Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate Ga0059261_0846 Ga0059261_0846 Zn-dependent alcohol dehydrogenases, class III
Query= BRENDA::C7R702 (374 letters) >FitnessBrowser__Korea:Ga0059261_0846 Length = 361 Score = 256 bits (655), Expect = 5e-73 Identities = 144/371 (38%), Positives = 213/371 (57%), Gaps = 17/371 (4%) Query: 9 KAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGVFPSILGHE 68 KAAV +EA +PL I ++ + P EV ++ A GVC +D + G P V P+I GHE Sbjct: 2 KAAVLFEAKRPLEIHDITIDKPGPREVLIRTAACGVCRSDLHFVDGAYPH-VMPTIPGHE 60 Query: 69 GGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLC-----QKIRETQGKGLM 123 G+VE+VG VT ++PGDHVI +T CG C+FC+SG+ +LC ++ +E + K + Sbjct: 61 ASGVVEAVGSEVTRLRPGDHVITFFTVFCGSCEFCVSGRPSLCVDGSTKRPKEGEPKLRL 120 Query: 124 PDGTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGMGAV 183 PDGT PI ++ S F+E ++ E + ++ PL+ LLGC V TG GA+ Sbjct: 121 PDGT--------PIAQFLNLSAFAEQMLVHENACVAISKDMPLDRAALLGCAVITGAGAI 172 Query: 184 MNTAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDCVNP 243 +KV G TVA+ G GGIGLSAV A +A A +IIAID K E+A+K+GAT + Sbjct: 173 FRDSKVTPGETVAVIGCGGIGLSAVNAAKIAGAGKIIAIDPVPEKREIARKMGATHVFDA 232 Query: 244 KDYDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEIST 303 D + + + ++TDGGVDY+ E +G N A +G G + I+G+ GQ +S Sbjct: 233 MADD--LVKQVAKLTDGGVDYAIEAVGRPNTAELAWNLLRRG-GTATILGMIAPGQSVSI 289 Query: 304 RPFQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFDLMH 363 +TG+ +G+ G ++ +LP V+ YL G LD + + LE IN AFD + Sbjct: 290 PGPTFLTGKKLQGSLLGSMRFPVDLPRLVQMYLDGLLDLDTMVAERIRLEDINHAFDNLR 349 Query: 364 EGKSIRSVIHY 374 +G ++RSVI + Sbjct: 350 KGDAVRSVIEF 360 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: 369 Number of extensions: 22 Number of successful extensions: 6 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: 361 Length adjustment: 30 Effective length of query: 344 Effective length of database: 331 Effective search space: 113864 Effective search space used: 113864 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