Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_002117405.1:WP_085772038.1 Length = 506 Score = 352 bits (904), Expect = e-101 Identities = 209/500 (41%), Positives = 287/500 (57%), Gaps = 23/500 (4%) Query: 10 KLPNGTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATA 69 KL ++ FI ++V + F +SP T I QV + D++ A++AA Sbjct: 8 KLKGSVAIKKRYDNFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHK 67 Query: 70 AFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFR 128 A +W + R +L K+A +D++ LA +E +DNGK + + D+ L +FR Sbjct: 68 A-KDAWGKTPAAERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFR 126 Query: 129 SCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTV 188 AG +GS+ E Y EP+GV GQIIPWNFP+LMA+WKL P L G V Sbjct: 127 YFAGCLRAQEGSLSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVV 186 Query: 189 LKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATG 248 LK AE TP+S L +A LI + PPGV+N+V+GFG AG P++S+ +I K+AFTG T TG Sbjct: 187 LKPAEQTPMSILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTG 245 Query: 249 RHIMKAAAESNLKKVTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCA 302 R IM+ AAE NL VTLELGGKSPNI F DDA + ++ + N GEVC Sbjct: 246 RLIMQYAAE-NLIPVTLELGGKSPNIFFADVMAEDDAFLDKALEGFAS-FALNQGEVCTC 303 Query: 303 GSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEG 362 SR VQ IYDK + + ++ G P T +GAQ S QL+KIL Y+DIG+KEG Sbjct: 304 PSRALVQRSIYDKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEG 363 Query: 363 ATVITGGERFG-----NKGYFIKPTIFGDVKEDH---QIVRDEIFGPVVTITKFKTVEEV 414 A V+ GGER +GY+++PT E H ++ ++EIFGPVV++T F+T EE Sbjct: 364 AKVLIGGERSVLEGELKEGYYMQPTAL----EGHNRMRVFQEEIFGPVVSVTTFETEEEA 419 Query: 415 IALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGRE 474 + +AND+ YGL AG+ T + S A I +G +W N Y+ + FGGY QSGIGRE Sbjct: 420 LQIANDTLYGLGAGLWTRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRE 479 Query: 475 MGEEALDNYTQVKAVRIGLS 494 + LD+Y Q K + + S Sbjct: 480 NHKMMLDHYQQTKNLLVSYS 499 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: 576 Number of extensions: 31 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: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 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 Apr 09 2024. 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