Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BPHYT_RS14810 BPHYT_RS14810 dioxygenase
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS14810 Length = 265 Score = 246 bits (628), Expect = 3e-70 Identities = 124/258 (48%), Positives = 170/258 (65%) Query: 3 KLLAAFSAVAALGLTAAQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQ 62 KL AA A + + AA A +++ V T PHA+I+ VVK + A+ G+++KI EF+DYVQ Sbjct: 8 KLAAALGAASLIAANAAYAEDTIKVGVTGGPHAQIMEVVKTVAARNGLNIKIVEFSDYVQ 67 Query: 63 PNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGA 122 PN ++ LDAN +QH PYL K +G L+ + P+G YS K K L EL GA Sbjct: 68 PNAALAGGDLDANSYQHDPYLQAQVKDRGYKLIRIADTVTYPMGIYSKKVKTLAELQPGA 127 Query: 123 TVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPRVL 182 + +PND TNGGRALLLL K G++KL+ + + ATP DIVDNPK +KI EL+AA +PR L Sbjct: 128 KIAVPNDPTNGGRALLLLQKQGLLKLRADAGLKATPLDIVDNPKKLKIVELDAAQIPRSL 187 Query: 183 TQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALHSA 242 VD A INTN+A+EA L P +DA+AIE PYVN++ R +K+ + KL A HS Sbjct: 188 NDVDAAAINTNFAMEAGLKPKQDAIAIEDPKGPYVNVIAIREADKNKPWVAKLVAAYHSP 247 Query: 243 EIKQFIQEKYKGAVVPAF 260 E+KQF++ K+ G+V+ A+ Sbjct: 248 EVKQFVESKFGGSVITAW 265 Lambda K H 0.314 0.131 0.354 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: 213 Number of extensions: 8 Number of successful extensions: 1 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: 260 Length of database: 265 Length adjustment: 25 Effective length of query: 235 Effective length of database: 240 Effective search space: 56400 Effective search space used: 56400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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