ++L R+ ++ +A+ G A +AQ + I ++ A ++G Sbjct: 64 EERIDILERIIAEYQKRFEDMAKAITEEMGAPAWLAQRAQAAMGIGHVQTAAA---VLKG 120 Query: 140 STVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKPAD 199 E D+ + +E IGV I WN+P+ K+GPA+ATGCT+VLKP++ Sbjct: 121 YKFE-------EDRGTTRIVKEPIGVCAFITPWNWPVNQIACKVGPAIATGCTMVLKPSE 173 Query: 200 ETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLIGK 259 P S E++ AG PAGVFN+V G G GAALSRHP VD ++FTGST G + K Sbjct: 174 IAPFSGYIWTEIMHAAGVPAGVFNLVNGDGPTVGAALSRHPEVDMVSFTGSTRAGIEVAK 233 Query: 260 AAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKHFD 319 A + RV ELGGKSP I++ DA+ A AG ++ N GQ C A +R+ V D Sbjct: 234 NAAPTVKRVHQELGGKSPNIILDDADFSRAVAGGVASVMMNSGQSCNAPTRMLVPGARMD 293 Query: 320 NVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGG----E 375 V+A A +G+ + +MGP++S Q +++ G I+ G + GAT+ GG E Sbjct: 294 EVIAIAKAAAESHTVGDP-NGNHKMGPVVSETQWNKIQGLIQKGIDEGATLVTGGVGRPE 352 Query: 376 GFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIWS 435 G GY+VKPTV +V + +EEIFGPV+ + +D +DE + + ND YGL A + Sbjct: 353 GLDKGYYVKPTVFANVTNEMTIAKEEIFGPVVSILGYDTVDEAVTVGNDTEYGLAAYVSG 412 Query: 436 NDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSVL 494 D V ++ R+++G V +N + D PFGGYKMSG GRE G A + E K++L Sbjct: 413 GDQDEVRKVASRLRAGQVTLN-GAGPDLMAPFGGYKMSGNGREWGDHAFGEFLETKAIL 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: 605 Number of extensions: 29 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: 479 Length adjustment: 34 Effective length of query: 463 Effective length of database: 445 Effective search space: 206035 Effective search space used: 206035 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