Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate 15361 b1241 fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase (NCBI)
Query= SwissProt::P0A9S1 (382 letters) >FitnessBrowser__Keio:15361 Length = 891 Score = 206 bits (525), Expect = 2e-57 Identities = 130/406 (32%), Positives = 222/406 (54%), Gaps = 39/406 (9%) Query: 7 LNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDG 66 L ++ +F RG++ DEV G+++ALIVTD+ L G ++T + AAG+ ++ Sbjct: 456 LPKSIYFRRGSLPIALDEVITDGHKRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFE 515 Query: 67 VVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPE---------FAD 117 V +PT+++V++G + + D +IA+GGGSP D K + ++ +PE F D Sbjct: 516 VEADPTLSIVRKGAELANSFKPDVIIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMD 575 Query: 118 VRSLEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFID 177 +R P ++A+ TT+GT +EVT V+TD+ +K+ D P +A +D Sbjct: 576 IRKRIYKFPKMGVKAKMIAVTTTSGTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVD 635 Query: 178 ADMMDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSV-AGDK 236 A+++ MP +L A G+DA+THA+E Y++ A +D ++A++++ L S G K Sbjct: 636 ANLVMDMPKSLCAFGGLDAVTHAMEAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSK 695 Query: 237 D--AGEEMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADF 294 + A E + +AG+ F+N LG+ H MAH LG+ ++ PHG+ANA+L+ +V+RYNA+ Sbjct: 696 NPVARERVHSAATIAGIAFANAFLGVCHSMAHKLGSQFHIPHGLANALLICNVIRYNAND 755 Query: 295 TGEK---------------YRDIARVMGVKVEGMSLEEARNAAVEAVFA----LNRDVGI 335 K Y +IA +G+ G + A +E + A L ++GI Sbjct: 756 NPTKQTAFSQYDRPQARRRYAEIADHLGLSAPG----DRTAAKIEKLLAWLETLKAELGI 811 Query: 336 PPHLRDVGVRKED----IPALAQAALDDVCTGGNPREATLEDIVEL 377 P +R+ GV++ D + L++ A DD CTG NPR + ++ ++ Sbjct: 812 PKSIREAGVQEADFLANVDKLSEDAFDDQCTGANPRYPLISELKQI 857 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: 813 Number of extensions: 35 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: 382 Length of database: 891 Length adjustment: 36 Effective length of query: 346 Effective length of database: 855 Effective search space: 295830 Effective search space used: 295830 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: 53 (25.0 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