Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate AZOBR_RS19465 AZOBR_RS19465 dioxygenase
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__azobra:AZOBR_RS19465 Length = 254 Score = 258 bits (660), Expect = 7e-74 Identities = 130/252 (51%), Positives = 175/252 (69%) Query: 9 SAVAALGLTAAQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQPNVQVS 68 + +A L +AE+L + TP PH +IL VKPL AKEG+DL + EF+DYV PN +S Sbjct: 3 AGIATLATAVGASAEALKIGVTPGPHGQILEKVKPLAAKEGLDLTVLEFSDYVIPNQALS 62 Query: 69 EKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGATVVIPN 128 + L+AN FQHQPYLD K +G +LV+V I P+G YS K K LDELP GA V IPN Sbjct: 63 QGDLNANSFQHQPYLDNQVKDRGYELVSVAKTVIFPMGVYSKKVKSLDELPDGAKVSIPN 122 Query: 129 DATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPRVLTQVDMA 188 D TNGGRALLLL G++K+K++ + A+P DI +NPK ++I EL+AA LPR L V +A Sbjct: 123 DPTNGGRALLLLQAKGLLKVKESAGLKASPLDISENPKKLQILELDAAQLPRSLDDVTVA 182 Query: 189 LINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALHSAEIKQFI 248 +INTN+A+E+ L+P KDA+A E S+SPY N++ R ++D + L K S E+KQFI Sbjct: 183 VINTNFAMESGLDPNKDAIAREASESPYANVIAVRKADQDKPWVATLVKVYQSDEVKQFI 242 Query: 249 QEKYKGAVVPAF 260 +++KGAVVPA+ Sbjct: 243 LDRFKGAVVPAW 254 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: 203 Number of extensions: 8 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: 254 Length adjustment: 24 Effective length of query: 236 Effective length of database: 230 Effective search space: 54280 Effective search space used: 54280 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