Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Dsui_2066 Dsui_2066 ABC-type metal ion transport system, periplasmic component/surface antigen
Query= TCDB::Q9HT68 (260 letters) >FitnessBrowser__PS:Dsui_2066 Length = 267 Score = 168 bits (426), Expect = 9e-47 Identities = 93/266 (34%), Positives = 158/266 (59%), Gaps = 7/266 (2%) Query: 1 MKKLLAAFSAVAALGLTAA----QAAESLTVAATPVPHAEILNV-VKPLLAKEGVDLKIK 55 MK + + A ALGL AA Q ++LT+ AT P+ + + + +KP+L K+G +K+ Sbjct: 1 MKLIRSLLVAGLALGLAAAPAFAQEKKNLTIGATAGPNFDQVKLGIKPILEKKGYSVKLV 60 Query: 56 EFTDYVQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKL 115 EF DYVQPN+ +++ LDAN FQH YL +F+ KG +L V V + P+G YS K K L Sbjct: 61 EFNDYVQPNLALAQGSLDANVFQHVIYLKKFSADKGLNLTDVVKVPVAPMGLYSKKAKSL 120 Query: 116 DELPSGATVVIPNDATNGGRALLLLDKAGVIKLKDN-KSITATPKDIVDNPKNIKIRELE 174 ++ G V +PND +N RAL L++ G+IK+K ++ AT KD+ +NP+ +++ +E Sbjct: 121 KDVKDGDRVTLPNDPSNLARALHFLEQNGLIKVKAGIDALKATEKDVAENPRKLQLTPIE 180 Query: 175 AATLPRVLTQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQK 234 AA LPR L + ++ N+A+ + L +A+++E + Y+N++ + ++++ Q Sbjct: 181 AAQLPRTLDDAGLVVVPGNFAIASGLK-LSEAISLEKTPDHYLNVVAVKTEDQNKAWAQD 239 Query: 235 LAKALHSAEIKQFIQEKYKGAVVPAF 260 + A SAE K + + ++G P + Sbjct: 240 IVAAFKSAEFKAVLDKHFQGYARPNY 265 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: 177 Number of extensions: 11 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: 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