Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_027178845.1 G496_RS0108130 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000429985.1:WP_027178845.1 Length = 494 Score = 386 bits (992), Expect = e-112 Identities = 203/473 (42%), Positives = 297/473 (62%), Gaps = 7/473 (1%) Query: 23 LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAF-HSSWSTSDPQ 81 +FIN +V S S KT ++P + I V E ED A++AA AAF + W+++ Sbjct: 6 MFINGSWVDSVSGKTREIINPYDQSVIAVVPEGSREDAALAIKAARAAFDNGKWASTPAC 65 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSV 141 R +++YKLA+LI+ + LA +E+LD GK++ S+ D+ A FR AG DK G V Sbjct: 66 DRGRLVYKLAELIERDREELAELESLDTGKTVEESRWDMDDIAGIFRYFAGLADKDGGEV 125 Query: 142 IETG-DTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200 I + + REP+GVCGQI PWN+PLL A+WKL P L G T V+K +E TPL+A+ Sbjct: 126 IASPVPDSASVVVREPVGVCGQISPWNYPLLQAAWKLAPALAAGNTVVMKPSEITPLTAI 185 Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260 + L +E G P GVVN+V G G GA +S + ++FTG ATG+ IM+AA SN+ Sbjct: 186 KVTQLAEECGFPQGVVNLVLGPGAEVGAELSESVDVDLISFTGGIATGKTIMRAAT-SNV 244 Query: 261 KKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320 KKV LELGGK+PNI+FDDAD + + + +F++ G++C AG+R+ +Q GI+D+ V Sbjct: 245 KKVALELGGKNPNIIFDDADFDVALDYALNAVFFHAGQICSAGARLMLQGGIHDRFVEAL 304 Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN----KG 376 K E + +G FK++T MG S L K+ Y+ + ++GA +I GG+R N KG Sbjct: 305 KARMEKIVMGSGFKKNTEMGPLISAEHLAKVESYMPVAVQDGAKIILGGKRPSNRELQKG 364 Query: 377 YFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLST 436 +F +PT+ D D +IV++E+FGPV+T+ +F+T EEV+ LAND+ YGL+AG T + Sbjct: 365 FFFEPTLITDCSSDMKIVQEEVFGPVITVERFQTEEEVVRLANDTIYGLSAGFWTRDPER 424 Query: 437 AISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 VS + GT+W+N +N + P+GGY QSG+GRE+G L+ YT+VK + Sbjct: 425 MERVSRALKFGTVWINDFNVYFVQAPWGGYKQSGLGRELGHVGLEEYTEVKHI 477 Lambda K H 0.316 0.133 0.389 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: 639 Number of extensions: 30 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: 495 Length of database: 494 Length adjustment: 34 Effective length of query: 461 Effective length of database: 460 Effective search space: 212060 Effective search space used: 212060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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