Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_085770042.1 B1812_RS01610 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_002117405.1:WP_085770042.1 Length = 474 Score = 289 bits (739), Expect = 2e-82 Identities = 165/475 (34%), Positives = 269/475 (56%), Gaps = 22/475 (4%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 +I+ +V+ +T ++P+TE + + D+D AV AA AF S+S + + R Sbjct: 8 YIDGHWVEPAELRTLEVINPATEAVCGHIALGSATDVDRAVAAAGEAF-KSFSRTSRRER 66 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKI----- 137 +++L ++ +++ + +A + G + + + + AA+F + + Sbjct: 67 LELLQRIVVELEKRHEDMARAITEEMGAPVWLAQRAQARMGAAHFSTAIEVLKRYEFEER 126 Query: 138 KGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPL 197 +G+ I +EPIGVCG I PWN+PL + K+ P L TGC VLK +E P Sbjct: 127 RGATIIV---------KEPIGVCGFITPWNWPLNQMACKIAPALATGCAMVLKPSEIAPF 177 Query: 198 SALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257 S + LA ++ AG PPGV N+V+G GPT GA ISSHP + V+FTGST G + K AA Sbjct: 178 SGIVLAEALEAAGTPPGVFNLVNGDGPTVGAAISSHPGVSMVSFTGSTRAGVEVAKNAAP 237 Query: 258 SNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317 + +K++ ELGGKSPNI+ +DAD+K+ + V + N+G+ C A +R+ ++++ Sbjct: 238 T-VKRICQELGGKSPNILLEDADMKAAVTAGVNAVMLNSGQSCNAPTRMLAPRKRMEEVI 296 Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG---ERFGN 374 ++AAE+ +GDP + MG S+ Q +K+ I G +EGA+++ GG Sbjct: 297 GFARSAAEATTVGDP-NGNAQMGPVVSEAQWNKVQGLIQKGLEEGASLVAGGLGKPEGLE 355 Query: 375 KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNL 434 KGY++KPT+F +V D I R+EIFGPV++I + V + I +AND+EYGL+A V + Sbjct: 356 KGYYVKPTVFANVTNDMTIAREEIFGPVLSILAYDRVADAIEIANDTEYGLSAYVSGADP 415 Query: 435 STAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 + + ++++ +G + +N+ M PFGGY SG GRE G+ A + + KA+ Sbjct: 416 ARLMETASRLRAGQVQLNS-APMDLMAPFGGYKMSGNGREWGDHAFAEFLETKAI 469 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: 503 Number of extensions: 22 Number of successful extensions: 6 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: 474 Length adjustment: 34 Effective length of query: 461 Effective length of database: 440 Effective search space: 202840 Effective search space used: 202840 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