Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate AO356_28570 AO356_28570 ABC transporter substrate-binding protein
Query= TCDB::Q9R9Q7 (423 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28570 Length = 424 Score = 362 bits (928), Expect = e-104 Identities = 180/403 (44%), Positives = 255/403 (63%), Gaps = 1/403 (0%) Query: 22 LAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLVTMPASSSEQFSQYRLWLAAGN 81 L+ AA L+++ + G L ++ + + K+TG+ V +V+ P S++E+ S Y+ L+A + Sbjct: 22 LSTAANLTISCGAVGAELQLCKEAVEAWSKQTGNSVEVVSTPNSATERLSFYQQILSAQS 81 Query: 82 KDVDVYQTDVIWAPQLAEQFVDLTEA-TKDVVGEHFPSIIQSQTVNGKLVALPFYTDAPA 140 D+D+ Q D++W LA+ +DL + D +F + + + TVNG+LV +P++TD+ Sbjct: 82 SDIDIIQIDMVWPGMLAKHLLDLRQVLAADATQGYFQAQVDNATVNGRLVTMPWFTDSGL 141 Query: 141 LYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSADIWGFVFQGNAYEGLTCNALE 200 LYYRKDLL+KY K P+TW+E+ TA+ VQ ERAAG+A+ WG++FQG AYEGLTCNALE Sbjct: 142 LYYRKDLLEKYNKPVPQTWEEMTTTARTVQQAERAAGNANAWGYIFQGRAYEGLTCNALE 201 Query: 201 WIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAPKGVLAYQEEESRGVWQTGNA 260 WI S G ++ G I VN++ + AA+ K W+G IAP+GVL Y EEE RGV+Q+GNA Sbjct: 202 WISSQPQGGLVNAQGDIVVNSQASRAALTLAKSWVGDIAPRGVLNYTEEEGRGVFQSGNA 261 Query: 261 VFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSSTLGGWNLAVSKYSDEQEAAI 320 +FMRNWPY +AL DSAVK K VAPLP +STLGGW LAVS+YS + A Sbjct: 262 LFMRNWPYVWALVQSQDSAVKDKVGVAPLPRGGATGTHASTLGGWGLAVSRYSANPKLAA 321 Query: 321 AFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPFMPHWKPIFQSAVPRPSAVAK 380 V +L SA+ QK RA+ + P I +LY DPE+ AA P+ I V RP+++ Sbjct: 322 ELVSYLSSAQQQKHRALVGAYNPVIESLYQDPELLAAMPYYSQLHSILNDGVMRPASITA 381 Query: 381 VKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKGDAW 423 +Y VS+ F+ VH L+G + L LE ELT +K W Sbjct: 382 DRYPRVSNAFFDQVHGVLAGERPVDQALAELESELTRIKRRNW 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: 445 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