Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate SMa1296 SMa1296 alcohol dehydrogenase
Query= BRENDA::Q97YM2 (349 letters) >FitnessBrowser__Smeli:SMa1296 Length = 340 Score = 136 bits (343), Expect = 7e-37 Identities = 107/345 (31%), Positives = 177/345 (51%), Gaps = 21/345 (6%) Query: 11 AALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPIILGH 70 AA++++F +PL IE+V +P+P +VLI+ GVC TDL KG + P I GH Sbjct: 5 AAVVREFGKPLVIEEVPVPQPGPGQVLIKYEATGVCHTDLHAAKGDWPVRP-NPPFIPGH 63 Query: 71 ENAGTIVEVG-ELAKVKKGDNVVV---YATWGDLTCRYCREGKFNICKNQIIPGQTTNGG 126 E G + ++G E+ ++K+GD V V + G C CR G +C +Q G + +G Sbjct: 64 EGVGYVAKLGAEVTRLKEGDRVGVPWLHTACG--CCTPCRTGWETLCGSQQNTGYSVDGT 121 Query: 127 FSEYMLVKSSRWLVKLNS-LSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIG 185 F++Y L ++ +L + L AAP+ AG T +++ ++ V+V+GIG Sbjct: 122 FAQYGLADPD-FVGRLPARLEFGPAAPVLCAGVTVYKGLKETEVRPGEW----VLVSGIG 176 Query: 186 GLAVYTIQILKALMKNITIVGISRSKKHRDFALELGADYVSEMK--DAESLINKLTDGL- 242 GL +Q KA+ ++ I K A +LGAD V + + DA + + T GL Sbjct: 177 GLGHMAVQYAKAMGMHVAAADIFPDKLA--LAEKLGADLVVDARAPDAVEEVQRRTGGLH 234 Query: 243 GASIAIDLVGTEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSL 302 GA + E Y++ L +G + LVG+ ++ L FDT + + GS G+ Sbjct: 235 GALVTAVSPKAMEQAYSM---LRSKGTMALVGLPPGQICLPVFDTVLKRITVRGSIVGTR 291 Query: 303 NDLEDVVRLSESGKIKPYIIKVPLDDINKAFTNLDEGRVDGRQVI 347 DLE+ + + GK+ + +++IN F ++EG++DGR V+ Sbjct: 292 QDLEEALEFAGEGKVAAHFSWDKIENINAIFERMEEGKIDGRIVL 336 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: 340 Length adjustment: 29 Effective length of query: 320 Effective length of database: 311 Effective search space: 99520 Effective search space used: 99520 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