Align Alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_040486164.1 N177_RS18515 alcohol dehydrogenase AdhP
Query= reanno::Cup4G11:RR42_RS34260 (342 letters) >NCBI__GCF_000496075.1:WP_040486164.1 Length = 342 Score = 475 bits (1222), Expect = e-139 Identities = 233/342 (68%), Positives = 272/342 (79%), Gaps = 1/342 (0%) Query: 1 MTAMMKAAVVREFGAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLP 60 M MMKAAVVRE G PL I+++ VP+ GRGQI +K+EASGVCHTDLHAA GDWPVKPT P Sbjct: 1 MAKMMKAAVVRELGKPLVIEDMKVPEVGRGQILMKVEASGVCHTDLHAASGDWPVKPTPP 60 Query: 61 FIPGHEGVGYVSAVGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSV 120 FIPGHEGVGYV+AVGA V+ VKEGDR+GVPWL++ACG+CEHC GWETLC QQ TGY+V Sbjct: 61 FIPGHEGVGYVAAVGAEVTAVKEGDRIGVPWLHTACGHCEHCRTGWETLCYDQQMTGYTV 120 Query: 121 NGGYGEYVVADPNYVGLLPDSVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGL 180 NGG+ EYV+ADPNYVG LPD++ F AP+LCAGVTVYKGLK TDT+PG WV +SGIGGL Sbjct: 121 NGGFAEYVLADPNYVGHLPDNLDFGAAAPVLCAGVTVYKGLKETDTKPGDWVTVSGIGGL 180 Query: 181 GHVAVQYARAMGLRVAAVDIDDKKLELARKLGAEVTVNARTTDPVAFL-QKEIGGAHGAL 239 GH+AVQYA+AMG V AVD+ + KL+LA +LGA+ TV+AR D V + Q GGAHG L Sbjct: 181 GHMAVQYAKAMGRHVVAVDVAEDKLKLAAELGADATVDARANDAVEQVRQITDGGAHGIL 240 Query: 240 VTAVSPKAFGQAIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSDLQES 299 VTAVS AF QA+ M RRGGT+++ GLPPGDFP PIFDVVL IT+RGSIVGTR DL E+ Sbjct: 241 VTAVSRPAFAQALAMTRRGGTMSMVGLPPGDFPLPIFDVVLNRITVRGSIVGTRQDLVEA 300 Query: 300 LDFAAHGAVKATVSTAPLEKINEIFTRMRAGDIEGRVVMDFA 341 L FA G V + S L+ IN+IF RMR G I+GRVVM A Sbjct: 301 LQFAGEGKVASHFSWDSLDNINDIFDRMRDGRIDGRVVMRIA 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: 433 Number of extensions: 12 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: 342 Length adjustment: 29 Effective length of query: 313 Effective length of database: 313 Effective search space: 97969 Effective search space used: 97969 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 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