Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate 201211 SO2054 alcohol dehydrogenase class III (NCBI ptt file)
Query= BRENDA::C7R702 (374 letters) >FitnessBrowser__MR1:201211 Length = 379 Score = 665 bits (1716), Expect = 0.0 Identities = 326/377 (86%), Positives = 351/377 (93%), Gaps = 3/377 (0%) Query: 1 MSNE---VIKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDP 57 MSNE IK KAAVAW +PL IEEV+V P+ GEV V+IVATGVCHTDAFTLSGDDP Sbjct: 1 MSNEKPQFIKSKAAVAWGPRQPLKIEEVDVMLPKAGEVLVRIVATGVCHTDAFTLSGDDP 60 Query: 58 EGVFPSILGHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRET 117 EGVFP+ILGHEGGGIVE VGEGVTSV+ GDHVIPLYTPECG+CKFCLSGKTNLCQKIR T Sbjct: 61 EGVFPAILGHEGGGIVEQVGEGVTSVQVGDHVIPLYTPECGECKFCLSGKTNLCQKIRAT 120 Query: 118 QGKGLMPDGTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVT 177 QGKGLMPDGTTRF +G+PI+HYMG STFSEYTVLPEISLAKVN APL+E+CLLGCGVT Sbjct: 121 QGKGLMPDGTTRFYKDGQPIFHYMGCSTFSEYTVLPEISLAKVNKTAPLKEICLLGCGVT 180 Query: 178 TGMGAVMNTAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGA 237 TGMGAVMNTAKVE GATVAIFGLGGIGLSA+IGA MAKASRIIAIDINESKFELA+KLGA Sbjct: 181 TGMGAVMNTAKVEAGATVAIFGLGGIGLSAIIGATMAKASRIIAIDINESKFELARKLGA 240 Query: 238 TDCVNPKDYDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGA 297 TDC+NPK++DKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGA Sbjct: 241 TDCINPKNFDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGA 300 Query: 298 GQEISTRPFQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKIND 357 GQEISTRPFQLVTGRVW+G+AFGGVKGRS+LP VE+YLAGEFKLDDFITHTM LE++N+ Sbjct: 301 GQEISTRPFQLVTGRVWRGSAFGGVKGRSQLPKIVEQYLAGEFKLDDFITHTMGLEQVNE 360 Query: 358 AFDLMHEGKSIRSVIHY 374 AFDLMHEGKSIRSVIH+ Sbjct: 361 AFDLMHEGKSIRSVIHF 377 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: 645 Number of extensions: 17 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: 379 Length adjustment: 30 Effective length of query: 344 Effective length of database: 349 Effective search space: 120056 Effective search space used: 120056 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 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