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_013459096.1 SULKU_RS01190 aldehyde dehydrogenase
Query= SwissProt::Q19A30 (505 letters) >NCBI__GCF_000183725.1:WP_013459096.1 Length = 471 Score = 246 bits (628), Expect = 1e-69 Identities = 154/460 (33%), Positives = 245/460 (53%), Gaps = 20/460 (4%) Query: 45 PATGRVLCQMVPCGAEEVDEAIMSAHAAYVQWSKKSGTERARVMLEAARIIRERREKIAK 104 P GRV+ + C A++ +A++ A A K + +R +L+ A ++E+RE+ A+ Sbjct: 23 PYDGRVVSRAAECSADDARQALIIAQNASKIAKKVALHQRCAWLLDVASKLKEQREEFAR 82 Query: 105 LEVINNGKSITEALVDIDVAWQCIEYYAGVAGTLAGQHFQ---LPGG--AFAYTRREPLG 159 + GK IT A +++D + I A T+ G+ +P G A AY RRE G Sbjct: 83 VLCDEVGKPITYARIEVDRCIETITLSAETMRTMHGESINTDAMPSGRAAHAYWRREAAG 142 Query: 160 VCVGIGAWNYPFQIAACKSAPALACGNAMVFKPSPFTPVTAVILAEIYKEA--GVPDGLF 217 V V I +N+P + A K APAL GNA+V KP+P P+ A LA+++ E+ PD L Sbjct: 143 VVVAITPFNFPLNLVAHKLAPALVAGNAVVLKPTPEAPLCAYKLAQLFIESPYATPDAL- 201 Query: 218 CVVQGGAETGSLLCNHPKVAKVSFTGSVPTGKKVMEMSAKGVKQVTLELGGKSPLIIFKD 277 VV G AE GS L +SFTGSV G + + G+K+++LELGG + I Sbjct: 202 SVVYGDAEVGSALVGSDIPRVISFTGSVGVGNIITRSA--GIKKISLELGGNAATYIDTS 259 Query: 278 CDLENAVKGALMANFLTQGQVCCNGTRVFVHKDILPQFLEEVVKRTKAIAVGDPLLDSTR 337 DLE A + F+ GQVC + R++V + +F ++ + T + VG P D T Sbjct: 260 ADLEYAAARCAIGAFVNSGQVCISLQRIYVDSSVYDEFALKMAEATSKLVVGSPYNDDTF 319 Query: 338 MGALITKPHLEKVLGFVRQAKKEGGRVLCGGEPFVPSDPKLKGGYFMSPCILDNCRDDMT 397 +G LI + + +V A +EG R L + P+ +G F PC++ + + M Sbjct: 320 LGPLINDEAASRAMSWVESAIEEGARAL--------TPPRCEGRIFY-PCVMADVTESMK 370 Query: 398 CVKEEIFGPVMSVLPFDTEEEVIRRANNTTFGLASGVFTRDISRAHRVAASLEAGTCFIN 457 V EE+F P++S++ D ++ I R NN+ +GL VFT ++S A + L+AG IN Sbjct: 371 IVCEEVFAPIVSLVRVDGIDDAITRMNNSPYGLQFSVFTNNLSHATKAIDELDAGGVVIN 430 Query: 458 NYNISPVEV-PFGGYKMSGFGRENGQVTIEYYSQLKTVVV 496 + ++ P+GG K+SG GRE + IE ++++K++V+ Sbjct: 431 DMPTLRFDIQPYGGVKLSGVGREGPRFAIEEFTEIKSIVI 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: 496 Number of extensions: 22 Number of successful extensions: 6 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 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