Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate RR42_RS04565 RR42_RS04565 dioxygenase
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__Cup4G11:RR42_RS04565 Length = 265 Score = 227 bits (578), Expect = 2e-64 Identities = 119/253 (47%), Positives = 162/253 (64%), Gaps = 4/253 (1%) Query: 12 AALGLTAAQAA----ESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQPNVQV 67 AALG T A A + + + T PHA+I+ VK + AK+G+++++ EF+DYVQPN + Sbjct: 13 AALGATLATGAMAQEKPIKIGVTGGPHAQIMEQVKKVAAKDGLNIQLVEFSDYVQPNAAL 72 Query: 68 SEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGATVVIP 127 + LDAN +QH PYL+ K +G + P+G YS K K LD+L GA V +P Sbjct: 73 AAGDLDANSYQHLPYLEAQIKDRGYKFTHIAFTVTFPMGVYSKKIKSLDQLKDGARVGVP 132 Query: 128 NDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPRVLTQVDM 187 ND TNGGR LLLL G+IKL+ + + ATP DIV NPK I+I EL+AA LPR L +D Sbjct: 133 NDPTNGGRGLLLLQSKGLIKLRPDAGLKATPLDIVSNPKKIRIVELDAAQLPRSLDDLDA 192 Query: 188 ALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALHSAEIKQF 247 A IN NYA A L+PTKDA+A+EG PY N++ R +K+ + KL KA HS EIKQ+ Sbjct: 193 AAINGNYAESAGLSPTKDAIAMEGPKGPYANLIAIREADKNKPWVAKLVKAYHSPEIKQY 252 Query: 248 IQEKYKGAVVPAF 260 +Q +K +V+ A+ Sbjct: 253 VQSTFKDSVITAW 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: 210 Number of extensions: 5 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