Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate AO356_25765 AO356_25765 carnitine dehydratase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25765 Length = 493 Score = 365 bits (938), Expect = e-105 Identities = 196/475 (41%), Positives = 294/475 (61%), Gaps = 5/475 (1%) Query: 25 INNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTSDPQVR 83 I E+V + S KTF +++P+ + ++ +A D++ AV+AA +AF S +W R Sbjct: 10 IGGEWVDALSGKTFESLNPALAQPWAELPDADEADVERAVQAAQSAFDSPAWRGLTATAR 69 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIE 143 K+L +L DLI E+ + LA +E+ DNGK + ++G V +F AG DK++G + Sbjct: 70 GKLLRRLGDLIAENKEQLAQLESRDNGKLIRETRGQVGYLPEFFHYTAGLADKLEGGTLP 129 Query: 144 TGDTH-FNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 F YT E +GV IIPWN PL + + KL P L G T V+K +E + L L Sbjct: 130 LDKPDLFAYTVHEAMGVVAAIIPWNSPLYLTAIKLAPALAAGNTIVIKPSEHASATVLEL 189 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 A L EAG PPGVVNVV+G+GP+ GA ++ HP ++K+AFTG AT RH+++++AE N K Sbjct: 190 ARLALEAGIPPGVVNVVTGYGPSTGAALTRHPLVRKIAFTGGAATARHVVRSSAE-NFAK 248 Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322 ++LELGGKSPNI+F DAD+ S I + GI+ +G+ C +GSR+ VQ+ IYD+ VS Sbjct: 249 LSLELGGKSPNIIFADADLDSAINGAIAGIYAASGQSCVSGSRLLVQDEIYDEFVSRLVE 308 Query: 323 AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN--KGYFIK 380 A+ ++IG+P ++ + MG + QL + + EGA + GG+R N G+F + Sbjct: 309 RAQRIRIGNPQEDASEMGPMATAQQLAVVEGLVADAIAEGARLRLGGKRPQNLGDGWFYE 368 Query: 381 PTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISV 440 PT+F + +I+++E+FGPV ++ +FK E +A+ANDS++GLAAG+ T +L A + Sbjct: 369 PTLFECDRNSMKIMQEEVFGPVASVIRFKDEAEALAIANDSQFGLAAGIWTRDLGRAHRL 428 Query: 441 SNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLSQ 495 + + SG IWVNTY M P GG+ SG GRE G +++ YT++K V I LSQ Sbjct: 429 ARDVRSGIIWVNTYRAVSAMAPIGGFKNSGYGRESGIDSVLAYTELKTVWINLSQ 483 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: 566 Number of extensions: 25 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