Align 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Gamma-aminobutyraldehyde dehydrogenase; EC 1.2.1.47; EC 1.2.1.3; EC 1.2.1.19 (characterized)
to candidate SMa1731 SMa1731 betaine aldehyde dehydrogenase
Query= SwissProt::Q9JLJ3 (494 letters) >FitnessBrowser__Smeli:SMa1731 Length = 489 Score = 452 bits (1163), Expect = e-131 Identities = 235/466 (50%), Positives = 316/466 (67%), Gaps = 9/466 (1%) Query: 24 DASGTE-KAFEPATGREIATFKCSGEKEVNLAVENAKAAFKIWSKKSGLERCQVLLEAAR 82 D +G E + P G IA + + A+ +AK A K W++K ER +VL AA Sbjct: 29 DRTGPEILSVNPVDGEIIAKLHGATSCIIEKAIASAKRAQKEWARKEPAERGRVLSRAAD 88 Query: 83 IIKERRDEIAIMETINNGKSIFEARL-DVDTSWQCLEYYAGLAASMAGEHIQLPGGSFGY 141 I++ R E++++ET + GK I E + D + CLEY+ +AA+++G+ IQ G + Y Sbjct: 89 IMRARNRELSVLETRDTGKPISETLVADAASGADCLEYFGAIAATLSGDSIQF-GEDWVY 147 Query: 142 TRREPLGVCLGIGAWNYPFQIACWKSAPALACGNAMIFKPSPFTPVSALLLAEIYTKAGA 201 TRREPLGVCLGIGAWNYP QIA WK+APALACGNAMIFKPS TP+SAL LAEI T+AG Sbjct: 148 TRREPLGVCLGIGAWNYPIQIAAWKAAPALACGNAMIFKPSEVTPLSALKLAEILTEAGL 207 Query: 202 PNGLFNVVQGGAATGQFLCQHRDVAKVSFTGSVPTGMKIMEMAAKGIKPITLELGGKSPL 261 P G+FN+VQG G L H +AKVS TGSV TG ++ A GI+P+T+ELGGKS L Sbjct: 208 PPGVFNIVQGAGDVGAELATHPAIAKVSLTGSVKTGARVASAAMAGIRPVTMELGGKSAL 267 Query: 262 IIFSDCNMKNAVKGALLANFLTQGQVCCNGTRVFVQKEIADAFTKEVVRQTQRIKIGDPL 321 I+F D +++ AV GA+L NF + GQ+C NGTRVF+Q+ I +AF ++ + +KIGDP+ Sbjct: 268 IVFDDADVEAAVSGAILGNFYSAGQICSNGTRVFLQRGIREAFLARLLARVAALKIGDPM 327 Query: 322 LEDTRMGPLINAPHLERVLGFVRSAKEQGATVLCGGEPYAPEDPKLKHGYYMTPCILTNC 381 E+T +GPL++A H RV +V A+ +GA + P D + P + TN Sbjct: 328 DEETDIGPLVSAAHRNRVATYVARAEVEGAYQMAPPRKLPPGDA------WHEPVVFTNV 381 Query: 382 TDDMTCVKEEIFGPVMSILTFETEAEVLERANDTTFGLAAGVFTRDIQRAHRVAAELQAG 441 TD MT +EE+FGPVM++L F+ E +V+ RAN T FGLAAG+FTRD+ RAHR+AAEL+AG Sbjct: 382 TDWMTLAREEVFGPVMAVLDFDDEQDVVARANATDFGLAAGIFTRDLVRAHRLAAELEAG 441 Query: 442 TCYINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEM 487 T +IN YN++P + FGG K+SG GRENGRV I++Y+QLK+V V M Sbjct: 442 TVWINAYNLTPAGMAFGGIKRSGIGRENGRVAIDHYTQLKSVFVSM 487 Lambda K H 0.319 0.136 0.408 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: 651 Number of extensions: 24 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: 494 Length of database: 489 Length adjustment: 34 Effective length of query: 460 Effective length of database: 455 Effective search space: 209300 Effective search space used: 209300 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