Align predicted periplasmic 3-ketoglycoside hydrolase (DUF1080) (characterized)
to candidate 352996 BT3469 conserved hypothetical protein (NCBI ptt file)
Query= reanno::Btheta:351685 (290 letters) >FitnessBrowser__Btheta:352996 Length = 449 Score = 159 bits (402), Expect = 1e-43 Identities = 92/232 (39%), Positives = 134/232 (57%), Gaps = 25/232 (10%) Query: 61 DGYITIFDGKTFNGWRGYGKDRVPSK-WTIEDGCIKFNGSGGGEAQDGDGGDLIFAHKFK 119 +G+ ++DGKT NGWRG + P K W +EDG +K SGG E+ +GGD++ K+K Sbjct: 239 EGWALLWDGKTNNGWRGAKLNAFPEKGWKMEDGILKVMKSGGAES--ANGGDIVTTRKYK 296 Query: 120 NFELEMEWKVSKGGNSGIFYLAQEVTSKDKDGNDVLEPIYISAPEYQVLDNDNHPDAKLG 179 NF L +++K+++G NSG+ Y +K +G+ + E+Q+LD+D HPDAKLG Sbjct: 297 NFILTVDFKITEGANSGVKYFVNPDLNKG-EGSAI-------GCEFQILDDDKHPDAKLG 348 Query: 180 KDNNRQSASLYDMIPAVPQNAKPFG--EWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQW 237 NR+ SLYD+IPA KPF ++N A I+V V H N ++EY T W Sbjct: 349 VKGNRKLGSLYDLIPA--PEKKPFNKKDFNTATIIVQDNHVEHWLNGVKLIEYTRNTDMW 406 Query: 238 TDLLQASKFSQDKWPLAFELLNNCGGENHEGFIGMQDHGDDVWFRNIRVKVL 289 L+ SK+ WP G + EG I +QDHGD+VWF+N+++K L Sbjct: 407 NALVAYSKYK--NWPNF--------GNSAEGNILLQDHGDEVWFKNVKIKEL 448 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: 401 Number of extensions: 23 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: 449 Length adjustment: 29 Effective length of query: 261 Effective length of database: 420 Effective search space: 109620 Effective search space used: 109620 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: 49 (23.5 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