Align 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized)
to candidate WP_041099671.1 SUTH_RS12545 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= SwissProt::P56533 (503 letters) >NCBI__GCF_000828635.1:WP_041099671.1 Length = 505 Score = 254 bits (648), Expect = 7e-72 Identities = 161/484 (33%), Positives = 239/484 (49%), Gaps = 16/484 (3%) Query: 19 DDLNYWGGRRIKSKDGATTEPVFEPATGRVLCQMVPCGAEEVDQAVQSAQAAYLKWSKMA 78 D + +W + G VF PA GRV Q+ +VD+AV +A+AA+ W A Sbjct: 10 DLVGHWINGHADAGAGTRVGEVFNPAEGRVARQVALATRADVDRAVAAARAAFADWGSAA 69 Query: 79 GIERSRVMLEAARIIRERRDNIAKLEVINNGKTITEAEYDIDAAWQCIEYYAGLAPTLSG 138 R+RVM + ++ + +IAKL +GKT+ +A ++ + IE+ G+ L G Sbjct: 70 PQRRARVMFKFRDLVDQYSTDIAKLLSAEHGKTLPDALGEVQRGLEVIEFACGIPQLLKG 129 Query: 139 QHIQ-LPGGAFAYTRREPLGVCAGILAWNYPFMIAAWKCAPALACGNAVVFKPSPMTPVT 197 QH + GG + +R PLGV AGI +N+PFM+ W ALACGN + KPS P Sbjct: 130 QHSHGIGGGIDHWNQRMPLGVTAGITPFNFPFMVPMWMAPMALACGNTFILKPSERDPSP 189 Query: 198 GVILAEIFHEAGVPVGLVNVVQGGAETGSLLCHHPNVAKVSFTGSVPTGKKVMEMSAKTV 257 + AE+ EAG+P G NV+QG E L HP V+ VSF GS P K + Sbjct: 190 SLFAAELLREAGLPAGAFNVIQGDKEAVDALLEHPFVSAVSFVGSTPIAKYIQAHGIAHG 249 Query: 258 KHVTLELGGKSPLLIFKDCELENAVRGALMANFLTQGQVCTNGTRVFVQREIMPQFLEEV 317 K V G K+ +++ D +L+ A + A + + G+ C + + V Sbjct: 250 KRVQALGGAKNHMVVMPDADLDGAADALIGAAYGSAGERCMAISVAVAVGSCADDLVARV 309 Query: 318 VKRTKAIVVGDPLLTETRMGGLISKPQLDKVLGFVAQAKKEGAR-VLCGGEPLTPSDPKL 376 + R K + VG MG L++ DKV G++A +EGA+ VL G E LT +L Sbjct: 310 LARAKKLKVGAGDAANVEMGPLVTAVHRDKVAGYIAAGVQEGAKLVLDGREGLT---GEL 366 Query: 377 KNGYFMSPCVLDNCRDDMTCVKEEIFGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRD 436 G+F++P + DN +M+ +EEIFGPV+ V+ T ++ N TF FTRD Sbjct: 367 AQGFFINPTLFDNVTPNMSIYQEEIFGPVLCVVRVPTFAAAVELINRHTFANGVACFTRD 426 Query: 437 ISRAHRVAANLEAGTCYINTYSISPVEVP-----FGGYKMSGFGREN--GQATVDYYSQL 489 A +E G IN P+ VP FGG+K S FG + G+ V +Y++ Sbjct: 427 GGTAQAFIQKIEVGMVGINV----PIPVPMAWHSFGGWKASLFGDHHIYGEEGVRFYTRY 482 Query: 490 KTVI 493 K ++ Sbjct: 483 KAIM 486 Lambda K H 0.319 0.135 0.404 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: 578 Number of extensions: 31 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: 503 Length of database: 505 Length adjustment: 34 Effective length of query: 469 Effective length of database: 471 Effective search space: 220899 Effective search space used: 220899 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 Apr 09 2024. 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