Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate GFF2223 Psest_2268 Alcohol dehydrogenase, class IV
Query= SwissProt::P0A9S1 (382 letters) >FitnessBrowser__psRCH2:GFF2223 Length = 387 Score = 244 bits (623), Expect = 3e-69 Identities = 133/371 (35%), Positives = 207/371 (55%), Gaps = 4/371 (1%) Query: 13 FGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPT 72 FG G ++ + G +K L+V+D +V G VA V ++ + ++ GV PNP Sbjct: 18 FGAGCRHSVGNCAANFGARKVLLVSDPGVVHAGWVADVQASLERQNIGHCLFTGVSPNPR 77 Query: 73 ITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSV 132 V G ++++ G + ++A+GGGSP D K IGI++ + + EG+ PS Sbjct: 78 CEEVMLGAELYRSEGCNVIVAVGGGSPMDCAKGIGIVAAHGRH--IYEFEGVDTLRVPSP 135 Query: 133 PILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPPALKAAT 192 P++ IPTTAGT+A+V+ +I+++++R KF V +P V+ ID + M P L A T Sbjct: 136 PLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAAVPDVSLIDPETTLSMDPFLSACT 195 Query: 193 GVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAG--EEMALGQYVAG 250 G+DAL HAIE +++ G LTD ++A+ +I G L +A D E++ LG AG Sbjct: 196 GIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPADIALREQIMLGSMQAG 255 Query: 251 MGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVKV 310 + FSN LG VH M+H LG + + PHGV NA+L+ HV+ +N D ++YR +A +G+ Sbjct: 256 LAFSNAILGAVHAMSHSLGGYLDLPHGVCNAVLVEHVVAFNYDAAPDRYRMVAETLGIDS 315 Query: 311 EGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVCTGGNPREAT 370 G+S + R V+ + L + +G L GV DIP L+Q A+ D C NPR +T Sbjct: 316 RGLSHRQVRERLVQHLIDLKQQIGFRETLGLHGVNLSDIPFLSQHAMQDPCILTNPRSST 375 Query: 371 LEDIVELYHTA 381 D+ +Y A Sbjct: 376 QRDVEVVYAEA 386 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: 395 Number of extensions: 20 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: 387 Length adjustment: 30 Effective length of query: 352 Effective length of database: 357 Effective search space: 125664 Effective search space used: 125664 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