Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate RR42_RS28475 RR42_RS28475 dioxygenase
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__Cup4G11:RR42_RS28475 Length = 267 Score = 201 bits (510), Expect = 2e-56 Identities = 110/255 (43%), Positives = 156/255 (61%), Gaps = 4/255 (1%) Query: 10 AVAALGLTAAQAAESLTVAATPV-PHAEILNVVKPLLAKEGVDLKIKEFTDYVQPNVQVS 68 A A + L AA AA+ + T P A+I VV+ + + G+D+KI EF DY QPN + Sbjct: 13 AAAMIVLPAAHAADQVVRLGTMSGPDAQIWEVVRTVAKRSGLDVKIIEFNDYAQPNAALD 72 Query: 69 EKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGATVVIPN 128 LDAN FQHQP+LD +A+ + V ++ P+G YS K K L LP GA V I N Sbjct: 73 AGDLDANSFQHQPFLDSQIEARHYKIANVGLTYVAPMGFYSKKLKSLKALPDGAKVGIQN 132 Query: 129 DATNGGRALLLLDKAGVIKLKD---NKSITATPKDIVDNPKNIKIRELEAATLPRVLTQV 185 D +NG RALLLL K G++ L+D ATP DI NP+ +KI EL++A LPR L + Sbjct: 133 DPSNGNRALLLLQKEGLVTLRDGAGKNGKNATPLDIKANPRKLKIVELDSAILPRSLDDL 192 Query: 186 DMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALHSAEIK 245 +A INT+YA++A L+P +DA+A E PY N++ R +KD ++ L A S E++ Sbjct: 193 AVASINTDYAVKAGLSPAQDAIATEDLRGPYANLIAVRTQDKDKPWVKPLVAAYQSQEVR 252 Query: 246 QFIQEKYKGAVVPAF 260 +F+ ++KGA++PAF Sbjct: 253 EFLATQFKGAILPAF 267 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: 182 Number of extensions: 8 Number of successful extensions: 2 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: 267 Length adjustment: 25 Effective length of query: 235 Effective length of database: 242 Effective search space: 56870 Effective search space used: 56870 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