Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate AZOBR_RS25910 AZOBR_RS25910 oxidoreductase
Query= BRENDA::A0A075B5H4 (258 letters) >FitnessBrowser__azobra:AZOBR_RS25910 Length = 257 Score = 188 bits (478), Expect = 8e-53 Identities = 111/255 (43%), Positives = 148/255 (58%), Gaps = 8/255 (3%) Query: 4 DLKGKRILITGSTEGIGMATAIELARYGAVVGLNSHVDPADPALLLGKLREAGGDGAF-F 62 DL+GKR+L+TGS+ GIG A A GA V L+ D A L AGG + Sbjct: 7 DLRGKRVLVTGSSRGIGAAVGTAFASLGARVALHGS-GGNDAAARLALALTAGGTEVYAV 65 Query: 63 RADITKTAECQRLVSAFVERFDGIDVLINNAGGLAGRSNLENIDDAFYDRVMDLNGRSVL 122 D + V A V+ G+D+L+NNAG + GR LE I D F D V+DLN RSV+ Sbjct: 66 TGDFRDPRAVESAVDAAVQALGGLDILVNNAGTMVGRVPLERIGDDFLDEVIDLNLRSVV 125 Query: 123 MMTKFAIPHLRASAKASGTTSAVISTGSIAAREGGGIGAGVYAASKAWLHDIHRNWVKEF 182 + + A+P LRAS A+++T SI+AR GG G+ +Y+ASKA++ R+ E Sbjct: 126 VACRRALPALRASG-----GGAIVNTVSISARTGGSPGSSIYSASKAFVSTFTRSLAAEL 180 Query: 183 TKDSIRFNIVAPGTVDTAFHAD-KSDELKTRIANSIPMGRFGTVQELAPAYVFFASHAAS 241 D IR N V+PGT+DT FH S E A IP+GR GT ++ AY+F AS A S Sbjct: 181 APDRIRVNAVSPGTIDTDFHQRYSSPEKLAATAARIPLGRLGTAEDCVGAYLFLASEALS 240 Query: 242 GYITGQILDVNGGQI 256 GYITGQ+++VNGGQ+ Sbjct: 241 GYITGQVIEVNGGQL 255 Lambda K H 0.320 0.136 0.397 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: 187 Number of extensions: 9 Number of successful extensions: 3 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: 258 Length of database: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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