Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-15732 (497 letters) >NCBI__GCF_001906585.1:WP_073950325.1 Length = 511 Score = 350 bits (897), Expect = e-101 Identities = 198/467 (42%), Positives = 268/467 (57%), Gaps = 12/467 (2%) Query: 32 SGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRLRPRERQNLLWRLAD 91 SGRT + +PATGE + A +DVD AV AAR+AF W+ P +R + L R A+ Sbjct: 34 SGRTHAVVDPATGEEVHTYELAGPDDVDAAVAAAREAFPG--WAGATPGDRSDALHRFAE 91 Query: 92 LMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEGSTVEASMPLMPN 151 ++ A A E L GK + + DV ID + AG A ++G + + Sbjct: 92 VLADRAEDFARAESLQCGKPLKLTREFDVPGTIDNAAFFAGAARHLQGQSAGEY-----S 146 Query: 152 DQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKPADETPLSVLKLAEL 211 +VRRE IGVVG+I WN+PL +A WK+ PA+A G TIVLKPA+ TPL+ L A+ Sbjct: 147 GDHTSYVRREPIGVVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLTSLLFAQA 206 Query: 212 VDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLIGKAAMDNMTRVTLE 271 EAG P GV N+VTGTG AG L HP V ++FTGST VGK + + A ++ R+ LE Sbjct: 207 ATEAGIPDGVINIVTGTGKEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIATASVKRLHLE 266 Query: 272 LGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKHFDNVVADIAGIANG 331 LGGK+P +V DA+L+ A GA N GQ C A +R YV R ++ VA A + Sbjct: 267 LGGKAPFVVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFVARTAALMET 326 Query: 332 MKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGGEG----FGPGYFVKPTV 387 ++LG+ P +GPLIS +DRV G+++ R A V GGE G + +PT+ Sbjct: 327 VRLGDPFAPGTDLGPLISHVHRDRVAGFVDRARAY-ARVVTGGEAPQGELKNGAYYRPTL 385 Query: 388 IVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIWSNDLAAVHRMIPR 447 I Q +VQ EIFGPVLV +PFD DE I +AND YGL AS WS D+ +R Sbjct: 386 IAGAAQDSEIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVYRANRATRE 445 Query: 448 IKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSVL 494 IK+G VWVN H + +P GG K SG G+++ + + E YT++K V+ Sbjct: 446 IKAGCVWVNDHIPIISEMPHGGSKQSGFGKDMSSYSFEEYTQIKHVM 492 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: 657 Number of extensions: 27 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: 511 Length adjustment: 34 Effective length of query: 463 Effective length of database: 477 Effective search space: 220851 Effective search space used: 220851 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 24 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