Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate H281DRAFT_03803 H281DRAFT_03803 alcohol dehydrogenase
Query= SwissProt::P0A9S1 (382 letters) >FitnessBrowser__Burk376:H281DRAFT_03803 Length = 387 Score = 192 bits (489), Expect = 1e-53 Identities = 116/356 (32%), Positives = 196/356 (55%), Gaps = 7/356 (1%) Query: 31 QKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPTITVVKEGLGVFQNSGADY 90 ++ +VTD L + G++ + A G + D V+ +P +V E +++GA+ Sbjct: 35 ERLCVVTDGFLHKSGLLDPALADLAAHGWNATVIDDVIADPPEHIVLEATARARSAGAEI 94 Query: 91 LIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSVPILAIPTTAGTAAEVTIN 150 ++ +GGGS D K I ++ + + + G++ +P++ +PTTAGT +EVT Sbjct: 95 VLGLGGGSSMDVAKLIAALAPQQQ-QQLSEMYGVNKVTVQRLPLVQMPTTAGTGSEVTAV 153 Query: 151 YVITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPPALKAATGVDALTHAIEGYITRGAW 210 ++T E R+ V V P I +A +DA++ G+P A AATG+DA+ HAIE Y + Sbjct: 154 SIVTVGEARKMGV-VAPQLIADLAILDAELTLGLPVAATAATGIDAMVHAIEAYTSAHLK 212 Query: 211 -ALTDALHIKAIEIIAGALRGSV--AGDKDAGEEMALGQYVAGMGFSNVGLGLVHGMAHP 267 ++D L IKA+E+++ L + ++DA E M LG AG F+N + VH +A+P Sbjct: 213 NPVSDMLAIKALELLSRNLLPACEDGNNRDAREAMLLGATFAGQAFANSPVAAVHALAYP 272 Query: 268 LGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVKVEGMSLEEARNAAVEAVF 327 +G Y+ PHG++NA++LPHV+R+NAD + Y ++A V+ G S + A +E + Sbjct: 273 IGGIYHVPHGLSNALVLPHVLRFNADSAADLYAELADVVVPGTTG-SARDKTQALIENLE 331 Query: 328 ALNRDVGIPPHLRDVGVRKEDIPALA-QAALDDVCTGGNPREATLEDIVELYHTAW 382 + + IP LRDVG+ +E + +A A L NPR + D + +Y+ A+ Sbjct: 332 RMIAETAIPARLRDVGIEREGLGRMASDAMLQTRLLVNNPRPVSEADALAIYNAAF 387 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: 389 Number of extensions: 19 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: 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