Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Echvi_4610 Echvi_4610 3-oxoacyl-(acyl-carrier-protein) reductase
Query= BRENDA::Q4J702 (264 letters) >FitnessBrowser__Cola:Echvi_4610 Length = 248 Score = 128 bits (322), Expect = 1e-34 Identities = 79/242 (32%), Positives = 123/242 (50%), Gaps = 4/242 (1%) Query: 11 GMNAVVLGASSGIGKAIAEMFSEMGGKVVLSDIDE-EGLKRLSDSLRSRGHEVNHMKCDI 69 G A++ GAS GIG+AIA +++ G V + + E + L L G + + D Sbjct: 6 GKTALITGASKGIGRAIALKYAQEGANVAFTFLSSVEKGQALEKELAEFGVKAKGFRSDA 65 Query: 70 TDLNQVKKLVNFSLSVYGNVDALYVTPSINVRKSIENYTYEDFEKVINVNLKGNFMVVKE 129 +D ++LVN + +G +D L + + E ++ V+N+NLK F VK Sbjct: 66 SDFKAAEELVNEVVKEFGALDVLINNAGVTRDNLLMRMNEEAWDDVMNINLKSCFNTVKA 125 Query: 130 FLSVMKNNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAAEYGKYNIRVNVI 189 + K G S++ +S+ G GQ+ YA +KAGII K A E G IR N + Sbjct: 126 ATRTLMKQKAG-SIINITSVVGIKGNAGQANYAASKAGIIGFTKSVALELGSRGIRSNAV 184 Query: 190 APGVVDTPLTRQIKSDPEWFKAYTEKTILKRWATPEEIANVALFLAMPASSYITGTVIYV 249 APG ++T +T + D + + + + +KR PEE+AN +FL SSY++G VI V Sbjct: 185 APGFIETEMTEVL--DEKTVQGWRDAIPMKRGGQPEEVANACVFLGSDMSSYVSGQVIQV 242 Query: 250 DG 251 DG Sbjct: 243 DG 244 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: 163 Number of extensions: 14 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: 248 Length adjustment: 24 Effective length of query: 240 Effective length of database: 224 Effective search space: 53760 Effective search space used: 53760 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 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