Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Cola:Echvi_3822 Length = 453 Score = 223 bits (568), Expect = 1e-62 Identities = 140/456 (30%), Positives = 221/456 (48%), Gaps = 8/456 (1%) Query: 40 TVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHAD 99 +++P T E + + + + ++ A++ A+ SW R ++ K ++ ++ D Sbjct: 3 SINPYTGELLEEFTDHTEQQVEAAIQKGQEAY-LSWRELPISQRADLMKKAGQVLRDNTD 61 Query: 100 TLAHIEALDNGKSLMCSKGDV---ALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREP 156 I +L+ GK + SK +V A Y+ A + + + I D P Sbjct: 62 KYGKIISLEMGKVITESKSEVEKCAWVCEYYAENA--EEMLADAPIALPDGKEAKVVYNP 119 Query: 157 IGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVV 216 +G+ ++PWNFP P L G +LK A + P AL + + +AG P GV Sbjct: 120 LGIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEGVF 179 Query: 217 NVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVF 276 + G A I +HP +K TGS G+ I A E +KK LELGG P IV Sbjct: 180 QSLL-IGSDKVANIIAHPDVKAATLTGSEKAGQKIAAQAGEQ-IKKTVLELGGSDPFIVL 237 Query: 277 DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKED 336 DADVK + G N G+ C A R +++ +YD+ ++ FK+A ES GDP E Sbjct: 238 KDADVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLDEK 297 Query: 337 TFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRD 396 ++ + ++ ++GA VI G + FIKP I G + D R+ Sbjct: 298 AGYACMARPDLAMELYEQVEASIQKGAEVILEGTKPEKGKAFIKPYILGKLTPDMPAYRE 357 Query: 397 EIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYND 456 E+FGPV ++ K V+E IA+ANDS +GL A + T + A +S KI SG +++N+ Sbjct: 358 ELFGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFINSMVA 417 Query: 457 FHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492 +P +PFGG +SG GRE+ E + + +K V +G Sbjct: 418 SNPYLPFGGIKKSGYGRELAENGIKEFMNIKTVYLG 453 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: 533 Number of extensions: 21 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: 495 Length of database: 453 Length adjustment: 33 Effective length of query: 462 Effective length of database: 420 Effective search space: 194040 Effective search space used: 194040 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