Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF3406 PS417_17430 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__WCS417:GFF3406 Length = 506 Score = 363 bits (933), Expect = e-105 Identities = 213/484 (44%), Positives = 289/484 (59%), Gaps = 17/484 (3%) Query: 16 TYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSW 75 +++Q G +I EFV S + F SP T E I + + + DID A++AA AA +W Sbjct: 14 SFKQRYGNYIGGEFVAPLSGEYFTNTSPVTGEVIAEFPRSNAADIDKALDAAHAAA-DAW 72 Query: 76 STSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWT 134 + PQ R VL K+AD I++H + LA E+ DNGK++ + DV L A +FR AG Sbjct: 73 GKTSPQDRSLVLLKIADRIEQHLEVLAVTESWDNGKAVRETLNADVPLAADHFRYFAGCI 132 Query: 135 DKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194 +G E + Y EP+GV GQIIPWNFPLLMA+WKL P L G VLK AE Sbjct: 133 RAQEGGAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQ 192 Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254 TPLS + A LI + PPGV+N+V GFG AG +++ +I K+AFTGST G HIM A Sbjct: 193 TPLSIMVFAELINDL-LPPGVLNIVQGFGREAGEALATSKRIAKIAFTGSTPIGAHIMHA 251 Query: 255 AAESNLKKVTLELGGKSPNIVFDDAD------VKSTIQHLVTGIFYNTGEVCCAGSRIYV 308 AAE NL T+ELGGKSPNI F+D ++ + LV F+N GEVC SR V Sbjct: 252 AAE-NLIPSTVELGGKSPNIFFEDIMQAEPQFIEKAAEGLVLA-FFNQGEVCTCPSRALV 309 Query: 309 QEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITG 368 QE IYD + +K G+P +T +GAQ S+ Q DKIL Y+ I ++EGA ++TG Sbjct: 310 QESIYDDFMKVVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLKIAQEEGAELLTG 369 Query: 369 G--ERFG---NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEY 423 G ER + GY+I+PT+ + ++ ++EIFGPVV IT FK E +A+ANDSE+ Sbjct: 370 GAAERLEGDLSSGYYIQPTLLKGHNK-MRVFQEEIFGPVVGITTFKDEAEALAIANDSEF 428 Query: 424 GLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNY 483 GL AG+ T +++ A + I +G +W N Y+ + FGGY +SG+GRE + LD+Y Sbjct: 429 GLGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRENHKMMLDHY 488 Query: 484 TQVK 487 Q K Sbjct: 489 QQTK 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: 621 Number of extensions: 25 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 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