Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate H281DRAFT_02499 H281DRAFT_02499 Acyl-CoA reductase
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__Burk376:H281DRAFT_02499 Length = 503 Score = 373 bits (958), Expect = e-108 Identities = 194/479 (40%), Positives = 286/479 (59%), Gaps = 10/479 (2%) Query: 20 KMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRLRP 79 ++ IG +W DA GRTL NPATGEV+G + +A A DVDRAV+A +AF+ W + Sbjct: 12 QLLIGGEWTDAEDGRTLDIVNPATGEVIGALASASARDVDRAVQAGHRAFEGGAWRDMSI 71 Query: 80 RERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEG 139 ++R +L R ADL E D Q +LE LNNG+ A + +L F RY A A Sbjct: 72 QQRARILNRFADLFEADLEQFYKLETLNNGRPIAETRAQISRLP-QFYRYFAALALTRRS 130 Query: 140 STVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKPAD 199 + P + + +R +GVV + ++N PL++ L PALATG ++V+K ++ Sbjct: 131 DVIPIEGPYLC------YTQRVPLGVVALMTSFNHPLMILSKSLAPALATGNSVVIKASE 184 Query: 200 ETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLIGK 259 +TPL+ ++L +L+ +AG P GV NVV G G AGAAL++HP + K+ FTG TEVG+ IG+ Sbjct: 185 QTPLTTVRLVKLLQDAGVPKGVVNVVNGEGRVAGAALAQHPLIRKVVFTGGTEVGRSIGE 244 Query: 260 AAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKHFD 319 AA N TLELGGK I+ D +++ A GA+ A F GQ C G+R+ V + + Sbjct: 245 AAARNFALTTLELGGKGAVILFDDFDIERAVNGASFAAFIGAGQTCVCGARILVQKSMYA 304 Query: 320 NVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGG---EG 376 + +++G+ D Q+GP+IS + + R+ +E ++ GA + GG + Sbjct: 305 AFLERFRAKVERIRVGDPTDAKTQLGPVISERSRQRILAMLERAQQAGAKLLTGGRVPQE 364 Query: 377 FGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIWSN 436 GYF++PTV+ D D + Q+E+FGPV V MPF+D + I +AND +GL ASIW+ Sbjct: 365 LTSGYFLEPTVVYDADPHSEIGQDEVFGPVTVVMPFEDEADAIRIANDTSFGLAASIWTQ 424 Query: 437 DLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSVLI 495 D+A HR+ R++ G VWVN H LDPA P+GG+K SGVGRE G + + ++E ++V I Sbjct: 425 DVARAHRVAGRLEFGMVWVNDHHRLDPASPWGGFKNSGVGRETGIESFDQFSEPRAVTI 483 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: 611 Number of extensions: 19 Number of successful extensions: 3 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: 503 Length adjustment: 34 Effective length of query: 463 Effective length of database: 469 Effective search space: 217147 Effective search space used: 217147 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