Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate Pf6N2E2_1646 Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE
Query= TCDB::Q9R9Q7 (423 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1646 Length = 450 Score = 358 bits (919), Expect = e-103 Identities = 179/407 (43%), Positives = 255/407 (62%), Gaps = 1/407 (0%) Query: 18 GAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLVTMPASSSEQFSQYRLWL 77 G L AA L+++ + G L ++ + + K+TG+ V +V+ P S++E+ S Y+ L Sbjct: 44 GFPSLCTAASLTISCGAVGAELQLCKEAVEAWSKQTGNSVEVVSTPNSATERLSFYQQIL 103 Query: 78 AAGNKDVDVYQTDVIWAPQLAEQFVDLTEATK-DVVGEHFPSIIQSQTVNGKLVALPFYT 136 +A + D+D+ Q D++W LA+ +DL E + +F + + + TVNG+LV +P++T Sbjct: 104 SAQSSDIDIIQIDMVWPGMLAKHLMDLREVLPANATQGYFQAQVDNATVNGRLVTMPWFT 163 Query: 137 DAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSADIWGFVFQGNAYEGLTC 196 D+ LYYRKDLL+KY K P+TW+E+ TA+ VQ ERAAG+A+ WG+VFQG AYEGLTC Sbjct: 164 DSGLLYYRKDLLEKYNKPVPQTWEEMTTTARAVQQAERAAGNANAWGYVFQGRAYEGLTC 223 Query: 197 NALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAPKGVLAYQEEESRGVWQ 256 NALEWI S G ++ G I VN++ + AA+ K W+G I+P+GVL Y EEE RGV+Q Sbjct: 224 NALEWISSQPQGGLVNQQGDIVVNSQASRAALTLAKSWVGDISPRGVLNYTEEEGRGVFQ 283 Query: 257 TGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSSTLGGWNLAVSKYSDEQ 316 +GNA+FMRNWPY +AL DS VK K VAPLP + +STLGGW LAVS+YS Sbjct: 284 SGNALFMRNWPYVWALVQSQDSVVKDKVGVAPLPRGGETGTHASTLGGWGLAVSRYSANP 343 Query: 317 EAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPFMPHWKPIFQSAVPRPS 376 + A V +L SA+ QK RA+ + P I +LY DPE+ AA P+ + I V RP+ Sbjct: 344 KLAAELVSYLSSAQQQKHRALVGAYNPVIESLYQDPELLAAMPYYSQLRSILNDGVMRPA 403 Query: 377 AVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKGDAW 423 ++ +Y VS+ F+ VH L+ + L LE ELT +K W Sbjct: 404 SITADRYPRVSNAFFDQVHGVLADERPVDQALAELESELTRIKRRNW 450 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: 461 Number of extensions: 16 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: 450 Length adjustment: 32 Effective length of query: 391 Effective length of database: 418 Effective search space: 163438 Effective search space used: 163438 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