Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate Pf6N2E2_1380 Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10)
Query= SwissProt::P0A9S1 (382 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1380 Length = 392 Score = 248 bits (632), Expect = 3e-70 Identities = 137/380 (36%), Positives = 212/380 (55%), Gaps = 4/380 (1%) Query: 4 RMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAI 63 R ++ FG G + + K G +K LIVTD ++ G VA V + A G+ + + Sbjct: 14 RKFVSPEIMFGAGCRHNVGNYAKTFGARKVLIVTDPGVIAAGWVADVEASLQAQGIDYCV 73 Query: 64 YDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEG 123 Y V PNP + V G +++ + D ++A+GGGSP D K IGI+ + ++ EG Sbjct: 74 YSAVSPNPRVEEVMLGADLYRENHCDVIVAVGGGSPMDCGKGIGIVVAHGR--NILEFEG 131 Query: 124 LSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADMMDG 183 + + PS P++ IPTTAGT+A+V+ +I+++++R KF V +P V+ ID + Sbjct: 132 VDTLHVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAAVPDVSLIDPETTLS 191 Query: 184 MPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAG--EE 241 M P L A TG+DAL HAIE +++ G LTD ++A+ +I L +A D E+ Sbjct: 192 MDPFLSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINSNLVQMIANPADIALREK 251 Query: 242 MALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRD 301 + LG AG+ FSN LG VH M+H LG F + PHG+ NA+L+ HV+ +N + E+++ Sbjct: 252 IMLGSMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAPERFKV 311 Query: 302 IARVMGVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVC 361 IA +G+ G++ + R VE + AL +G L GV DIP L+Q A+ D C Sbjct: 312 IAETLGIDCRGLNHRQIRTRLVEHLIALKHTIGFHETLGLHGVSTSDIPFLSQHAMHDPC 371 Query: 362 TGGNPREATLEDIVELYHTA 381 NPRE++ D+ +Y A Sbjct: 372 ILTNPRESSQRDVEVVYGEA 391 Lambda K H 0.319 0.136 0.404 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: 417 Number of extensions: 24 Number of successful extensions: 3 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: 382 Length of database: 392 Length adjustment: 30 Effective length of query: 352 Effective length of database: 362 Effective search space: 127424 Effective search space used: 127424 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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