Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_085770964.1 B1812_RS07050 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_002117405.1:WP_085770964.1 Length = 505 Score = 334 bits (856), Expect = 5e-96 Identities = 205/507 (40%), Positives = 287/507 (56%), Gaps = 22/507 (4%) Query: 1 MSLPLFVPIKLPN-GTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSED 59 M+ P FV P YE FI E++ ++ + F V+P + +V + D Sbjct: 1 MTRPEFVRCSSPKFKACYEN----FIGGEWLAPRAGRYFENVTPVNGRMLCEVPRSDEID 56 Query: 60 IDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKG 118 I+ A++AA AA +W + R ++L +AD ++++ LA E+ DNGK + + Sbjct: 57 IELALDAAHAA-KEAWGRTSVAARSRLLNAVADRMEQNLAALAEAESWDNGKPIRETTAA 115 Query: 119 DVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLG 178 D+ L +FR A +G V E Y EP+GV GQIIPWNFPLLMA+WKL Sbjct: 116 DIPLAIDHFRYFASVIRAQEGGVSELDHDTVAYHFHEPLGVVGQIIPWNFPLLMAAWKLA 175 Query: 179 PVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKK 238 P L G VLK AE TP S L A L+ + PPGVVN+V+GFG AG P++S +I K Sbjct: 176 PALAAGNCVVLKPAEPTPASILVWAELVGDL-LPPGVVNIVNGFGLEAGKPLASSSRIAK 234 Query: 239 VAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDD--ADVKSTIQHLVTGIFY-- 294 +AFTG T TGR I + AA NL TLELGGKSPNI F D AD + + + G Sbjct: 235 IAFTGDTGTGRLIGEYAAR-NLIPATLELGGKSPNIFFADVMADDDAFLDKALEGFAMFA 293 Query: 295 -NTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILK 353 N GEVC SR V IYD+ + ++ GDP + T +GAQ S+ Q++KIL Sbjct: 294 LNQGEVCTCPSRALVHRSIYDRFMERALKRVGAIVQGDPLDKRTMVGAQASREQMEKILA 353 Query: 354 YIDIGKKEGATVITGGERFG-----NKGYFIKPTIF-GDVKEDHQIVRDEIFGPVVTITK 407 YIDIG+KEGA ++ GG R + GY+++PT+ G+ K ++ ++EIFGPV+++T Sbjct: 354 YIDIGRKEGAEILIGGGRADLGADLSGGYYVRPTVLLGNNKM--RVFQEEIFGPVLSVTV 411 Query: 408 FKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYS 467 F T EE A+AND+ +GL AGV T +++ A + I +G +W N Y+ + FGGY Sbjct: 412 FDTDEEAAAIANDTVFGLGAGVWTRDINRAYRMGRAIQAGRVWTNCYHAYPAHAAFGGYK 471 Query: 468 QSGIGREMGEEALDNYTQVKAVRIGLS 494 QSG+GRE LD+Y Q K + + S Sbjct: 472 QSGVGRENHRMMLDHYQQTKNLLVSYS 498 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: 589 Number of extensions: 35 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: 505 Length adjustment: 34 Effective length of query: 461 Effective length of database: 471 Effective search space: 217131 Effective search space used: 217131 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