Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_041303771.1 BTUS_RS05345 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000092905.1:WP_041303771.1 Length = 497 Score = 429 bits (1103), Expect = e-124 Identities = 214/499 (42%), Positives = 327/499 (65%), Gaps = 7/499 (1%) Query: 1 MSLPLFVPIKLPNGTTYEQ--PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSE 58 M+ L +P+ L T+ + P + I +V S S +TF +V P++ E + +Y A Sbjct: 1 MTSTLKLPVVLDRVRTFMESGPKKMLIGGRWVPSASGQTFQSVDPASGEVLCTLYAADDP 60 Query: 59 DIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSK 117 D++ AV+AA A W P R ++L++L+DL++ HA+ L+ +E+LD GK + S Sbjct: 61 DVEAAVQAARRALDGPWKNISPMERARLLWRLSDLLEAHAEELSQLESLDTGKPIAETSA 120 Query: 118 GDVALTAAYFRSCAGWTDKIKGSVIETG--DTHFNYTRREPIGVCGQIIPWNFPLLMASW 175 D+ +FR AGWT K+ G + + YTRREP+GV G I+PWNFPL++ SW Sbjct: 121 VDIPYAIDHFRYFAGWTTKLSGENLPVSMPGQYLVYTRREPVGVVGAIVPWNFPLMITSW 180 Query: 176 KLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPK 235 K+ P L G T VLK +E TPL+AL L L EAG PPGV+NVV G+G TAGA ++ H Sbjct: 181 KVAPALACGNTVVLKPSELTPLTALRLGELALEAGIPPGVLNVVPGYGHTAGAALTHHRG 240 Query: 236 IKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYN 295 + K++FTGST GR I+ A+A ++ K+++LELGGKSPNIVF DAD+ ++ IF+N Sbjct: 241 VDKISFTGSTRVGREIVHASA-ADFKRLSLELGGKSPNIVFPDADLDMVAGGIMMSIFFN 299 Query: 296 TGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYI 355 GEVCCAGSR+Y+ + +YD+++ A++++ G T MG S+ ++++L YI Sbjct: 300 QGEVCCAGSRLYLHKQVYDRVLEAIVRRAKTIRQGAGVDPATQMGPLVSEQHMNRVLGYI 359 Query: 356 DIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVI 415 + G +EGA +TGG R G+ GYF++PT+ + ++D I R+E+FGPV+ + F+ V +V+ Sbjct: 360 EKGLEEGAKRLTGGVRKGSSGYFVEPTVL-EARDDMTIAREEVFGPVLAVMPFEDVRDVV 418 Query: 416 ALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREM 475 AND+EYGLAAG+ T+++ AI V++++ +GT+W+N YN P P+GG+ QSG+GREM Sbjct: 419 RRANDTEYGLAAGIWTSDVRRAIRVAHELRAGTVWINGYNLLDPTSPWGGFKQSGLGREM 478 Query: 476 GEEALDNYTQVKAVRIGLS 494 G AL++YT++K+V + L+ Sbjct: 479 GRYALEHYTEMKSVWVNLT 497 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: 628 Number of extensions: 22 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: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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