Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_011648831.1 RL_RS33110 ABC transporter substrate-binding protein
Query= TCDB::Q9R9Q7 (423 letters) >NCBI__GCF_000009265.1:WP_011648831.1 Length = 420 Score = 680 bits (1755), Expect = 0.0 Identities = 328/413 (79%), Positives = 369/413 (89%), Gaps = 3/413 (0%) Query: 11 ISCAAIAGAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLVTMPASSSEQF 70 IS A AG++ AAE+S AAN+TGKN+ FL +Q+A FEK TG+ V LVTMP+SSSEQF Sbjct: 11 ISVAIAAGSV---RAAEISFAANTTGKNVEFLHNQLAIFEKNTGNHVKLVTMPSSSSEQF 67 Query: 71 SQYRLWLAAGNKDVDVYQTDVIWAPQLAEQFVDLTEATKDVVGEHFPSIIQSQTVNGKLV 130 SQYRLWLAAGNKDVDVYQTDVIWAPQLA+QFVDL EA KDVVG+ FPSII SQTVNG+LV Sbjct: 68 SQYRLWLAAGNKDVDVYQTDVIWAPQLADQFVDLKEAAKDVVGQFFPSIIASQTVNGRLV 127 Query: 131 ALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSADIWGFVFQGNA 190 ALP +TDAPAL+YRKDLL+KYGK PPKTWDE+AATAKE+QDKER AG D+WG+VFQGN+ Sbjct: 128 ALPLFTDAPALFYRKDLLEKYGKQPPKTWDEMAATAKEIQDKERQAGQKDLWGYVFQGNS 187 Query: 191 YEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAPKGVLAYQEEE 250 YEGLTCN LEW+KSSGGGQI+EPDGTIS+NNEKAAAA+E+ K+WIGTI+P GVLAYQEEE Sbjct: 188 YEGLTCNGLEWVKSSGGGQIVEPDGTISINNEKAAAALERAKDWIGTISPPGVLAYQEEE 247 Query: 251 SRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSSTLGGWNLAVS 310 SRGVWQTGNAVFMRNWPYAY+LGNG DSAVKGKF+V LP A GD+PSSTLGGWNLAVS Sbjct: 248 SRGVWQTGNAVFMRNWPYAYSLGNGADSAVKGKFDVMTLPVAAVGDKPSSTLGGWNLAVS 307 Query: 311 KYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPFMPHWKPIFQS 370 KYS++Q+AAIA VKFL S + QK RAIELSNLPT+ LYDD +VAAAQPFMP+WKPIFQ Sbjct: 308 KYSEQQDAAIALVKFLASKDVQKARAIELSNLPTLTDLYDDKDVAAAQPFMPNWKPIFQD 367 Query: 371 AVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKGDAW 423 AVPRPSA AKVKYNEVSSKFW+AVHNTLSG+G+AAENLELLE +LT LKGDAW Sbjct: 368 AVPRPSATAKVKYNEVSSKFWTAVHNTLSGSGSAAENLELLEADLTTLKGDAW 420 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: 657 Number of extensions: 20 Number of successful extensions: 1 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: 420 Length adjustment: 32 Effective length of query: 391 Effective length of database: 388 Effective search space: 151708 Effective search space used: 151708 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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