Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate PP_3646 PP_3646 Aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Putida:PP_3646 Length = 493 Score = 366 bits (939), Expect = e-105 Identities = 199/474 (41%), Positives = 292/474 (61%), Gaps = 5/474 (1%) Query: 25 INNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTSDPQVR 83 I+ ++ ++S KTF +++P+T + Q+ +A D++ AV+AA AF S +W + R Sbjct: 10 IDGQWRDAQSGKTFDSLNPATAQAWAQLPDADEADVELAVQAAQRAFDSKAWRSITATAR 69 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIE 143 K+L +L DLI E+ + LA +E+ DNGK + ++G V +F AG DK++G + Sbjct: 70 GKLLRRLGDLIAENKEHLAQLESRDNGKLIRETRGQVGYLPEFFHYTAGLADKLEGGTLP 129 Query: 144 TGDTH-FNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 F YT EPIGV IIPWN PL + + KL P L G T VLK +E + L L Sbjct: 130 LDKPDLFAYTVHEPIGVVAGIIPWNSPLYLTAIKLAPALAAGNTIVLKPSEHASATILEL 189 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 A L EAG P GVVNVV+G+GP+ GA ++ HP ++K+AFTG AT RH+++++AE N K Sbjct: 190 ARLALEAGFPAGVVNVVTGYGPSTGAALTRHPLVRKIAFTGGAATARHVVRSSAE-NFAK 248 Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322 ++LELGGKSPNI+F DAD+ S I V GI+ +G+ C AGSR+ VQ+ I+D+ V Sbjct: 249 LSLELGGKSPNIIFADADLDSAINGAVAGIYAASGQSCVAGSRLLVQDEIFDEFVERLIA 308 Query: 323 AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGER--FGNKGYFIK 380 A+ ++IG+P + + MG + QL + + K EGA + GG+R G+F + Sbjct: 309 RAKRIRIGNPQDDASEMGPMATAQQLAVVEGLVAAAKAEGAKLHMGGKRADVEGDGWFYE 368 Query: 381 PTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISV 440 PT+F I+++E+FGPV + +FKT EE +A+ANDS++GLAAG+ T +L A + Sbjct: 369 PTLFECDSNAMTIMQEEVFGPVAAVIRFKTEEEALAMANDSQFGLAAGIWTRDLGRAHRL 428 Query: 441 SNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLS 494 + + SG IWVNTY M P GG+ SG GRE G +++ YT++K V I LS Sbjct: 429 ARDVRSGIIWVNTYRAVSAMAPIGGFKNSGYGRESGIDSVLAYTELKTVWINLS 482 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: 563 Number of extensions: 26 Number of successful extensions: 5 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: 493 Length adjustment: 34 Effective length of query: 461 Effective length of database: 459 Effective search space: 211599 Effective search space used: 211599 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