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_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= SwissProt::P56533 (503 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 487 bits (1254), Expect = e-142 Identities = 247/469 (52%), Positives = 328/469 (69%), Gaps = 8/469 (1%) Query: 36 TTEPVFEPATGRVLCQMVPCGAEEVDQAVQSAQAAYLKWSKMAGIERSRVMLEAARIIRE 95 T PV PATG + + VD+A+ +A A W+ M+G ER R++ AA ++RE Sbjct: 24 TPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKAWAAMSGTERGRILRRAADMMRE 83 Query: 96 RRDNIAKLEVINNGKTITEA-EYDIDAAWQCIEYYAGLAPTLSGQHIQLPGGAFAYTRRE 154 R +++ LE + GK E D + +EY+ GLA +L+G+HIQL G + YTRRE Sbjct: 84 RNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLTGEHIQL-GEDWVYTRRE 142 Query: 155 PLGVCAGILAWNYPFMIAAWKCAPALACGNAVVFKPSPMTPVTGVILAEIFHEAGVPVGL 214 PLGVC GI AWNYP IA WK APALACGNA+VFKPS TP+ + +AEI HEAG+P G+ Sbjct: 143 PLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALKVAEILHEAGLPAGI 202 Query: 215 VNVVQGGAETGSLLCHHPNVAKVSFTGSVPTGKKVMEMSAKTVKHVTLELGGKSPLLIFK 274 NVVQG E G+ L P VAKVS TGSVPTGKKV +A+ +KHVT+ELGGKSPLLIF Sbjct: 203 YNVVQGLGEVGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMKHVTMELGGKSPLLIFD 262 Query: 275 DCELENAVRGALMANFLTQGQVCTNGTRVFVQREIMPQFLEEVVKRTKAIVVGDPLLTET 334 D +LENAV GA++ NF + GQVC+NGTRVFVQ+ I FL+ + +R VVGDPL T Sbjct: 263 DADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTERLSTAVVGDPLDEAT 322 Query: 335 RMGGLISKPQLDKVLGFVAQAKKEGARVLCGGEPLTPSDPKLKNGYFMSPCVLDNCRDDM 394 G ++S+ Q+ VL ++ + + EGAR++ GG L ++G+++ P V + +DDM Sbjct: 323 NFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLN------RDGFYLQPTVFADVKDDM 376 Query: 395 TCVKEEIFGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRDISRAHRVAANLEAGTCYI 454 +EEIFGPVM+VL F+TEEE + RAN+T FGL++GVFTRD+SRAHRV A LEAG+C+I Sbjct: 377 IIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVIAQLEAGSCFI 436 Query: 455 NTYSISPVEVPFGGYKMSGFGRENGQATVDYYSQLKTVIVEMGDVDSLF 503 N+Y+ +PVE PFGG KMSG GREN +A +++YS++K+V V MGDV++ F Sbjct: 437 NSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVRMGDVEAPF 485 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: 716 Number of extensions: 26 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: 485 Length adjustment: 34 Effective length of query: 469 Effective length of database: 451 Effective search space: 211519 Effective search space used: 211519 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