Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_067912398.1 AQZ52_RS14300 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_001519075.1:WP_067912398.1 Length = 500 Score = 325 bits (834), Expect = 2e-93 Identities = 193/476 (40%), Positives = 270/476 (56%), Gaps = 17/476 (3%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI+ +F+ S + F +P + +V + + DI+ A++AA A +W T+ R Sbjct: 16 FISGKFLPPASGRYFANPTPVDGTVLCEVARSDAADIELALDAAHRAA-PNWGTTSAAER 74 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSVI 142 +L ++AD ++E+ LA E+ DNGK L S D+ L +FR AG +G + Sbjct: 75 AGILNRIADRMEENLALLAQAESWDNGKPLRESMAADLPLAIDHFRYFAGCIRAQQGGLS 134 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 E Y EP+GV GQIIPWNFPLLMA+WK+ P L G VLK AE TP S + Sbjct: 135 EIDSQTVAYHFHEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQTPASIMIW 194 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 A L+ + P GV+N+V+GFG AG P++S P+I K+AFTG T+TGR IM+ A+E N+ Sbjct: 195 AELVGDL-LPAGVINIVNGFGLEAGKPLASSPRISKIAFTGETSTGRLIMQYASE-NIIP 252 Query: 263 VTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316 VTLELGGKSPNI F DD + I+ V N GEVC SR + E IYD+ Sbjct: 253 VTLELGGKSPNIFFADVAQEDDEFLDKAIEGFVM-FALNQGEVCTCPSRALIHESIYDRF 311 Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG--- 373 + +K G P +T +GAQ S Q++KIL Y+D+G+ EGA + GG R Sbjct: 312 MERALARVAQIKQGHPLDMETMIGAQASTEQVEKILSYLDLGEMEGALTLIGGGRASVPP 371 Query: 374 --NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHT 431 G +I+PT+ ++ ++EIFGPVV +T FK E +++AND+ YGL AGV + Sbjct: 372 ALKGGNYIQPTVLKG-HNGMRVFQEEIFGPVVCVTTFKDEAEALSIANDTLYGLGAGVWS 430 Query: 432 TNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487 ++ST + I +G +W N Y+ + FGGY QSGIGRE L +Y Q K Sbjct: 431 RDISTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHLMMLSHYQQTK 486 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: 570 Number of extensions: 24 Number of successful extensions: 7 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: 500 Length adjustment: 34 Effective length of query: 461 Effective length of database: 466 Effective search space: 214826 Effective search space used: 214826 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