Align 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= SwissProt::Q19A30 (505 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 239 bits (611), Expect = 1e-67 Identities = 149/463 (32%), Positives = 248/463 (53%), Gaps = 26/463 (5%) Query: 45 PATGRVLCQMVPCGAEEVDEAIMSAHAAYVQWSKKSGTERARVMLEAARIIRERREKIAK 104 P G V + V C A++ +A+ A A + SK + +R +L+ A + + +E IAK Sbjct: 23 PYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDIAK 82 Query: 105 LEVINNGKSITEALVDIDVAWQCIEYYAGVAGTLAGQHFQLPG-GAFA-------YTRRE 156 GK IT + ++++ +CIE A T+ H + AFA + R Sbjct: 83 TITDEVGKPITYSRIEVE---RCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSRV 139 Query: 157 PLGVCVGIGAWNYPFQIAACKSAPALACGNAMVFKPSPFTPVTAVILAEIYKEA--GVPD 214 P GV V I +N+P + A K APAL GNA++ KP+P P+TA A+++ E+ + D Sbjct: 140 PCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKD 199 Query: 215 GLFCVVQGGAETGSLLCNHPKVAKVSFTGSVPTGKKVMEMSAKGVKQVTLELGGKSPLII 274 L VV G A+ G L +SFTGSV G+ + + + G+K+V+LELGG + I Sbjct: 200 AL-SVVYGDADVGGTLVTSEIPRVISFTGSVGVGEIITKSA--GIKKVSLELGGNAATFI 256 Query: 275 FKDCDLENAVKGALMANFLTQGQVCCNGTRVFVHKDILPQFLEEVVKRTKAIAVGDPLLD 334 K +L+ A + + F+ GQVC + R++VHKDI +F ++ + TK + VG P + Sbjct: 257 DKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYEE 316 Query: 335 STRMGALITKPHLEKVLGFVRQAKKEGGRVLCGGEPFVPSDPKLKGGYFMSPCILDNCRD 394 T MG L+ ++ + +V+ A KEG + +P+++G F PC++ + ++ Sbjct: 317 DTFMGPLVNDEAAKRAMEWVQSAIKEGATPIL--------EPRVEGRVFY-PCVMADVKE 367 Query: 395 DMTCVKEEIFGPVMSVLPFDTEEEVIRRANNTTFGLASGVFTRDISRAHRVAASLEAGTC 454 DM V +E+F P++S++ +E + NN+ +GL +FT D++ R L+AG Sbjct: 368 DMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGI 427 Query: 455 FINNYNISPVEV-PFGGYKMSGFGRENGQVTIEYYSQLKTVVV 496 IN+ ++ P+GG K+SG GRE + IE S++K+V++ Sbjct: 428 VINDMPTLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470 Lambda K H 0.320 0.136 0.410 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: 532 Number of extensions: 27 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: 505 Length of database: 471 Length adjustment: 34 Effective length of query: 471 Effective length of database: 437 Effective search space: 205827 Effective search space used: 205827 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