Align Alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate HSERO_RS04830 HSERO_RS04830 alcohol dehydrogenase
Query= reanno::Cup4G11:RR42_RS34260 (342 letters) >FitnessBrowser__HerbieS:HSERO_RS04830 Length = 341 Score = 477 bits (1227), Expect = e-139 Identities = 233/339 (68%), Positives = 270/339 (79%) Query: 1 MTAMMKAAVVREFGAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLP 60 MT MMKAAVVREFG PL+I++VPVP P GQI VK EASGVCHTDLHAA GDWPVKPT P Sbjct: 1 MTQMMKAAVVREFGKPLSIEQVPVPTPAPGQILVKFEASGVCHTDLHAAHGDWPVKPTPP 60 Query: 61 FIPGHEGVGYVSAVGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSV 120 FIPGHEG GYV+AVGAGV VKEGDRVGVPWL++ACG C C GWETLC +QQNTGYSV Sbjct: 61 FIPGHEGTGYVAAVGAGVKHVKEGDRVGVPWLHTACGCCSPCRTGWETLCAEQQNTGYSV 120 Query: 121 NGGYGEYVVADPNYVGLLPDSVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGL 180 NG + EY +ADP +VG LPD++ F AP+LCAGVTVYKGLK T+ RPG+WVVISGIGGL Sbjct: 121 NGSFAEYGLADPKFVGHLPDNLDFGPAAPVLCAGVTVYKGLKETEVRPGEWVVISGIGGL 180 Query: 181 GHVAVQYARAMGLRVAAVDIDDKKLELARKLGAEVTVNARTTDPVAFLQKEIGGAHGALV 240 GH+AVQYA+AMG+ V A DI + KL LA+KLGA++TV+ R + VA +Q+ IGGAHGALV Sbjct: 181 GHMAVQYAKAMGMHVVAADIHEDKLALAKKLGADLTVDGRNHNAVAEVQRIIGGAHGALV 240 Query: 241 TAVSPKAFGQAIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSDLQESL 300 TAVSPKA QA G +R GT+AL GLPPGD P+F+ VLK IT+RGSIVGTR DL+ESL Sbjct: 241 TAVSPKAMEQAFGFLRARGTMALVGLPPGDISLPVFNTVLKRITVRGSIVGTRQDLEESL 300 Query: 301 DFAAHGAVKATVSTAPLEKINEIFTRMRAGDIEGRVVMD 339 FAA G V A + L+ IN IF RM G I+GR+V+D Sbjct: 301 VFAAEGKVAAHFTWDKLDNINAIFARMEEGKIDGRIVLD 339 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: 436 Number of extensions: 10 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: 341 Length adjustment: 29 Effective length of query: 313 Effective length of database: 312 Effective search space: 97656 Effective search space used: 97656 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