Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043529919.1 JH15_RS10235 SDR family oxidoreductase
Query= BRENDA::A0A075B5H4 (258 letters) >NCBI__GCF_000759345.1:WP_043529919.1 Length = 254 Score = 213 bits (543), Expect = 2e-60 Identities = 107/259 (41%), Positives = 163/259 (62%), Gaps = 6/259 (2%) Query: 1 MFSDLKGKRILITGSTEGIGMATAIELARYGAVVGLNSHVDPADPALLLGKLREAGGDGA 60 MF +L+GKR+LITG++ GIG A A + GA V ++ H + ++ AGG Sbjct: 1 MFDELRGKRVLITGASRGIGAAVAKRMGALGAHVAVHYHSSEGPAKAVCEEIEAAGGKAV 60 Query: 61 FFRADITKTAECQRLVSAFVERFDGIDVLINNAGGLAGRSNLENIDDAFYDRVMDLNGRS 120 + D+++++E R+V + G+D+L+NNAG + GR +L +IDD YDRV+DLN RS Sbjct: 61 CLKGDVSRSSEAVRVVEEAAKALGGLDILVNNAGDMLGRVSLADIDDDHYDRVLDLNVRS 120 Query: 121 VLMMTKFAIPHLRASAKASGTTSAVISTGSIAAREGGGIGAGVYAASKAWLHDIHRNWVK 180 V+ ++ A+P+ R + + +I T SIAAR GGG GAG+YA++K ++ + RN K Sbjct: 121 VIAASRAALPYFRQQGRGN-----IIHTSSIAARNGGGPGAGLYASAKGFVSTLTRNMAK 175 Query: 181 EFTKDSIRFNIVAPGTVDTAFHADKSDELKTRIAN-SIPMGRFGTVQELAPAYVFFASHA 239 E D+IR N VAPGT+ T FH S++ + A +IP GR G+ ++ AY+F A+ A Sbjct: 176 ELAGDNIRVNAVAPGTIATDFHERHSNDAQLEAARATIPQGRLGSAEDCVGAYLFLATDA 235 Query: 240 ASGYITGQILDVNGGQICP 258 S Y+TGQ+++VNGGQ+ P Sbjct: 236 LSDYVTGQVIEVNGGQLMP 254 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: 165 Number of extensions: 6 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: 254 Length adjustment: 24 Effective length of query: 234 Effective length of database: 230 Effective search space: 53820 Effective search space used: 53820 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 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