Align D-gluconate TRAP transporter, periplasmic component (characterized)
to candidate H281DRAFT_05542 H281DRAFT_05542 tripartite ATP-independent transporter solute receptor, DctP family
Query= reanno::psRCH2:GFF2082 (338 letters) >FitnessBrowser__Burk376:H281DRAFT_05542 Length = 339 Score = 117 bits (294), Expect = 3e-31 Identities = 88/286 (30%), Positives = 145/286 (50%), Gaps = 13/286 (4%) Query: 31 PRMIRFGYGLNEDSNQGRAA--KLLAEEVAKASGGKLKVRTFASASLGSD-DQMQNALIG 87 P +RF + D N + L E + K+ G +++V F + LG + D +Q +G Sbjct: 30 PVQLRFSSTMTPDENSAHYIYYQRLQENLKKSVGDQIRVDFFPNGQLGKEADVVQQVRLG 89 Query: 88 GAQEMMVGSTATLVGISKEMAVWDTPFLFTDPRQADQVLDGPVGRQVMDKL-EEKGLVGL 146 M+ GS+ + E A+ D FLF + + +D V + DKL + + + Sbjct: 90 SIDMMITGSSIWATALP-EFALLDLGFLFDNWAHVGKSVDHGVA-DIYDKLLQARTGCSV 147 Query: 147 VYWENGFRNVTNSARP-IEKLEDFNGVKLRVMPNPVFIDTFKRMGANAVPLPFSELFTAL 205 V W + F + +P I+ + VKLRV+P FI+TFK MGA P+ F+E++TA+ Sbjct: 148 VGWGSHFSARSVYTKPAIKDIAQLKNVKLRVLPTQAFIETFKLMGAIPTPIAFNEVYTAV 207 Query: 206 ETKAVDGQENPFNTILSSKFYEVQKYLSVTNHVYSPWIVTVSKRWWDGLSATEQGI---L 262 +T V+G E+ ++LS+K EV + TNH++SP I + KR GLS I Sbjct: 208 QTGVVEGFEHDAASVLSNKLNEVVQNSWQTNHLFSPCITVIGKR---GLSKIPDAIKPQF 264 Query: 263 MEAAEKARDAEREDTRREASQALAALKERGMQINEVSPDEIQRMRE 308 EAA +A +R+ + + A+A+LK+ GM ++ E +R+ Sbjct: 265 CEAAHEASLYQRQAAATKGADAIASLKKAGMTFYPMADAERANIRK 310 Lambda K H 0.315 0.131 0.368 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: 197 Number of extensions: 9 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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: 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