Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate WP_054343403.1 Nant_RS19780 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
Query= BRENDA::C7R702 (374 letters) >NCBI__GCF_001305295.1:WP_054343403.1 Length = 376 Score = 685 bits (1767), Expect = 0.0 Identities = 327/374 (87%), Positives = 355/374 (94%) Query: 1 MSNEVIKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGV 60 M+N+ IK KAA+AW +PLSIEEV+V PPQKGEVRV+IVA+GVCHTDAFTLSGDDPEG+ Sbjct: 1 MNNKTIKSKAAIAWGPNQPLSIEEVDVMPPQKGEVRVRIVASGVCHTDAFTLSGDDPEGI 60 Query: 61 FPSILGHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRETQGK 120 FP+ILGHEG GIVES+GEGVTSV GDHVIPLYTPECG+CKFC SGKTNLCQKIRETQGK Sbjct: 61 FPAILGHEGAGIVESIGEGVTSVAVGDHVIPLYTPECGECKFCKSGKTNLCQKIRETQGK 120 Query: 121 GLMPDGTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGM 180 GLMPDGTTRF +G+PI+HYMG STFSEYTVLPEISLAKVN APLEE+CLLGCGVTTGM Sbjct: 121 GLMPDGTTRFHKDGQPIFHYMGCSTFSEYTVLPEISLAKVNKDAPLEEICLLGCGVTTGM 180 Query: 181 GAVMNTAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDC 240 GAVMNTAKVEEGATVAIFG+GGIGLSA+IGA MAKASRIIAIDINESKFELA+KLGATDC Sbjct: 181 GAVMNTAKVEEGATVAIFGIGGIGLSAIIGATMAKASRIIAIDINESKFELARKLGATDC 240 Query: 241 VNPKDYDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQE 300 +NPKDYDKPIQ+VIVE+TDGGVDYSFECIGNVNVMRSALECCHKGWGESV+IGVAGAGQE Sbjct: 241 INPKDYDKPIQDVIVELTDGGVDYSFECIGNVNVMRSALECCHKGWGESVVIGVAGAGQE 300 Query: 301 ISTRPFQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFD 360 ISTRPFQLVTGRVW+G+AFGGVKGRSELPD+VERY+ GEFKLDDFITHTM LE+IN AFD Sbjct: 301 ISTRPFQLVTGRVWRGSAFGGVKGRSELPDFVERYMKGEFKLDDFITHTMTLEEINTAFD 360 Query: 361 LMHEGKSIRSVIHY 374 LMHEGKSIRSVIH+ Sbjct: 361 LMHEGKSIRSVIHF 374 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: 653 Number of extensions: 16 Number of successful extensions: 2 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: 376 Length adjustment: 30 Effective length of query: 344 Effective length of database: 346 Effective search space: 119024 Effective search space used: 119024 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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