Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_086509091.1 BZY95_RS06145 SDR family NAD(P)-dependent oxidoreductase
Query= BRENDA::A0A075B5H4 (258 letters) >NCBI__GCF_002151265.1:WP_086509091.1 Length = 254 Score = 230 bits (587), Expect = 2e-65 Identities = 120/259 (46%), Positives = 165/259 (63%), Gaps = 6/259 (2%) Query: 1 MFSDLKGKRILITGSTEGIGMATAIELARYGAVVGLNSHVDPADPALLLGKLREAGGDGA 60 MF + KGKR+L+TG++ GIG A A + GA V ++ H ++ +R AGG+ Sbjct: 1 MFEEWKGKRVLVTGASRGIGAAVARRMGALGASVAVHYHASSEAAEEVVKAIRTAGGEAF 60 Query: 61 FFRADITKTAECQRLVSAFVERFDGIDVLINNAGGLAGRSNLENIDDAFYDRVMDLNGRS 120 D+++++E QR+V ER G+++LINNAG + GR LE IDDA YDRVMDLN RS Sbjct: 61 ALTGDLSRSSEAQRVVDEAAERLGGLELLINNAGDMLGRVALEEIDDAHYDRVMDLNARS 120 Query: 121 VLMMTKFAIPHLRASAKASGTTSAVISTGSIAAREGGGIGAGVYAASKAWLHDIHRNWVK 180 V+M+T+ A+PH R + + VI T SIAAR GGG GAG+YAA+K ++ + RN K Sbjct: 121 VVMVTRAALPHFRHAGGGN-----VIHTTSIAARNGGGPGAGLYAAAKGFVSTLTRNMAK 175 Query: 181 EFTKDSIRFNIVAPGTVDTAFHADKSDELKTRIANS-IPMGRFGTVQELAPAYVFFASHA 239 E + IR N VAPGT+ T FH S+E A + IPMGR GT +E AY+F S + Sbjct: 176 ELAAERIRVNAVAPGTIATDFHVRHSNEAHLATARAGIPMGRLGTAEECVGAYLFLGSES 235 Query: 240 ASGYITGQILDVNGGQICP 258 S Y+TGQ+++VNGGQ+ P Sbjct: 236 LSAYVTGQVIEVNGGQLMP 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: 171 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: 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 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