Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate PP_2487 PP_2487 putative aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Putida:PP_2487 Length = 503 Score = 391 bits (1005), Expect = e-113 Identities = 201/479 (41%), Positives = 303/479 (63%), Gaps = 8/479 (1%) Query: 22 GLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQ 81 GLFI+N++V ++ +T ++P+ + +T + A + D+D AV+AA AF +W T+ P Sbjct: 22 GLFIDNQWVTAEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAF-VTWRTTSPA 80 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGS 140 R L K+ADL++ AD A +E LD GK + S+ D+ L +FR AG Sbjct: 81 ERANALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGVIRSQSDE 140 Query: 141 VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200 + + + EP+GV GQ+IPWNFPLLMA+WK+ P + G T V+K +E TP++ L Sbjct: 141 AVMLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTPVTIL 200 Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260 LA + + P GVVN+V+G G T G + HP ++K+AFTGST G + AAA+ + Sbjct: 201 ELAKIFAKV-LPAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVGELVANAAAKKII 259 Query: 261 KKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320 TLELGGKS NIVF DA+ ++ V I +N G+VC +G+R++V E IY++ ++E Sbjct: 260 P-ATLELGGKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFLAEL 318 Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG----NKG 376 K+ E++++GDP DT MGAQ S+ Q+++IL Y+DI K+EGA V+ GG R + G Sbjct: 319 KHKFEAVRVGDPLNPDTMMGAQVSKTQMERILGYVDIAKEEGAEVLIGGGRLTGADYDAG 378 Query: 377 YFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLST 436 +FI+PTI V+ D ++ +EIFGPV+ + FK EVIA+ANDSEYGLA V T +++ Sbjct: 379 FFIQPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQDINR 438 Query: 437 AISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLSQ 495 A+ V+ + +G +WVNTY++ PFGGY +SG+GRE + L+ Y+Q K + + L++ Sbjct: 439 ALRVARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYSQKKNIYVSLNE 497 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: 595 Number of extensions: 29 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: 503 Length adjustment: 34 Effective length of query: 461 Effective length of database: 469 Effective search space: 216209 Effective search space used: 216209 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