Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate Synpcc7942_0459 Synpcc7942_0459 glutathione-dependent formaldehyde dehydrogenase
Query= BRENDA::C7R702 (374 letters) >FitnessBrowser__SynE:Synpcc7942_0459 Length = 369 Score = 606 bits (1562), Expect = e-178 Identities = 286/369 (77%), Positives = 331/369 (89%) Query: 6 IKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGVFPSIL 65 +K +AA+AW AG+PL+IEEV+VQ PQ GEV VK+VATGVCHTDAFTLSG DPEG+FP IL Sbjct: 1 MKSRAAIAWAAGQPLTIEEVDVQAPQAGEVMVKLVATGVCHTDAFTLSGADPEGIFPCIL 60 Query: 66 GHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRETQGKGLMPD 125 GHEG GIV VGEGVTSV GDHVIPLYTPECG+CKFC SGKTNLCQ IR TQGKGLMPD Sbjct: 61 GHEGAGIVVEVGEGVTSVAVGDHVIPLYTPECGECKFCKSGKTNLCQAIRATQGKGLMPD 120 Query: 126 GTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGMGAVMN 185 GT+RFS+NG+PIYH+MGTSTFSEYTVLPEI++AK+NP A L++VCLLGCG+TTG+GAV+N Sbjct: 121 GTSRFSLNGQPIYHFMGTSTFSEYTVLPEIAIAKINPAAALDKVCLLGCGITTGIGAVLN 180 Query: 186 TAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDCVNPKD 245 TAKVE G+TVA+FGLGG+GLS + GAV+AKASRI+AIDIN K E AK+LGATD +NPKD Sbjct: 181 TAKVEPGSTVAVFGLGGVGLSVIQGAVLAKASRILAIDINPDKAEFAKQLGATDFINPKD 240 Query: 246 YDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEISTRP 305 YD+PIQEVIVE+TDGGVDYSFE IGNVN MR+ALE CHKGWGES IIGVAGAGQEISTRP Sbjct: 241 YDRPIQEVIVELTDGGVDYSFEAIGNVNTMRAALESCHKGWGESTIIGVAGAGQEISTRP 300 Query: 306 FQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFDLMHEG 365 FQLVTGRVW+G+AFGGVKGRS+LP YVE+YL G+ K+D+F+T T PLE+IN+AF+ MH G Sbjct: 301 FQLVTGRVWRGSAFGGVKGRSQLPGYVEQYLNGQIKVDEFVTETRPLEEINEAFEDMHAG 360 Query: 366 KSIRSVIHY 374 K IR+VI + Sbjct: 361 KVIRTVITF 369 Lambda K H 0.317 0.137 0.413 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: 571 Number of extensions: 13 Number of successful extensions: 1 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: 374 Length of database: 369 Length adjustment: 30 Effective length of query: 344 Effective length of database: 339 Effective search space: 116616 Effective search space used: 116616 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