Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate H281DRAFT_05508 H281DRAFT_05508 Alcohol dehydrogenase, class IV
Query= SwissProt::P0A9S1 (382 letters) >FitnessBrowser__Burk376:H281DRAFT_05508 Length = 383 Score = 192 bits (488), Expect = 1e-53 Identities = 116/368 (31%), Positives = 199/368 (54%), Gaps = 10/368 (2%) Query: 16 GAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPTITV 75 G + + ++ G L+V+D+ + G++ + +G+A + V +P+ Sbjct: 17 GVAARIGEVLEPLGVNSVLLVSDRGVKNAGLLEAPMAHLRTSGIAVECFFDVEADPSAAT 76 Query: 76 VKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSVPIL 135 V+ + ++SG D ++AIGGGSP D K +++ + D+ + G+ T P + ++ Sbjct: 77 VQAAAQLARSSGVDCVVAIGGGSPMDVAKLAALLAKSG--VDLEDIYGIHKTEGPRLRLV 134 Query: 136 AIPTTAGTAAEVT-INYVITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPPALKAATGV 194 +PTTAGT +E T I+ V T +++ VC P +P +A +DA++ G+P + AATG+ Sbjct: 135 LVPTTAGTGSEATPISIVTTGAGEKKGVVC--PVLLPDIAVLDAELTIGLPKHVSAATGI 192 Query: 195 DALTHAIEGYITRGAW-ALTDALHIKAIEIIAGALRGSVAG--DKDAGEEMALGQYVAGM 251 DA+ HAIE Y +R L+D L +A+ ++ L A D + + M LG +AGM Sbjct: 193 DAMVHAIEAYTSRSLKNPLSDCLAREALRLLGPHLERVCAQGHDVETRQAMLLGANLAGM 252 Query: 252 GFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVKVE 311 F+N + VH +A+P+GA ++ PHG++N+++LP V+R+N Y ++A ++ Sbjct: 253 AFANAPVAAVHALAYPIGARFHVPHGLSNSLMLPAVLRFNMTSAESLYAELASLLVPNAI 312 Query: 312 GMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALA-QAALDDVCTGGNPREAT 370 G S EE A + + L +G+P LRDVG+ ED+P LA A NPRE Sbjct: 313 G-SPEELTRALLAYLTELPVKLGLPVRLRDVGITAEDLPDLAIDAMKQSRLLVNNPREVG 371 Query: 371 LEDIVELY 378 +D + +Y Sbjct: 372 YDDALAMY 379 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: 396 Number of extensions: 27 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: 383 Length adjustment: 30 Effective length of query: 352 Effective length of database: 353 Effective search space: 124256 Effective search space used: 124256 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