Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 218 bits (554), Expect = 5e-61 Identities = 148/457 (32%), Positives = 228/457 (49%), Gaps = 13/457 (2%) Query: 43 TGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRLRPRERQNLLWRLADLMERDARQLAE 102 +G+V V DA+ ++A+ AA +A + P + +P ERQ +L +LA Sbjct: 28 SGKVATRVAVPDAKATEQAIAAAVKAAE--PMRQFKPWERQAVLQHCVQRFTERRDELAY 85 Query: 103 LECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEGSTVEASMPLMPNDQFHGFVRREA 162 C+ GK + +V I+ A A + G T+ + N +HG+ RR Sbjct: 86 ALCVEAGKPIKDS-AGEVTRLIETFGIAAEEAVRTNGETINLEIAKRLNG-YHGYTRRVP 143 Query: 163 IGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKPADETPLSVLKLAELVDEAGYPAGVF 222 +G V I +NFPL L K+ PA+A GC VLKPA+ TP+ L + E++ E P G F Sbjct: 144 LGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKGAF 203 Query: 223 NVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMP 282 +++ G +A + L P L+FTGS L +A +VTLELGG + IV Sbjct: 204 SILNLDGKHA-SPLVEDPRFKLLSFTGSQIGWDLKTRA---GHKKVTLELGGNAACIVDA 259 Query: 283 D--ANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKHFDNVVADIAGIANGMKLGNGLDP 340 D L F+ GQ C + R+Y H +D + + G+K G+ Sbjct: 260 DQLPRLDHVIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKAGDPKKK 319 Query: 341 AVQMGPLISAKQQDRVTGYIELGRELGATVACGGEGFGPGYFVKPTVIVDVDQRHRLVQE 400 +GP+I +R+ G+IE R+ G V CGG+ GP ++ T++ +V ++ ++ Sbjct: 320 ETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGKRKGP--MLEATLMENVRGDAKVNRQ 377 Query: 401 EIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIWSNDLAAVHRMIPRIKSGSVWVN-CHS 459 E+FGP + PF LDE I M ND+ YGL A I+++ LA R ++ G V VN S Sbjct: 378 EVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGVIVNDVPS 437 Query: 460 ALDPALPFGGYKMSGVGREVGAAAIEHYTELKSVLIK 496 +P+GG K+SG GRE AIE TE++ ++++ Sbjct: 438 FRVDNMPYGGVKLSGAGREGVRYAIEDMTEIRLMVMR 474 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: 496 Number of extensions: 26 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: 476 Length adjustment: 34 Effective length of query: 463 Effective length of database: 442 Effective search space: 204646 Effective search space used: 204646 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