Align predicted periplasmic 3-ketoglycoside hydrolase (DUF1080) (characterized)
to candidate Echvi_1840 Echvi_1840 Domain of Unknown Function (DUF1080).
Query= reanno::Btheta:351685 (290 letters) >FitnessBrowser__Cola:Echvi_1840 Length = 252 Score = 170 bits (430), Expect = 3e-47 Identities = 97/289 (33%), Positives = 149/289 (51%), Gaps = 37/289 (12%) Query: 1 MKKVFYPLACCLAAGVLVSCSGQKKAGSAQEEQSANEVAVSYSKSLKAAEMDSLQLPVDA 60 MKK L+ G+L S G + G ++E EVAV K+ A++ + Sbjct: 1 MKKSILSLS---VLGLLASACGSAEKGDTEKESVQEEVAV---KTETASQEE-------- 46 Query: 61 DGYITIFDGKTFNGWRGYGKDRVPSKWTIEDGCIKFNGSGGGEAQDGDGGDLIFAHKFKN 120 + +F+G+ +GW Y K+ V W +EDG + + S Q GGD++ + N Sbjct: 47 --WTPLFNGQNLDGWTSYNKETVGPAWKVEDGVLYLDASNKENWQVNGGGDIVTDKVYGN 104 Query: 121 FELEMEWKVSKGGNSGIFYLAQEVTSKDKDGNDVLEPIYISAPEYQVLDNDNHPDAKLGK 180 F L+++WK+S+ GNSGI +L QE+ D + + + PEYQ+LDND HPD K+ K Sbjct: 105 FHLKLDWKISENGNSGIIFLVQEL--------DKYKHSWNTGPEYQLLDNDGHPDGKIEK 156 Query: 181 DNNRQSASLYDMIPAVPQNAKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQWTDL 240 ++ LYD+I A + P GEWN ++I+V +G + N +E LW W +L Sbjct: 157 ---HRTGDLYDLIKATEEAENPVGEWNTSEIIVNQGKLTFKLNGVTTVETTLWNDSWNEL 213 Query: 241 LQASKFSQDKWPLAFELLNNCGGENHEGFIGMQDHGDDVWFRNIRVKVL 289 + SKF + G+ EG I +QDHG++VWF+NI +K L Sbjct: 214 IANSKFKNTEG----------FGQYQEGKIALQDHGNNVWFKNIMIKEL 252 Lambda K H 0.315 0.135 0.418 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: 276 Number of extensions: 24 Number of successful extensions: 5 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: 290 Length of database: 252 Length adjustment: 25 Effective length of query: 265 Effective length of database: 227 Effective search space: 60155 Effective search space used: 60155 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: 42 (22.0 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