Align Alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate N515DRAFT_2489 N515DRAFT_2489 alcohol dehydrogenase, propanol-preferring
Query= reanno::Cup4G11:RR42_RS34260 (342 letters) >FitnessBrowser__Dyella79:N515DRAFT_2489 Length = 343 Score = 546 bits (1406), Expect = e-160 Identities = 261/342 (76%), Positives = 294/342 (85%) Query: 1 MTAMMKAAVVREFGAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLP 60 M+ MKAAVVR FG PL+IDEVPVP PG G++ VKIEA GVCHTDLHA +GDWPVKP P Sbjct: 1 MSKTMKAAVVRAFGQPLSIDEVPVPTPGLGEVLVKIEACGVCHTDLHAVDGDWPVKPKPP 60 Query: 61 FIPGHEGVGYVSAVGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSV 120 FIPGHEGVGYV A+G GV+ +KEGDRVG+PWLYSACG+CEHCL GWETLCE QQNTGYSV Sbjct: 61 FIPGHEGVGYVVAIGPGVTHLKEGDRVGIPWLYSACGHCEHCLGGWETLCESQQNTGYSV 120 Query: 121 NGGYGEYVVADPNYVGLLPDSVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGL 180 NGG+ EY +A +YVG LPD +GFVEIAP+LCAGVTVYKGLKVTDTRPG WVVISGIGGL Sbjct: 121 NGGFAEYALAAADYVGHLPDGIGFVEIAPVLCAGVTVYKGLKVTDTRPGNWVVISGIGGL 180 Query: 181 GHVAVQYARAMGLRVAAVDIDDKKLELARKLGAEVTVNARTTDPVAFLQKEIGGAHGALV 240 GH+AVQYA AMGL VAAVDIDD KL+LAR+LGA++ +NAR DPVA ++KEIGGAHGALV Sbjct: 181 GHMAVQYAAAMGLNVAAVDIDDAKLDLARRLGAQLIINARHADPVAVVKKEIGGAHGALV 240 Query: 241 TAVSPKAFGQAIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSDLQESL 300 TAVSPKAFGQA+ MVRRGGT++LNGLPPG F IFD+VL G+T+RGSIVGTR DLQESL Sbjct: 241 TAVSPKAFGQAMNMVRRGGTVSLNGLPPGSFDLSIFDMVLNGVTVRGSIVGTRLDLQESL 300 Query: 301 DFAAHGAVKATVSTAPLEKINEIFTRMRAGDIEGRVVMDFAA 342 DFA G VKATV+T LE INE+F RM G IEGRVV+D A+ Sbjct: 301 DFAKAGKVKATVTTDRLENINEVFRRMHQGQIEGRVVLDMAS 342 Lambda K H 0.319 0.138 0.420 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: 457 Number of extensions: 15 Number of successful extensions: 1 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: 342 Length of database: 343 Length adjustment: 29 Effective length of query: 313 Effective length of database: 314 Effective search space: 98282 Effective search space used: 98282 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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