Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BWI76_RS15025 BWI76_RS15025 NLPA lipoprotein
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__Koxy:BWI76_RS15025 Length = 268 Score = 220 bits (560), Expect = 3e-62 Identities = 125/259 (48%), Positives = 165/259 (63%), Gaps = 8/259 (3%) Query: 5 LAAFSAVAALGLTAAQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQPN 64 LA + +L T+AQAA +L VAA PVPHAEILN +K + +DLKI E T V N Sbjct: 8 LAGVALSLSLAWTSAQAA-ALRVAADPVPHAEILNYIKKI--DPSLDLKIVELTSGVNAN 64 Query: 65 VQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGATV 124 ++ +DAN+FQH PYL + KA G VHIEPLG YS K+K LP ATV Sbjct: 65 ELLANGDVDANYFQHVPYLKDQEKALGKTFAVAATVHIEPLGIYSRKHKDFKSLPENATV 124 Query: 125 VIPNDATNGGRALLLLDKAGVIKL----KDNKSITATPKDIVDNPKNIKIRELEAATLPR 180 +PN+ TN RAL LL G+IKL D + ATPKDIV+NPK++KI E+E+ +PR Sbjct: 125 AVPNNTTNLSRALFLLQNQGLIKLAAKFTDPATTLATPKDIVENPKHLKILEIESPQIPR 184 Query: 181 VLTQVDMALINTNYALEAKLNPTKDALAIE-GSDSPYVNILVARPDNKDSDAMQKLAKAL 239 L VD+A+IN NYALEA L P KDAL +E +++PY NILV P + ++ LAK L Sbjct: 185 SLDDVDLAVINGNYALEAGLVPAKDALGLESATNNPYANILVTTPALANDPRIKALAKDL 244 Query: 240 HSAEIKQFIQEKYKGAVVP 258 S ++ +FI+++Y G+V+P Sbjct: 245 TSPQVAEFIRKQYNGSVIP 263 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: 216 Number of extensions: 8 Number of successful extensions: 4 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: 268 Length adjustment: 25 Effective length of query: 235 Effective length of database: 243 Effective search space: 57105 Effective search space used: 57105 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