Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011777673.1 MVAN_RS01790 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000015305.1:WP_011777673.1 Length = 499 Score = 331 bits (848), Expect = 4e-95 Identities = 184/463 (39%), Positives = 274/463 (59%), Gaps = 13/463 (2%) Query: 42 SPSTEEEITQVYEAFSEDIDDAVEAATAAF-HSSWSTSDPQVRMKVLYKLADLIDEHADT 100 SP+TEE + V + +D AV AA AF +W + P R ++ +A+ + + Sbjct: 24 SPATEELVATVAKGDVSHVDAAVAAARGAFDEGTWRRTPPAERAALINTVAERLAARTEE 83 Query: 101 LAHIEALDNGKSLMCSKG-DVALTAAYFRSCAG----WTDKIKGSVIETGDTHFNYTRRE 155 LA +++ +NG ++ + V L+AA + A + + G IE RE Sbjct: 84 LAALQSRENGATIRITGALHVGLSAAQLQYVAAIARDYEWETTGPAIEPVPAA-GIVVRE 142 Query: 156 PIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGV 215 PIGV I+PWN PLL WK+GP L G + VLK E PL L LA AG PPG+ Sbjct: 143 PIGVVAAIVPWNIPLLTTVWKIGPALAAGNSVVLKPDEHAPLLPLELAREFDAAGLPPGI 202 Query: 216 VNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIV 275 +NVV+G G GA +S HP ++KVAFTGSTA G+ I++ +A+S +++VTLELGGK NI+ Sbjct: 203 LNVVTGDGEPVGAHLSGHPGVRKVAFTGSTAVGKSILRQSADS-IRRVTLELGGKGANII 261 Query: 276 FDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKE 335 DDAD++ + + N GE C AG+R+ + D+I+++ A +L++GDP + Sbjct: 262 LDDADIEMAVDGALFACMANNGEACEAGTRLLIPRSRRDEILAKLLARASTLRLGDPLQP 321 Query: 336 DTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG---ERFG-NKGYFIKPTIFGDVKEDH 391 T +G S Q D+IL Y +I K EGATV GG + G +KGY+++PTIF DV + Sbjct: 322 TTHVGPIISAHQRDRILDYFEIAKAEGATVALGGGVPDGPGFDKGYWVEPTIFVDVTNNM 381 Query: 392 QIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWV 451 +I R+E+FGPV+ + + + +E I +AND+ YGL+AGV + A+ V+ +++SG +WV Sbjct: 382 RIAREEVFGPVLVVLTYDSTDEAIKIANDTNYGLSAGVWGSE-ENALQVARRLDSGMVWV 440 Query: 452 NTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLS 494 N ++ HP PFGGY +SG+GRE G A+D Y + K + I S Sbjct: 441 NNWHVIHPAYPFGGYKESGLGREGGPHAIDEYVEEKFISIDRS 483 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: 617 Number of extensions: 27 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: 499 Length adjustment: 34 Effective length of query: 461 Effective length of database: 465 Effective search space: 214365 Effective search space used: 214365 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