Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate GFF2231 Psest_2276 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__psRCH2:GFF2231 Length = 506 Score = 327 bits (839), Expect = 5e-94 Identities = 192/485 (39%), Positives = 269/485 (55%), Gaps = 23/485 (4%) Query: 23 IGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRLRPRER 82 IG ++ G +P GEV+ E P + AED+++A+ AA A D W + ++R Sbjct: 23 IGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEKALDAAHAAAD--AWGKTSVQDR 80 Query: 83 QNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEGSTV 142 +L ++AD +E + +LA E +NGK+ DV LA D RY AG EGS Sbjct: 81 ALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGSAA 140 Query: 143 EASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKPADETP 202 E N+ + E +GVVG I+ WNFPLL+A WKL PALA G IVLKPA++TP Sbjct: 141 EI------NEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTP 194 Query: 203 LSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLIGKAAM 262 LS++ E+V + P GV N+V G G AG AL+ + K+ FTGST VG I + A Sbjct: 195 LSIMVFIEVVGDL-LPPGVLNIVQGFGREAGQALATSTRIAKIAFTGSTPVGSHIMRCAA 253 Query: 263 DNMTRVTLELGGKSPTIVMPD------ANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRK 316 +N+ T+ELGGKSP I D A +++AA G A FFNQG+VC SR + Sbjct: 254 ENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLA-FFNQGEVCTCPSRALIQES 312 Query: 317 HFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGG-- 374 F+ + + +K GN LD +G S +Q D++ Y+E+ ++ GA + GG Sbjct: 313 IFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQQEGAQILTGGAA 372 Query: 375 ---EG-FGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLG 430 EG GY+V+PT+I + R+ QEEIFGPV+ F D E + +AND +GLG Sbjct: 373 EKLEGSLSTGYYVQPTLIKG-HNKMRVFQEEIFGPVVGVATFKDEAEALAIANDTEFGLG 431 Query: 431 ASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTEL 490 A +W+ D+ +RM IK+G VW NC+ FGGYK SGVGRE ++HY + Sbjct: 432 AGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQT 491 Query: 491 KSVLI 495 K++LI Sbjct: 492 KNLLI 496 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: 614 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: 506 Length adjustment: 34 Effective length of query: 463 Effective length of database: 472 Effective search space: 218536 Effective search space used: 218536 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