Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate SMa1296 SMa1296 alcohol dehydrogenase
Query= BRENDA::Q8L3C9 (344 letters) >FitnessBrowser__Smeli:SMa1296 Length = 340 Score = 451 bits (1160), Expect = e-131 Identities = 217/337 (64%), Positives = 268/337 (79%) Query: 5 TMKAAVIREFGSLLKIEEVEVKRPGRNEILVKVIASGVCHTDLHAVEGDWPVKPKMPLIP 64 TM AAV+REFG L IEEV V +PG ++L+K A+GVCHTDLHA +GDWPV+P P IP Sbjct: 2 TMTAAVVREFGKPLVIEEVPVPQPGPGQVLIKYEATGVCHTDLHAAKGDWPVRPNPPFIP 61 Query: 65 GHEAVGYVVAVGQEVKNVKEGDAVGVPWLYSACGGCDQCITGWETLCDTQQNGGYSVDGG 124 GHE VGYV +G EV +KEGD VGVPWL++ACG C C TGWETLC +QQN GYSVDG Sbjct: 62 GHEGVGYVAKLGAEVTRLKEGDRVGVPWLHTACGCCTPCRTGWETLCGSQQNTGYSVDGT 121 Query: 125 FAEYVIADARYVGLLPSNVNFMEMAPILCAGVTVYKGLKETEVKPGEWVAISGIGGLGHV 184 FA+Y +AD +VG LP+ + F AP+LCAGVTVYKGLKETEV+PGEWV +SGIGGLGH+ Sbjct: 122 FAQYGLADPDFVGRLPARLEFGPAAPVLCAGVTVYKGLKETEVRPGEWVLVSGIGGLGHM 181 Query: 185 AVQYAKAMGMHVAAIDVADDKLDLAKKLGADLVVNAKNQNPGEFLKKEVGGMHGALITAV 244 AVQYAKAMGMHVAA D+ DKL LA+KLGADLVV+A+ + E +++ GG+HGAL+TAV Sbjct: 182 AVQYAKAMGMHVAAADIFPDKLALAEKLGADLVVDARAPDAVEEVQRRTGGLHGALVTAV 241 Query: 245 SPIAFKQGLETLRRKGTMALNGLPPGNFDLSIFDTVLNRITIRGSIVGTRKDMKEAIEFA 304 SP A +Q LR KGTMAL GLPPG L +FDTVL RIT+RGSIVGTR+D++EA+EFA Sbjct: 242 SPKAMEQAYSMLRSKGTMALVGLPPGQICLPVFDTVLKRITVRGSIVGTRQDLEEALEFA 301 Query: 305 VEGKVKATVTPAKLENINEVFDKMKKGQIEGRVVLEI 341 EGKV A + K+ENIN +F++M++G+I+GR+VL++ Sbjct: 302 GEGKVAAHFSWDKIENINAIFERMEEGKIDGRIVLDL 338 Lambda K H 0.318 0.137 0.404 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: 415 Number of extensions: 8 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: 344 Length of database: 340 Length adjustment: 29 Effective length of query: 315 Effective length of database: 311 Effective search space: 97965 Effective search space used: 97965 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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