Align Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= curated2:A6UVT6 (465 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 292 bits (747), Expect = 2e-83 Identities = 166/459 (36%), Positives = 265/459 (57%), Gaps = 15/459 (3%) Query: 13 IEVKNPYNNEIIGYIPSLSRNETKEAIKIAEEHKSTMKNLSPTIRYNILMKIASELSKNK 72 ++V + Y+ ++ + T++AI A + M+ P R +L ++ + Sbjct: 21 MDVLDKYSGKVATRVAVPDAKATEQAIAAAVKAAEPMRQFKPWERQAVLQHCVQRFTERR 80 Query: 73 RELAKLITIDVGKPIKQSIIEVDRTITTFKFSAFYSRELRGETIPFDDGMVI------TK 126 ELA + ++ GKPIK S EV R I TF +A + GETI + + T+ Sbjct: 81 DELAYALCVEAGKPIKDSAGEVTRLIETFGIAAEEAVRTNGETINLEIAKRLNGYHGYTR 140 Query: 127 REPVGLVGAITPFNFPLNLFAHKIAPAIAMGNSIVAHPSSKAPMITIELTKIIEKVLKSK 186 R P+G V ITPFNFPLNL AHK+APAIA G V P+ + P+ + II +VL Sbjct: 141 RVPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGAL----IIGEVLAET 196 Query: 187 KIPLGVFNLLTGEGHIVGDEIVKNNKINKLSFTGSVEVGESITKKAGFKKITLELGGNNP 246 +P G F++L +G +V++ + LSFTGS ++G + +AG KK+TLELGGN Sbjct: 197 DLPKGAFSILNLDGKHASP-LVEDPRFKLLSFTGS-QIGWDLKTRAGHKKVTLELGGNAA 254 Query: 247 MIILKDA--NINKAVESCMSGKFLNSGQVCISVGRVLIEQEVADEFINKIVEKVKKLKIG 304 I+ D ++ +E + G F SGQ CISV R+ + + DE ++V VK LK G Sbjct: 255 CIVDADQLPRLDHVIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKAG 314 Query: 305 NPLDEDTNISSLISLDSAERVEKLINKSIGQGGKLICGGKRENSIIYPTILE-ITADNIL 363 +P ++T + +I +AER+ I ++ GGK++CGGKR+ ++ T++E + D + Sbjct: 315 DPKKKETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGKRKGPMLEATLMENVRGDAKV 374 Query: 364 ANIEIFAPVLPIIRVNDMNEALNQANNSNYGLHSGVFTQDINKALYFADNLEYGGVLINN 423 E+F P + ++EA+ N+S+YGL +G+FT + A+ + LE GGV++N+ Sbjct: 375 NRQEVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGVIVND 434 Query: 424 SPTFRIDNMPFGGIKHSGLGREGIKYAIDEMSEIKTIIV 462 P+FR+DNMP+GG+K SG GREG++YAI++M+EI+ +++ Sbjct: 435 VPSFRVDNMPYGGVKLSGAGREGVRYAIEDMTEIRLMVM 473 Lambda K H 0.316 0.136 0.377 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: 512 Number of extensions: 28 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: 465 Length of database: 476 Length adjustment: 33 Effective length of query: 432 Effective length of database: 443 Effective search space: 191376 Effective search space used: 191376 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 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