Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate AO353_25115 AO353_25115 ABC transporter substrate-binding protein
Query= TCDB::Q9R9Q7 (423 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25115 Length = 424 Score = 364 bits (935), Expect = e-105 Identities = 183/421 (43%), Positives = 269/421 (63%), Gaps = 4/421 (0%) Query: 7 VRTLISCAAI---AGAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLVTMP 63 ++TL+ A + AG +++AA+L+++ + G L ++ + + K+TG+ V +V+ P Sbjct: 4 LKTLLPAALLTLFAGLPSVSSAADLTISCGAVGAELQLCKEAVEAWSKQTGNNVEVVSTP 63 Query: 64 ASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQLAEQFVDLTEATK-DVVGEHFPSIIQS 122 S++E+ S Y+ L+A + D+D+ Q D++W LA+ +DL E + +F + + + Sbjct: 64 NSATERLSFYQQILSAQSTDIDIIQIDMVWPGMLAKHLMDLREVLPANATQGYFQAQVDN 123 Query: 123 QTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSADIW 182 TVNG+LV +P++TD+ LYYRKDLL+KY K P+TW+E+ ATA++VQ ER AG+ D+W Sbjct: 124 ATVNGRLVTMPWFTDSGLLYYRKDLLEKYNKQVPQTWEEMTATARDVQQAERNAGNPDVW 183 Query: 183 GFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAPKG 242 G++FQG AYEGLTCNALEWI S G ++ P G I VN++ + AA+ K W+G I+P+G Sbjct: 184 GYIFQGRAYEGLTCNALEWISSQPEGGLVNPRGDIVVNSQASRAALTLAKSWVGDISPRG 243 Query: 243 VLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSSTL 302 VL Y EEE RGV+Q+GNA+FMRNWPY +AL +SAVK K VAPLP + +STL Sbjct: 244 VLNYTEEEGRGVFQSGNALFMRNWPYVWALVQSQNSAVKDKVGVAPLPRGGETGNHASTL 303 Query: 303 GGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPFMP 362 GGW LAVS+YS + A V +L SA+ QK RA+ + P I +LY DPE+ AA P+ Sbjct: 304 GGWGLAVSRYSAHPKLAADLVSYLTSAQQQKHRALIGAYNPVIESLYQDPELLAAMPYYG 363 Query: 363 HWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKGDA 422 I V RP+++ +Y VS+ F+ VH L+G + L LE ELT +K Sbjct: 364 QLHSILNDGVMRPASITADRYPRVSNAFFDRVHGVLAGELPVDQALAELESELTRIKRRN 423 Query: 423 W 423 W Sbjct: 424 W 424 Lambda K H 0.313 0.129 0.383 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: 459 Number of extensions: 18 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: 423 Length of database: 424 Length adjustment: 32 Effective length of query: 391 Effective length of database: 392 Effective search space: 153272 Effective search space used: 153272 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: 51 (24.3 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