Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_057508430.1 ABB28_RS09665 NAD(P)-dependent alcohol dehydrogenase
Query= BRENDA::Q8H0L8 (359 letters) >NCBI__GCF_001431535.1:WP_057508430.1 Length = 350 Score = 338 bits (866), Expect = 2e-97 Identities = 177/346 (51%), Positives = 228/346 (65%), Gaps = 6/346 (1%) Query: 13 AFGWATRHTSGVLSPFNFSRRVTGEKHVQFKVMYCGICHSDLHQLKNEWGNTKYPMVPGH 72 A +A T+ L PF F RR V+ +++Y GICHSDLHQ +++WG KYPMVPGH Sbjct: 4 AKAYAAHSTTAPLVPFTFERRAVAAGDVRIEILYSGICHSDLHQARDDWGGAKYPMVPGH 63 Query: 73 EVVGVVIEVGSKVEKFKVGDKVGVGCMVGSCRKCENCTVDLENYCPR-QIPTYNGYSL-D 130 E++G V+EVG++V K KVGD GVGCMV SCR CE C DLE YC TYNG Sbjct: 64 EIIGKVVEVGAEVTKLKVGDFAGVGCMVDSCRHCEACNADLEQYCAEGSTFTYNGTDRHT 123 Query: 131 GTLTFGGYSDMMVSDEHFVVRWPENLSMD-AAPLLCAGITTYSPLKYFGLDKPGMHIGVV 189 G T GGYSD +V ++ FVV+ E L + AAPLLCAGITTYSPLK+F + PG +GV+ Sbjct: 124 GEPTQGGYSDHIVVEQRFVVKVSETLDLKAAAPLLCAGITTYSPLKHFKVG-PGQKVGVI 182 Query: 190 GLGGLGHMAVKFAKAFGTKVTVISTSANKKQEAIERLGADSFLISRDPEQMKAAMNTLDG 249 GLGGLGHM VKFAKA G V +I+T+ K +A RLGAD L+SRDPEQMKA + D Sbjct: 183 GLGGLGHMGVKFAKALGAHVVMITTTPEKGADA-TRLGADEVLVSRDPEQMKAHAGSFDF 241 Query: 250 IIDTVSAVHPILPLLMLMKSHGKLVMVGA-PEKPVELPVFPLLMGRKLVAGSCIGGMKET 308 +++T+ H P + L+K + +VG E L ++ GRK + GS IGGM ET Sbjct: 242 LLNTIPVGHDTNPYMGLLKRDATMCLVGVLTELDPPLTGVSVIFGRKHLTGSAIGGMAET 301 Query: 309 QEMLDFAAKHNITPDIEVVPMDYVNTALERLLKSDVKYRFVLDIGN 354 QEM+DF A+H I D+EV+ + VN A ER+ K+DV+YRFV+D+ + Sbjct: 302 QEMMDFCAEHGIVSDVEVINIQDVNEAWERMAKNDVRYRFVIDMAS 347 Lambda K H 0.320 0.137 0.417 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: 364 Number of extensions: 25 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: 359 Length of database: 350 Length adjustment: 29 Effective length of query: 330 Effective length of database: 321 Effective search space: 105930 Effective search space used: 105930 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: 49 (23.5 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