Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate H281DRAFT_03016 H281DRAFT_03016 aldehyde dehydrogenase (acceptor)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Burk376:H281DRAFT_03016 Length = 483 Score = 395 bits (1016), Expect = e-114 Identities = 194/456 (42%), Positives = 287/456 (62%), Gaps = 3/456 (0%) Query: 41 VSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADT 100 ++P+TEE I V + + D+D AV AA AA W+ R ++L +LA L+ + D Sbjct: 30 INPATEEPIAHVAQGSAADVDTAVRAARAAL-KVWNGIKAAERGRILSRLAGLMRANLDE 88 Query: 101 LAHIEALDNGKSLMC-SKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGV 159 LA +E+LD GK + + DV AGW DKI G V+ YT REP+GV Sbjct: 89 LAALESLDAGKPIAAVMRQDVPAAIDTLEYYAGWCDKINGQVVPVRPDALTYTLREPVGV 148 Query: 160 CGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVV 219 I+PWNFPL++ WK+ P L GCT ++K AE TPLSAL + L EAG PPGV+N+V Sbjct: 149 VAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLSALRIGELALEAGVPPGVLNIV 208 Query: 220 SGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDA 279 +G G G + +HP + KV FTGS + GR I++ AA N K+VTLELGGKS N++F DA Sbjct: 209 TGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAA-GNFKRVTLELGGKSANLIFPDA 267 Query: 280 DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFM 339 ++ + ++ +GIF+NTG+VC AGSRI +YD++V A+S+K+GDP +T M Sbjct: 268 NLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLAARAKSIKVGDPSSRETSM 327 Query: 340 GAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRDEIF 399 G S Q+ +L Y+D G+ EGA+++TGG R G +G+F++PT+F +V+ + +I ++EIF Sbjct: 328 GPLISAAQMKTVLGYVDAGRSEGASLVTGGGRIGERGFFVEPTVFANVEHEMRISQEEIF 387 Query: 400 GPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHP 459 GPV ++ +F + I +AN + Y LAAGV + ++ V+ + +GT+W+NTY Sbjct: 388 GPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHRVARDLRAGTVWINTYGYTDV 447 Query: 460 MVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLSQ 495 +P+GG SG GRE G+ A++N+T+ KAV + + Q Sbjct: 448 RLPWGGSGDSGFGREHGDVAIENFTEPKAVWLAIDQ 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: 610 Number of extensions: 25 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: 483 Length adjustment: 34 Effective length of query: 461 Effective length of database: 449 Effective search space: 206989 Effective search space used: 206989 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 17 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