Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate RR42_RS27780 RR42_RS27780 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS27780 Length = 483 Score = 401 bits (1031), Expect = e-116 Identities = 195/456 (42%), Positives = 291/456 (63%), Gaps = 3/456 (0%) Query: 41 VSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADT 100 ++P+TE I V + + D+D AV AA AA W R ++LY+ ADL++ + + Sbjct: 30 INPATELPIALVAQGSAADVDLAVSAARAAL-KVWCGLRAAERGRILYRFADLLEANQEE 88 Query: 101 LAHIEALDNGKSLMC-SKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGV 159 L +E+LD GK L + D+ R AGW DKI G V+ T YT REP+GV Sbjct: 89 LTALESLDAGKPLAAVRRQDMPAVIDTVRYYAGWADKINGQVVPTRPGALTYTVREPVGV 148 Query: 160 CGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVV 219 I+PWNFPL++ WK+ P L GCT ++K AE TPL+AL + L +AG PPGV+N+V Sbjct: 149 VAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLTALRVGELALQAGLPPGVLNIV 208 Query: 220 SGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDA 279 +G G G + +HP I KV FTGS GR IM+ AA +N K++TLELGGKS N++F DA Sbjct: 209 TGKGSVVGNALVAHPGIDKVTFTGSPGVGRGIMQGAA-ANFKRITLELGGKSANLIFADA 267 Query: 280 DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFM 339 +V + ++ +GIF+N G+VC AGSRI Q +YD++V + A S+++GDP DT M Sbjct: 268 NVDAAVRAAASGIFFNAGQVCSAGSRILAQREVYDEVVEKLAARAASIRVGDPAAPDTTM 327 Query: 340 GAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRDEIF 399 G S Q+ +L Y++IGK+EGA +TGGER G KGY+++PT+F +V + ++ ++EIF Sbjct: 328 GPLVSSTQMKTVLDYVEIGKREGAIAVTGGERVGGKGYYVQPTVFANVGHEMRVSQEEIF 387 Query: 400 GPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHP 459 GPV ++ +F+ + + +AN + + LAAGV + ++ V+ ++ +GT+W+NTY Sbjct: 388 GPVASVIRFEDEADAVRIANGTAFSLAAGVWSADIGRVHQVAAELKAGTVWINTYGHTDV 447 Query: 460 MVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLSQ 495 +P+GG SG+GRE G+ A+DN+T+ KA+ + L Q Sbjct: 448 RLPWGGAGDSGLGREHGDAAIDNFTEPKAIWLSLRQ 483 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: 593 Number of extensions: 27 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: 483 Length adjustment: 34 Effective length of query: 461 Effective length of database: 449 Effective search space: 206989 Effective search space used: 206989 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 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