Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate HSERO_RS23780 HSERO_RS23780 dioxygenase
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS23780 Length = 276 Score = 190 bits (482), Expect = 3e-53 Identities = 103/259 (39%), Positives = 153/259 (59%), Gaps = 7/259 (2%) Query: 9 SAVAALGLTAAQAAES-LTVAATPVPHAEILNVVKPLLAKE--GVDLKIKEFTDYVQPNV 65 S +A+L L A AA+ + V T PHA+I + + ++ G +KI EF DY+QPN Sbjct: 18 SMLASLVLNAQAAADQVIRVGVTSGPHAQIFEQARRVFERDNPGYKVKIIEFNDYIQPNA 77 Query: 66 QVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGATVV 125 + LDAN +QH+P+L+ K +G L A I P+ YS KY+KL+++P GA + Sbjct: 78 ALDAGELDANSYQHRPFLNAQIKTRGYKLYAEGKTMIGPMAIYSRKYRKLEDVPVGARIG 137 Query: 126 IPNDATNGGRALLLLDKAGVIKLKDN----KSITATPKDIVDNPKNIKIRELEAATLPRV 181 IPND N R LLLL K G IKL+ ATP DI +NPK K E++AA LPR Sbjct: 138 IPNDPANESRVLLLLQKHGFIKLRAGIDPLTGTNATPIDITENPKKWKFVEIDAAQLPRT 197 Query: 182 LTQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALHS 241 L +D + +N +YA +A LNP +D+L +E DSPY ++ R ++ + KL +A S Sbjct: 198 LDDLDASAVNADYAAKAGLNPARDSLVVESGDSPYACLIAVREKDRAQPWLGKLVQAYQS 257 Query: 242 AEIKQFIQEKYKGAVVPAF 260 E+K++I+ ++KG ++ A+ Sbjct: 258 PEVKRYIETEFKGGILAAW 276 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: 176 Number of extensions: 6 Number of successful extensions: 3 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: 276 Length adjustment: 25 Effective length of query: 235 Effective length of database: 251 Effective search space: 58985 Effective search space used: 58985 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