Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate PfGW456L13_1342 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1342 Length = 506 Score = 362 bits (929), Expect = e-104 Identities = 208/483 (43%), Positives = 287/483 (59%), Gaps = 15/483 (3%) Query: 16 TYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSW 75 +++ G +I EFV + F SP + I + + +EDID A++AA AA +W Sbjct: 14 SFKAKYGNYIGGEFVAPVKGQYFTNTSPVNGQPIAEFPRSTAEDIDKALDAAHAAA-DAW 72 Query: 76 STSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWT 134 + Q R VL K+AD I+++ + LA E+ DNGK++ + D+ L A +FR AG Sbjct: 73 GATSAQARSLVLLKIADRIEQNLELLAITESWDNGKAVRETLNADIPLAADHFRYFAGCI 132 Query: 135 DKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194 +GS E Y EP+GV GQIIPWNFP+LMA+WKL P L G VLK AE Sbjct: 133 RAQEGSAAEIDGNTVAYHIHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQ 192 Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254 TPL L LI + PPGV+N+V GFG AG +++ +I K+AFTGST G HIMK Sbjct: 193 TPLGITVLVELIGDL-LPPGVLNIVQGFGKEAGEALATSKRIAKIAFTGSTPVGSHIMKC 251 Query: 255 AAESNLKKVTLELGGKSPNIVFDDA--DVKSTIQHLVTGI---FYNTGEVCCAGSRIYVQ 309 AAE N+ T+ELGGKSPNI F+D S I+ G+ F+N GEVC SR VQ Sbjct: 252 AAE-NIIPSTVELGGKSPNIFFEDIMKAEPSFIEKAAEGLVLAFFNQGEVCTCPSRALVQ 310 Query: 310 EGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG 369 E IYD+ ++ +K GDP DT +GAQ S+ Q DKIL Y++I K EGA ++TGG Sbjct: 311 ESIYDEFMAVVMKKVLQIKRGDPLDTDTMVGAQASEQQFDKILSYLEIAKGEGAELLTGG 370 Query: 370 E---RFGN--KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYG 424 + GN GY+I+PT+ + ++ ++EIFGPVV+IT FK E +A+AND+E+G Sbjct: 371 KVEKLEGNLASGYYIQPTLLKGTNK-MRVFQEEIFGPVVSITTFKDEAEALAIANDTEFG 429 Query: 425 LAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYT 484 L AG+ T +++ A + I +G +W N Y+ + FGGY +SG+GRE + LD+Y Sbjct: 430 LGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQ 489 Query: 485 QVK 487 Q K Sbjct: 490 QTK 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: 633 Number of extensions: 28 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