Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000021485.1:WP_012536996.1 Length = 506 Score = 345 bits (886), Expect = 2e-99 Identities = 202/476 (42%), Positives = 280/476 (58%), Gaps = 17/476 (3%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI +V + F +SP + Q+ + +EDI+ A++AA AA +W + R Sbjct: 22 FIGGRWVAPVRGEYFDNISPINGKPFCQIPRSSAEDIELALDAAHAA-KDAWGRTSVTAR 80 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142 +L K+AD ID + + LA E DNGK++ + DV L++ +FR AG +G++ Sbjct: 81 SNILLKIADRIDANLEMLAVAETWDNGKAVRETLNADVPLSSDHFRYFAGCLRAQEGTIG 140 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 E + Y EP+GV GQIIPWNFPLLMA WKL P L G VLK AE TP S L + Sbjct: 141 EIDENTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASILVM 200 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 LI + P GV+NVV+G+G AG +++ +I K+AFTGST G IMK AAE N+ Sbjct: 201 MELIADL-LPAGVLNVVNGYGVEAGKALATSKRIAKIAFTGSTPVGSLIMKYAAE-NIIP 258 Query: 263 VTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316 T+ELGGKSPNI F +DA V ++ V F+N GEVC SR+ +QE IY+K Sbjct: 259 STVELGGKSPNIFFADVLDQEDAFVSKAVEGAVLA-FFNQGEVCTCPSRLLIQESIYEKF 317 Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG--ERFGN 374 + + +K G+P + +GAQ SQ Q DKIL YI IGK EGA VITGG E Sbjct: 318 IGMVVERSAQIKRGNPLDTEVMVGAQASQEQYDKILSYIQIGKDEGAEVITGGAVETMSA 377 Query: 375 ---KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHT 431 +GY+I+PT+ + ++ ++EIFGPVV++T FK E +A+AND E+GL AGV T Sbjct: 378 DYCEGYYIQPTLLKGTN-NMRVFQEEIFGPVVSVTTFKDEAEALAIANDIEFGLGAGVWT 436 Query: 432 TNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487 +++ A + I +G +W N Y+ + FGGY +SG+GRE + LD+Y Q K Sbjct: 437 RDMNRAYRMGRGIQAGRVWTNCYHMYPAHAAFGGYKKSGVGRETHKMMLDHYQQTK 492 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: 607 Number of extensions: 23 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