Align alcohol dehydrogenase (EC 1.1.1.1); aryl-alcohol dehydrogenase (EC 1.1.1.90); aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) (characterized)
to candidate WP_043769493.1 U743_RS15500 NAD(P)-dependent alcohol dehydrogenase
Query= BRENDA::W6CX26 (339 letters) >NCBI__GCF_000733765.1:WP_043769493.1 Length = 338 Score = 373 bits (957), Expect = e-108 Identities = 182/335 (54%), Positives = 237/335 (70%), Gaps = 2/335 (0%) Query: 1 MSIIKSYAAKEAGSELELYEYDAGELRPEDVEVQVDYCGICHSDLSMIDNEWGFSQYPLV 60 M+ I+++AA+ AG LE ++YDAG L + VE+ V++CG+CHSDLSM+DNEWG SQYPLV Sbjct: 1 MTQIRAWAAQTAGGALEEWQYDAGPLADDGVEIAVEHCGLCHSDLSMLDNEWGQSQYPLV 60 Query: 61 AGHEVIGRVAALGSAAQEKGVKVGQRVGVGWTARSCGHCDACISGNQINCLEGAVATILN 120 GHEV+GRV ALG A +G++VGQRVG+GW A SC HC C G+ C I Sbjct: 61 PGHEVVGRVRALGRDA--RGLEVGQRVGLGWIAGSCLHCRPCTGGDHHLCPSVEGTIIGR 118 Query: 121 RGGFAEKLRADWQWVIPLPESIDIESAGPLLCGGITVFKPLLMHHITATSRVGVIGIGGL 180 GGFAE +RA W+WV PLPE++ GPL CGGITVF PL I T RVGV+GIGGL Sbjct: 119 HGGFAEAVRAHWRWVTPLPEALAPAEVGPLFCGGITVFSPLREFGIRPTDRVGVVGIGGL 178 Query: 181 GHIAIKLLHAMGCEVTAFSSNPSKEQEVLAMGADKVVNSRDPDALNALAGQFDLIINTVN 240 GH+A++ A GCEVTAF+S+P+K +E MGA +VV+S D AL A AG+FDLI+ TVN Sbjct: 179 GHLALQFARAWGCEVTAFTSSPAKAEEARKMGAHEVVDSTDDAALKACAGRFDLILVTVN 238 Query: 241 VDLDWQPYFEALAYGGHFHTVGAVMKPLPVPAFTLIAGDRSISGSATGTPYELRKLMKFA 300 L W+ Y ALA G H VGAV++P+ V F L+ RS+S S TG+P + ++ FA Sbjct: 239 ATLPWKRYISALAPRGRLHFVGAVLEPVQVTVFQLLGAQRSVSASPTGSPAAIADMLDFA 298 Query: 301 GRSKVSPTTELFPMSQINEAIQHVRDGKARYRVVL 335 R ++PTTE FP++++N+AIQH+RDGKARYRV++ Sbjct: 299 ARHDIAPTTEHFPVARVNDAIQHLRDGKARYRVIV 333 Lambda K H 0.320 0.137 0.415 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: 329 Number of extensions: 13 Number of successful extensions: 2 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: 339 Length of database: 338 Length adjustment: 28 Effective length of query: 311 Effective length of database: 310 Effective search space: 96410 Effective search space used: 96410 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