Align D-gluconate TRAP transporter, periplasmic component (characterized)
to candidate H281DRAFT_03761 H281DRAFT_03761 tripartite ATP-independent transporter solute receptor, DctP family
Query= reanno::psRCH2:GFF2082 (338 letters) >FitnessBrowser__Burk376:H281DRAFT_03761 Length = 341 Score = 167 bits (422), Expect = 5e-46 Identities = 105/337 (31%), Positives = 167/337 (49%), Gaps = 2/337 (0%) Query: 2 KRLLISTLAAALLGSTLSLGYAQAADDIRPRMIRFGYGLNEDSNQGRAAKLLAEEVAKAS 61 +R L+ AAA + L A + ++G L A+ A ++ +AS Sbjct: 6 RRALLRAAAAAPVAGALGFPAIVRAASGPEFVFKYGNNLPLTHPLNVRAQEAANQIREAS 65 Query: 62 GGKLKVRTFASASLGSDDQMQNALIGGAQEMMVGSTATLVGISKEMAVWDTPFLFTDPRQ 121 G++++R F + LG D M + G EM S + ++ +A+ F F D Q Sbjct: 66 KGRMEIRIFPNNQLGGDTDMLAQVRSGGIEMFTPSALVVSTLAPSVAINAVGFAFNDYNQ 125 Query: 122 ADQVLDGPVGRQVMDKLEEKGLVGLV-YWENGFRNVTNSARPIEKLEDFNGVKLRVMPNP 180 +DG +G V +++ GL W+NGFR T S PI ++ G+K+RV +P Sbjct: 126 VWAAMDGKLGAYVRAAMQKAGLESFEKMWDNGFRQTTTSNGPITSAQNMRGLKIRVPVSP 185 Query: 181 VFIDTFKRMGANAVPLPFSELFTALETKAVDGQENPFNTILSSKFYEVQKYLSVTNHVYS 240 + ID FK +GA L FSE++++L+T VD QENP + +K YEVQKY S+TNH++ Sbjct: 186 LSIDMFKGLGAAPTSLQFSEVYSSLQTHIVDAQENPLPIVQVAKLYEVQKYCSLTNHMWD 245 Query: 241 PWIVTVSKRWWDGLSATEQGILMEAAEKARDAEREDTRREASQALAALKERGMQINEVSP 300 + ++ R W L QGI +A + +RED R+ A+A L+ +G+ IN +P Sbjct: 246 GYWFVLNPRAWQRLPKDLQGIASDAFNQCALKQREDVRKLNDAAVADLQSKGLAINRPAP 305 Query: 301 DEIQRMREKAQPAIQTVIDAVGQELFDQVQAEVEKAA 337 D + +A Q D G + +D ++ V K A Sbjct: 306 DSFRAALRQAGFYAQWK-DKFGNQAWDLLEQSVGKLA 341 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: 226 Number of extensions: 10 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: 341 Length adjustment: 28 Effective length of query: 310 Effective length of database: 313 Effective search space: 97030 Effective search space used: 97030 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