Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate GFF3713 Psest_3782 Alcohol dehydrogenase, class IV
Query= SwissProt::P0A9S1 (382 letters) >FitnessBrowser__psRCH2:GFF3713 Length = 388 Score = 248 bits (634), Expect = 2e-70 Identities = 141/389 (36%), Positives = 223/389 (57%), Gaps = 11/389 (2%) Query: 1 MANRMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLA 60 M++R++L G GA L +K G + LIVTD+ +V+ G VA++ ++ AG+A Sbjct: 1 MSHRIVLPRLMEVGAGASQQLARVLKELGCNRPLIVTDRMMVELGYVARIAGQLGEAGIA 60 Query: 61 WAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISN-NPEFADVR 119 + +P PT ++ G+ + + D ++A+GGGSP D+ KAIGI+ E D R Sbjct: 61 SQCFADTLPEPTAASIRAGVEMVRQGDFDSIVALGGGSPIDSAKAIGILGKFGGEMRDYR 120 Query: 120 SLEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDAD 179 +S + +P++AIPTTAGT +E T +ITDE K +C +P A ID + Sbjct: 121 FPRDVS---EAGLPLIAIPTTAGTGSEATRFTIITDETSDEKMLCAGLGFMPIAALIDYE 177 Query: 180 MMDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSV--AGDKD 237 + +PP + A TG+DALTHAIE Y++R A +DA ++A+ ++A LR + G++ Sbjct: 178 LTLSLPPRVTADTGIDALTHAIEAYVSRKASLYSDAQALEAMRLLAPNLRAAFHEPGNRA 237 Query: 238 AGEEMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGE 297 A E M LG +AG+ FSN + LVHGM+ P+GAF++ PHG++NA+LLP + ++ E Sbjct: 238 AREAMMLGATLAGIAFSNASVALVHGMSRPIGAFFHVPHGLSNAMLLPAITAFSIPAAPE 297 Query: 298 KYRDIARVMGVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDI----PALA 353 +Y D AR MGV + S+ A + + + A+N+++ +P G+ +E +A Sbjct: 298 RYADCARAMGVAAQTDSVGVANDKLLAELRAINQELQVPSP-EQFGISRERFFELRETMA 356 Query: 354 QAALDDVCTGGNPREATLEDIVELYHTAW 382 + AL G NPR T +I++LY T W Sbjct: 357 RQALASGSPGNNPRVPTEAEIIDLYKTVW 385 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: 416 Number of extensions: 21 Number of successful extensions: 4 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: 388 Length adjustment: 30 Effective length of query: 352 Effective length of database: 358 Effective search space: 126016 Effective search space used: 126016 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