Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_083924329.1 D471_RS0125445 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000341125.1:WP_083924329.1 Length = 467 Score = 343 bits (881), Expect = 6e-99 Identities = 180/454 (39%), Positives = 263/454 (57%), Gaps = 6/454 (1%) Query: 41 VSPSTEEEITQVYEAFSEDIDDAVEAATAAF-HSSWSTSDPQVRMKVLYKLADLIDEHAD 99 + P+ +T V E D +DA+ AA AF H W ++ R +VL ++ADL+ Sbjct: 2 LDPADGSVLTIVSEGGRADAEDAIAAARRAFDHGEWRSTTATERGRVLERIADLLQRDRH 61 Query: 100 TLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGV 159 +A +E+LD GK++ DV FR AG DK G ++ + + EP+GV Sbjct: 62 EIAVMESLDTGKTIEEGGIDVDDVTNVFRHYAGLADKDAGRLVSAPEGVQSRVVYEPVGV 121 Query: 160 CGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVV 219 CG I PWN+PLL +WK+ P + G T V+K +E TP++ L L EAG P GVVN+V Sbjct: 122 CGMITPWNYPLLQLAWKMAPAIAAGNTMVIKPSEITPVTTAKLVELSTEAGVPAGVVNLV 181 Query: 220 SGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDA 279 G GP AGAP+S HP + ++FTG TGR IM AAA + +KK+ LELGGK+PNI+F D Sbjct: 182 LGSGPDAGAPLSEHPDVDLISFTGGLVTGRRIM-AAASATVKKIALELGGKNPNIIFPDV 240 Query: 280 DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFM 339 D+ + + + ++ F+++G+VC AG+R+ V I+D +E AE+++IG E Sbjct: 241 DLDTAVDYALSAAFFHSGQVCSAGARLIVHNDIHDAFTTELARRAEAIRIGRGQVEGVRC 300 Query: 340 GAQTSQLQLDKILKYIDIGKKEGATVITGGERFG----NKGYFIKPTIFGDVKEDHQIVR 395 G S K+ + G +EGA VI GG+R GYF +PT+F D IV+ Sbjct: 301 GPLVSAEHRSKVEAAVARGVEEGARVIAGGKRPDAPELADGYFYRPTVFVDCDRSMDIVQ 360 Query: 396 DEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYN 455 E+FGPVVT+ +F+T + I L ND++YGL+ GV T + + V+ + GT+WVN Y Sbjct: 361 TEVFGPVVTVERFETEAQAIELGNDTDYGLSGGVWTNDTARGERVAAALRHGTVWVNDYG 420 Query: 456 DFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 + P +GG+ QSG+GRE+G LD Y + K + Sbjct: 421 PYFPGAEWGGFGQSGVGRELGLAGLDEYREAKHI 454 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: 561 Number of extensions: 20 Number of successful extensions: 3 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: 467 Length adjustment: 34 Effective length of query: 461 Effective length of database: 433 Effective search space: 199613 Effective search space used: 199613 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: 51 (24.3 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