Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate RR42_RS25005 RR42_RS25005 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__Cup4G11:RR42_RS25005 Length = 495 Score = 412 bits (1060), Expect = e-119 Identities = 214/491 (43%), Positives = 305/491 (62%), Gaps = 10/491 (2%) Query: 11 TRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFD 70 T AF+ ++ IG W AASG+ NPATGEV+ + AD D+DRAV AARQAF+ Sbjct: 10 TPAFVGGTKRLFIGGAWVPAASGKAFDTVNPATGEVIARLAQADQTDIDRAVTAARQAFE 69 Query: 71 DSPWSRLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYM 130 PW++ +RQ LL R+ D++E+ +LA +E L+ G + + L L+ + Sbjct: 70 -GPWNQWTHSDRQRLLIRIHDVVEKHFDELALIETLDMGAPLVRTRGLKSFL----LQLI 124 Query: 131 AGWATKIEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATG 190 +A++ V+ + +P +F + +GVV I+ WN PLL W LG LATG Sbjct: 125 LFYASQTAAGGVQTPLNALPG-KFATLKIKAPVGVVAGIIPWNGPLLSQWWILGATLATG 183 Query: 191 CTIVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGS 250 CT VLKPA++ LS L++AEL+ EAG PAGV NVVTG G AG+AL+ HPGVD++ FTGS Sbjct: 184 CTAVLKPAEDASLSALRMAELLQEAGVPAGVINVVTGYGGEAGSALAEHPGVDRIAFTGS 243 Query: 251 TEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSR 310 E G+ I +A+ N RV++ELGGKSP IV DANL +A G A +F N GQ+C AG+R Sbjct: 244 PETGRRIVRASAGNFKRVSVELGGKSPDIVFDDANLDKAVPGVAMGVFTNTGQICAAGTR 303 Query: 311 LYVHRKHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATV 370 + V R+ +D + + + +K+GNGLDP VQ+GP++S +Q DRV Y+++G + GA + Sbjct: 304 VLVQRRIYDEFIERLKAFSTSLKIGNGLDPQVQLGPIVSQRQLDRVMHYVDVGGQEGAEL 363 Query: 371 ACGGEGFG----PGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNP 426 ACGG G GYFV+PTV V + +EEIFGPV MPFD ++ + +AND Sbjct: 364 ACGGRRLGGELAAGYFVEPTVFTGVHNDMTIAREEIFGPVASVMPFDTPEQALRIANDTS 423 Query: 427 YGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEH 486 +GL +W+ +L+ HR I++G++WVNC+ LDP + FGGYK+SG G + A ++ Sbjct: 424 FGLAGGVWTQNLSTAHRFAQGIQAGTIWVNCYGVLDPQVGFGGYKLSGYGWKGAAEQVDS 483 Query: 487 YTELKSVLIKL 497 Y K+V + L Sbjct: 484 YLYQKAVYMNL 494 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: 668 Number of extensions: 20 Number of successful extensions: 4 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: 495 Length adjustment: 34 Effective length of query: 463 Effective length of database: 461 Effective search space: 213443 Effective search space used: 213443 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