Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 17721 b3661 cytoplasmic membrane lipoprotein-28 (NCBI)
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__Keio:17721 Length = 272 Score = 181 bits (460), Expect = 1e-50 Identities = 94/216 (43%), Positives = 140/216 (64%), Gaps = 2/216 (0%) Query: 47 KEGVDLKIKEFTDYVQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLG 106 K G+D+++ F+ + PN + LDAN FQH+P+L++ N+A G LVAV + P+ Sbjct: 57 KYGLDVELVGFSGSLLPNDATNHGELDANVFQHRPFLEQDNQAHGYKLVAVGNTFVFPMA 116 Query: 107 AYSSKYKKLDELPSGATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPK 166 YS K K + ++ GATV IPND TN GRALLLL K +I LK+ K + T DI DNP+ Sbjct: 117 GYSKKIKTVAQIKEGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPR 176 Query: 167 NIKIRELEAATLPRVL--TQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARP 224 +++I ELE A LPRVL +VD+A+I+T Y + L+P D++ IE +SPYVNILVAR Sbjct: 177 HLQIMELEGAQLPRVLDDPKVDVAIISTTYIQQTGLSPVHDSVFIEDKNSPYVNILVARE 236 Query: 225 DNKDSDAMQKLAKALHSAEIKQFIQEKYKGAVVPAF 260 DNK+++ +++ ++ S E+ + + + G VP + Sbjct: 237 DNKNAENVKEFLQSYQSPEVAKAAETIFNGGAVPGW 272 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: 206 Number of extensions: 8 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: 272 Length adjustment: 25 Effective length of query: 235 Effective length of database: 247 Effective search space: 58045 Effective search space used: 58045 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