Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate HSERO_RS04830 HSERO_RS04830 alcohol dehydrogenase
Query= BRENDA::Q97YM2 (349 letters) >FitnessBrowser__HerbieS:HSERO_RS04830 Length = 341 Score = 134 bits (336), Expect = 4e-36 Identities = 104/344 (30%), Positives = 169/344 (49%), Gaps = 17/344 (4%) Query: 10 KAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPIILG 69 KAA++++F +PLSIE V +P P ++L++ +GVC TDL G + P I G Sbjct: 6 KAAVVREFGKPLSIEQVPVPTPAPGQILVKFEASGVCHTDLHAAHGDWPVKPTP-PFIPG 64 Query: 70 HENAGTIVEVGELAK-VKKGDNVVV---YATWGDLTCRYCREGKFNICKNQIIPGQTTNG 125 HE G + VG K VK+GD V V + G C CR G +C Q G + NG Sbjct: 65 HEGTGYVAAVGAGVKHVKEGDRVGVPWLHTACG--CCSPCRTGWETLCAEQQNTGYSVNG 122 Query: 126 GFSEYMLVKSSRWLVKLNSLSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIG 185 F+EY L ++L AAP+ AG T +++ ++ V+++GIG Sbjct: 123 SFAEYGLADPKFVGHLPDNLDFGPAAPVLCAGVTVYKGLKETEVRPGEW----VVISGIG 178 Query: 186 GLAVYTIQILKALMKNITIVGISRSKKHRDFALELGADYVSEMKDAESL--INKLTDGLG 243 GL +Q KA+ ++ I K A +LGAD + ++ ++ + ++ G Sbjct: 179 GLGHMAVQYAKAMGMHVVAADIHEDKLA--LAKKLGADLTVDGRNHNAVAEVQRIIGGAH 236 Query: 244 ASIAIDLVGTEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSLN 303 ++ + V + G L A+ G + LVG+ +SL F+T + + GS G+ Sbjct: 237 GAL-VTAVSPKAMEQAFGFLRAR-GTMALVGLPPGDISLPVFNTVLKRITVRGSIVGTRQ 294 Query: 304 DLEDVVRLSESGKIKPYIIKVPLDDINKAFTNLDEGRVDGRQVI 347 DLE+ + + GK+ + LD+IN F ++EG++DGR V+ Sbjct: 295 DLEESLVFAAEGKVAAHFTWDKLDNINAIFARMEEGKIDGRIVL 338 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: 290 Number of extensions: 18 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: 341 Length adjustment: 29 Effective length of query: 320 Effective length of database: 312 Effective search space: 99840 Effective search space used: 99840 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