Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Dsui_2064 Dsui_2064 ABC-type metal ion transport system, periplasmic component/surface antigen
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__PS:Dsui_2064 Length = 269 Score = 172 bits (437), Expect = 5e-48 Identities = 98/268 (36%), Positives = 154/268 (57%), Gaps = 9/268 (3%) Query: 1 MKKLLAAFSAVAALGLTAA------QAAESLTVAATPVPHAEILNV-VKPLLAKEGVDLK 53 MK + +A +LGL AA Q ++LT+ AT P+ + L + +KP+L K+G +K Sbjct: 1 MKIIHTLLAAALSLGLAAAAPGALAQEKKNLTLGATAGPNFDQLKLGIKPILEKKGYSVK 60 Query: 54 IKEFTDYVQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYK 113 + EF DYVQPN+ +++ LDAN FQH YL +F KG +LV V I PLG YS K Sbjct: 61 LVEFNDYVQPNLALAQGSLDANLFQHVIYLKKFAADKGLNLVDVIKAPIAPLGLYSKKRA 120 Query: 114 KLDELPSGATVVIPNDATNGGRALLLLDKAGVIKLKDNKS-ITATPKDIVDNPKNIKIRE 172 L EL G + +PND +N RAL+ L++ G++K+K + AT KD+ +NP +K+ Sbjct: 121 SLKELKDGDRITLPNDPSNLARALVFLEQNGLLKVKPGTDPLKATEKDVAENPHKLKLTP 180 Query: 173 LEAATLPRVLTQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAM 232 +EAA LPR L +IN N+A+ + L +A+A+E + Y+N++ + +++ Sbjct: 181 IEAAQLPRTLDDAAFVVINGNFAIASGLK-LSEAIALENTPDHYLNVVAVKAEDQHKPWT 239 Query: 233 QKLAKALHSAEIKQFIQEKYKGAVVPAF 260 Q + A S E K + + ++G PA+ Sbjct: 240 QDIVAAFKSPEYKAVLDKHFQGYARPAY 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: 175 Number of extensions: 10 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: 269 Length adjustment: 25 Effective length of query: 235 Effective length of database: 244 Effective search space: 57340 Effective search space used: 57340 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