Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_085771999.1 B1812_RS13135 glucose 1-dehydrogenase
Query= BRENDA::Q4J702 (264 letters) >NCBI__GCF_002117405.1:WP_085771999.1 Length = 249 Score = 129 bits (325), Expect = 5e-35 Identities = 81/252 (32%), Positives = 133/252 (52%), Gaps = 10/252 (3%) Query: 9 VKGMNAVVLGASSGIGKAIAEMFSEMGGKVVLSDIDEEGLKRLSDSLRSRGHEVNHMKCD 68 + G AVV G +SGIG + A++F+ G +V++ + L ++ GH ++ D Sbjct: 4 LSGKVAVVTGGNSGIGLSTAQLFAAEGAHLVVTGRRKA---ELDTAVAEIGHGAVGVQGD 60 Query: 69 ITDLNQVKKLVNFSLSVYGNVDALYVTPSINVRKSIENYTYEDFEKVINVNLKGNFMVVK 128 ++ L + L S +G +D L+ + + + E F+KV ++N+KG V+ Sbjct: 61 VSKLADLDALYAEVKSKFGRIDILFANAGVCELAPLVGVSEEHFDKVFDINVKGLLFTVQ 120 Query: 129 EFLSVMKNNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAAEYGKYNIRVNV 188 + L + + GGS++L SS+ T P VY+ TKA + A+ +E NIRVNV Sbjct: 121 KALPLFAD---GGSIILNSSVANTTGIPAFGVYSATKAAVRSFARTWTSELKDRNIRVNV 177 Query: 189 IAPGVVDTPLTRQIKSDPEWFKAY----TEKTILKRWATPEEIANVALFLAMPASSYITG 244 I+PG ++TP+ ++ E + + + K L R+ PEEIA ALFLA +SY+ G Sbjct: 178 ISPGPIETPIFGKVGLSAEQLQEFDAQISAKVPLGRFGKPEEIAKAALFLASDDASYVAG 237 Query: 245 TVIYVDGGWTAI 256 +YVDGG A+ Sbjct: 238 ADLYVDGGLVAV 249 Lambda K H 0.317 0.134 0.381 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: 173 Number of extensions: 11 Number of successful extensions: 4 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: 264 Length of database: 249 Length adjustment: 24 Effective length of query: 240 Effective length of database: 225 Effective search space: 54000 Effective search space used: 54000 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 (21.6 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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