Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate PP_2680 PP_2680 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Putida:PP_2680 Length = 506 Score = 353 bits (907), Expect = e-102 Identities = 204/478 (42%), Positives = 286/478 (59%), Gaps = 17/478 (3%) Query: 22 GLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQ 81 G FI EFVQ + + F SP + I + + ++D++ A++AA AA + W + Q Sbjct: 20 GNFIGGEFVQPLAGQYFINSSPVNGQPIAEFPRSTAQDVERALDAAHAAAEA-WGKTSVQ 78 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGS 140 R +VL K+AD I+++ + LA E+ DNGK++ + DV L A +FR AG +G Sbjct: 79 DRARVLLKIADRIEQNLEVLAVTESWDNGKAIRETLNADVPLAADHFRYFAGCIRAQEGG 138 Query: 141 VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200 V E + Y EP+GV GQIIPWNFPLLMA+WKL P L G VLK AE TPLS Sbjct: 139 VGEINEGTVAYHIHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCVVLKPAEQTPLSIT 198 Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260 A LI + P GV+N+V GFG AG +++ +I K+AFTGST G HIMK AAE N+ Sbjct: 199 VFAELIADL-LPAGVLNIVQGFGREAGEALATSKRIAKIAFTGSTPVGSHIMKCAAE-NI 256 Query: 261 KKVTLELGGKSPNIVFDD------ADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYD 314 T+ELGGKSPNI F+D A ++ + LV F+N GEVC SR +QE IY+ Sbjct: 257 IPSTVELGGKSPNIFFEDIMQAEPAFIEKAAEGLVLA-FFNQGEVCTCPSRALIQESIYE 315 Query: 315 KIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG--ERF 372 ++E + G+P +T +GAQ S+ Q DKIL Y++I ++EGA ++TGG ER Sbjct: 316 PFMAEVMKKIAKITRGNPLDTETMVGAQASEQQYDKILSYLEIAREEGAQLLTGGGAERL 375 Query: 373 GN---KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGV 429 GY+I+PT+ ++ ++EIFGPVV +T FK E +A+ANDSE+GL AG+ Sbjct: 376 QGDLASGYYIQPTLLKG-NNKMRVFQEEIFGPVVGVTTFKDEAEALAIANDSEFGLGAGL 434 Query: 430 HTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487 T +++ A + I +G +W N Y+ + FGGY +SG+GRE + LD+Y Q K Sbjct: 435 WTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQTK 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: 625 Number of extensions: 30 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