Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate Synpcc7942_0459 Synpcc7942_0459 glutathione-dependent formaldehyde dehydrogenase
Query= BRENDA::Q97YM2 (349 letters) >FitnessBrowser__SynE:Synpcc7942_0459 Length = 369 Score = 118 bits (296), Expect = 2e-31 Identities = 116/380 (30%), Positives = 180/380 (47%), Gaps = 50/380 (13%) Query: 7 VKSKAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPI 66 +KS+AA+ +PL+IE+V++ PQ EV++++ GVC TD G + + F P Sbjct: 1 MKSRAAIAWAAGQPLTIEEVDVQAPQAGEVMVKLVATGVCHTDAFTLSGADPEGIF--PC 58 Query: 67 ILGHENAGTIVEVGE-LAKVKKGDNVVVYATWGDLTCRYCREGKFNICK-------NQII 118 ILGHE AG +VEVGE + V GD+V+ T C++C+ GK N+C+ ++ Sbjct: 59 ILGHEGAGIVVEVGEGVTSVAVGDHVIPLYTPECGECKFCKSGKTNLCQAIRATQGKGLM 118 Query: 119 PGQTT----NG----------GFSEYMLVKSSRWLVKLNSLSPVEAAPLADAG-TTSMGA 163 P T+ NG FSEY ++ + K+N + ++ L G TT +GA Sbjct: 119 PDGTSRFSLNGQPIYHFMGTSTFSEYTVLPEIA-IAKINPAAALDKVCLLGCGITTGIGA 177 Query: 164 IRQALPFISKFAEP--VVIVNGIGGLAVYTIQILKALMKNITIVGISRSKKHRDFALELG 221 + EP V V G+GG+ + IQ L K I+ I + +FA +LG Sbjct: 178 VLNTAK-----VEPGSTVAVFGLGGVGLSVIQ-GAVLAKASRILAIDINPDKAEFAKQLG 231 Query: 222 ADYVSEMKD----AESLINKLTDGLGASIAIDLVGTEETTYNLGKLLAQ---EGAIILVG 274 A KD + +I +LTDG G + + +G T + + E II V Sbjct: 232 ATDFINPKDYDRPIQEVIVELTDG-GVDYSFEAIGNVNTMRAALESCHKGWGESTIIGVA 290 Query: 275 MEGKRVSLEAFDTA---VWNKKLLGSNYGSLNDLEDVVRLSESGKIK--PYIIKV-PLDD 328 G+ +S F VW G G + L V +G+IK ++ + PL++ Sbjct: 291 GAGQEISTRPFQLVTGRVWRGSAFGGVKGR-SQLPGYVEQYLNGQIKVDEFVTETRPLEE 349 Query: 329 INKAFTNLDEGRVDGRQVIT 348 IN+AF ++ G+V R VIT Sbjct: 350 INEAFEDMHAGKVI-RTVIT 368 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: 322 Number of extensions: 23 Number of successful extensions: 4 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: 369 Length adjustment: 29 Effective length of query: 320 Effective length of database: 340 Effective search space: 108800 Effective search space used: 108800 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