Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_013403448.1 CALHY_RS07935 ABC transporter substrate-binding protein
Query= TCDB::Q9HT68 (260 letters) >NCBI__GCF_000166355.1:WP_013403448.1 Length = 283 Score = 306 bits (785), Expect = 2e-88 Identities = 154/244 (63%), Positives = 190/244 (77%) Query: 17 TAAQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQPNVQVSEKRLDANF 76 T + ++ V ATPVPHAEILNVVKP+L K+G++L I EFTDYVQPN++++EK LDANF Sbjct: 40 TTVKKKITIKVGATPVPHAEILNVVKPILEKKGINLNIVEFTDYVQPNLKLAEKELDANF 99 Query: 77 FQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGATVVIPNDATNGGRA 136 FQH PYL++F+K +L + VHIEP+G YS K KKL++L GAT+ IPNDATNGGRA Sbjct: 100 FQHIPYLEDFSKEHRLNLTYIAKVHIEPMGIYSQKVKKLNQLKQGATIAIPNDATNGGRA 159 Query: 137 LLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPRVLTQVDMALINTNYAL 196 LLLL AG+IKLK N I A DI+ NPK IKI ELEAATLPRVL VD A+INTNYAL Sbjct: 160 LLLLQSAGLIKLKPNVGIKAKVSDIIKNPKKIKIIELEAATLPRVLPDVDAAVINTNYAL 219 Query: 197 EAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALHSAEIKQFIQEKYKGAV 256 EAKL PTKDAL IE ++SPYVN+L R ++ +++LAKAL+S E+K+FI +KYKGAV Sbjct: 220 EAKLVPTKDALFIENANSPYVNVLAVRKGDEFRPELKELAKALNSPEVKKFINKKYKGAV 279 Query: 257 VPAF 260 +PAF Sbjct: 280 IPAF 283 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: 266 Number of extensions: 11 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: 283 Length adjustment: 25 Effective length of query: 235 Effective length of database: 258 Effective search space: 60630 Effective search space used: 60630 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 24 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