Align predicted 3-ketoglycoside hydrolase (DUF1080) (characterized)
to candidate Ga0059261_0549 Ga0059261_0549 Domain of Unknown Function (DUF1080)
Query= reanno::Cola:Echvi_2921 (251 letters) >FitnessBrowser__Korea:Ga0059261_0549 Length = 271 Score = 197 bits (502), Expect = 1e-55 Identities = 104/219 (47%), Positives = 135/219 (61%), Gaps = 13/219 (5%) Query: 38 PVPPVVTPGEENHMPPSDAIVLFDGSDLSAWKSVKTGGEAEWTVHDGIFTVKP-----GT 92 P P VVTP PSDAIVL AW+ G A WTV G+ TV P G Sbjct: 47 PAPVVVTPATLPGGAPSDAIVLSP----DAWQ----GQLAPWTVAGGVMTVPPRPAGGGD 98 Query: 93 GEIATKEKFGDVQVHIEWKAPDVVKGEGQGRGNSGLFFCERYEVQILDSYQNRTYSNGQA 152 + +++ FGDVQ+H+E+++P+ K Q RGNSG++F +RYEVQILD Y+N TY++G Sbjct: 99 NNLVSRQSFGDVQLHLEFRSPNPPKDTSQDRGNSGVWFMQRYEVQILDGYRNPTYADGTV 158 Query: 153 ASLYKEGIPLANAMRSPQEWNTYDVFFTAPRFNKDGMVISPAYVTVIHNGVLVQNHYEVK 212 + Y PL NA R P EW +YD+ F PRF DG ++ PAYVT NGVLVQN + Sbjct: 159 GAAYGWKPPLVNAARKPGEWQSYDIVFERPRFAADGKLLRPAYVTAFLNGVLVQNRQALL 218 Query: 213 GSTAYIGVHKYEAHETELPIKLQDHGNLVNFRNIWVRKL 251 G+T + V Y+AH P++LQDHG+ V+FRNIWVR L Sbjct: 219 GTTVWRKVAAYQAHPDAAPLQLQDHGSPVSFRNIWVRPL 257 Lambda K H 0.317 0.135 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: 255 Number of extensions: 11 Number of successful extensions: 2 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: 251 Length of database: 271 Length adjustment: 25 Effective length of query: 226 Effective length of database: 246 Effective search space: 55596 Effective search space used: 55596 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