Align Alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 3607519 Dshi_0931 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= reanno::Cup4G11:RR42_RS34260 (342 letters) >FitnessBrowser__Dino:3607519 Length = 339 Score = 426 bits (1095), Expect = e-124 Identities = 221/337 (65%), Positives = 250/337 (74%), Gaps = 2/337 (0%) Query: 3 AMMKAAVVREFGAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLPFI 62 +MMKAA+V +F PL I EV P G I VKIEA GVCHTDLHAA GDWPVKP PFI Sbjct: 2 SMMKAALVTDFSKPLEIREVRKPTVTDGNILVKIEACGVCHTDLHAARGDWPVKPEPPFI 61 Query: 63 PGHEGVGYVSAVGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQ-QNTGYSVN 121 PGHEGVG V VG V+ VKEGDRVGVPWL+ ACG+C C+ GWETLC + + TGY+VN Sbjct: 62 PGHEGVGVVVEVGHNVTSVKEGDRVGVPWLHHACGHCTACVTGWETLCRTEPEYTGYTVN 121 Query: 122 GGYGEYVVADPNYVGLLPDSVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGLG 181 GG+ EYV ADP YVG LPD + F APILCAGVTVYKGLK D PGQ VVISGIGGLG Sbjct: 122 GGFAEYVEADPTYVGHLPDKLDFAPAAPILCAGVTVYKGLKECDLHPGQTVVISGIGGLG 181 Query: 182 HVAVQYARAMGLRVAAVDIDDKKLELARKLGAEVTVNARTTDPVAFLQKEIGGAHGALVT 241 H+AVQYARAMGL V AVD+ + KL LAR LGA V +NA T DPVA + + +GGA G LVT Sbjct: 182 HLAVQYARAMGLHVIAVDVAEDKLALARDLGAGVAINAATQDPVAEVAR-LGGAEGVLVT 240 Query: 242 AVSPKAFGQAIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSDLQESLD 301 AVS AF Q +GM+ GGT++L GLPPGDFP IFDVVL TIRGSIVGTR+DL ESL Sbjct: 241 AVSNTAFSQGVGMLAPGGTMSLVGLPPGDFPLNIFDVVLNRKTIRGSIVGTRADLAESLS 300 Query: 302 FAAHGAVKATVSTAPLEKINEIFTRMRAGDIEGRVVM 338 FAA G V + +T L+ IN IF +M G IEGR+VM Sbjct: 301 FAAEGKVASHYATDSLDNINGIFDQMEQGRIEGRIVM 337 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: 412 Number of extensions: 16 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: 342 Length of database: 339 Length adjustment: 28 Effective length of query: 314 Effective length of database: 311 Effective search space: 97654 Effective search space used: 97654 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