Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_043769867.1 U743_RS16355 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000733765.1:WP_043769867.1 Length = 494 Score = 390 bits (1001), Expect = e-113 Identities = 199/477 (41%), Positives = 297/477 (62%), Gaps = 7/477 (1%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTSDPQV 82 FI E+ + P++E + + + + +D AV AA AF+ +WS P Sbjct: 19 FIAGEWRDESGAERITVTDPASETVLGDIPCSSAATVDKAVRAARKAFNDPAWSNLAPME 78 Query: 83 RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGS- 140 R +L++LA L+++HAD LA IE+LDNGK + S DV L+A + AGW K+ G Sbjct: 79 REALLHRLAALVEQHADDLATIESLDNGKPIAFSSTLDVPLSAQWLHYFAGWPSKLSGRS 138 Query: 141 ---VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPL 197 ++ +H YT R+P+GV G I+PWNFPL++A WKL P L G T V+K AE TP Sbjct: 139 MHPAVQPTGSHHAYTLRQPVGVVGAIVPWNFPLVLAIWKLAPALAAGNTVVIKPAEQTPY 198 Query: 198 SALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257 S L LA LI+ AG PPGVVNVV G G T G I HP + K++FTGSTA G+H++ +AA Sbjct: 199 SLLKLAELIEAAGFPPGVVNVVLGDGRTTGQAIVDHPGVDKISFTGSTAVGKHLLTSAA- 257 Query: 258 SNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 ++LK+VTLELGGKSP ++ DAD+++ I +F N+G++C AG+R++ +D+I+ Sbjct: 258 NDLKRVTLELGGKSPTVILPDADLETAIPGAAQAVFVNSGQICFAGTRLFAPRKHFDRIL 317 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGY 377 AA+S +G ++ +G SQ Q+D IL ++ G K GA+ GG R +GY Sbjct: 318 EGVAEAAKSFPVGAGLDPNSMLGPVVSQQQMDSILGKVEAGVKAGASTFCGGGRLDREGY 377 Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437 F++PTI + R+EIFGPV+T T++ ++++IA+ANDSEYGL+A ++T++ A Sbjct: 378 FLEPTILVTDDAQNPAYREEIFGPVLTATRYDELDDIIAMANDSEYGLSANLYTSHFGLA 437 Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLS 494 ++ ++ +GT+W+NT P +PFGG+ QSG GRE GE+ +YT+ K+V L+ Sbjct: 438 HRLAAQLQAGTVWINTQLSPDPHIPFGGFKQSGWGRENGEDVFAHYTETKSVIASLA 494 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: 620 Number of extensions: 19 Number of successful extensions: 3 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: 494 Length adjustment: 34 Effective length of query: 461 Effective length of database: 460 Effective search space: 212060 Effective search space used: 212060 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