Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate H281DRAFT_01171 H281DRAFT_01171 alcohol dehydrogenase, propanol-preferring
Query= BRENDA::Q97YM2 (349 letters) >FitnessBrowser__Burk376:H281DRAFT_01171 Length = 356 Score = 129 bits (325), Expect = 9e-35 Identities = 106/344 (30%), Positives = 168/344 (48%), Gaps = 23/344 (6%) Query: 20 PLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVE----------AKQGFRLPIILG 69 PL P P+G EV++R+ +G+C TDL +W G +++G P+ LG Sbjct: 12 PLQARLRETPVPKGREVVLRVTHSGLCHTDLHLWHGYFDLGGGRRAPLSERGLVPPLTLG 71 Query: 70 HENAGTIVEVGE-LAKVKKGDNVVVYATWGDLTCRYCREGKFNICKNQIIPGQTTNGGFS 128 HE G + VG+ + V G + + C C +G+ +C Q G GGF+ Sbjct: 72 HEPLGIVEAVGDAVTGVAPGARCLAFPWIACGACWACDKGRTELCARQRNLGIGLPGGFA 131 Query: 129 EYMLVKSSRWLVKLNSLSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIGGLA 188 +++V +R+LV ++ + AA LA +G TS A+ + LP + A+ V V G GG+ Sbjct: 132 THLVVPDARYLVNVDGIDDAFAATLACSGVTSYAAVSK-LPTLE--ADDHVAVIGCGGVG 188 Query: 189 VYTIQILKALMKNI-TIVGISRSKKHRDFALELGADYVSEMKDAE---SLINKLTDGLGA 244 + I IL+A + I I+ S++ + A LGA AE +L+ + LG Sbjct: 189 LTAISILRA--RGIERIIACDVSEEKLEAARSLGAAQALRTDSAEAAQALMELAGNMLGG 246 Query: 245 SIAIDLVGTEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSLND 304 A+D VG T L + G +L G+ G + ++ A + ++GS GS+ D Sbjct: 247 --ALDFVGIPSTLDLAYTALRKGGTYVLCGLHGGQATIPIPPIAQRSLSIVGSFVGSIAD 304 Query: 305 LEDVVRLSESGKIKPYIIKV-PLDDINKAFTNLDEGRVDGRQVI 347 LE V L+++GK+ I+ +IN A + LD GRV GR VI Sbjct: 305 LEATVELAKAGKLARLPIQTCDAREINTALSALDAGRVIGRTVI 348 Lambda K H 0.317 0.136 0.389 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: 277 Number of extensions: 16 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: 349 Length of database: 356 Length adjustment: 29 Effective length of query: 320 Effective length of database: 327 Effective search space: 104640 Effective search space used: 104640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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