Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate WP_106710601.1 CU102_RS08085 ABC transporter substrate-binding protein
Query= TCDB::Q9R9Q7 (423 letters) >NCBI__GCF_003010955.1:WP_106710601.1 Length = 420 Score = 598 bits (1541), Expect = e-175 Identities = 281/423 (66%), Positives = 347/423 (82%), Gaps = 3/423 (0%) Query: 1 MNVKPFVRTLISCAAIAGAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLV 60 M K FV TL++ +A A AA+LS+ + TG FLR Q+ RFEKETG+KV++V Sbjct: 1 MIAKSFVTTLLATTLLASG---AFAADLSIVSGDTGNGREFLRKQLDRFEKETGNKVSIV 57 Query: 61 TMPASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQLAEQFVDLTEATKDVVGEHFPSII 120 MPA+SS+ F Q+RLWLAAGN D+DVY+TDVIWAPQLA+QF+DL +A KDV+ +H PSII Sbjct: 58 AMPANSSDNFGQFRLWLAAGNTDIDVYRTDVIWAPQLADQFLDLKDAAKDVIDQHIPSII 117 Query: 121 QSQTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSAD 180 +SQTVNGKLVA+P +TDAPALYYRKDLL+KY K PKTWDE+AATAKE+QD ERAAG+ Sbjct: 118 ESQTVNGKLVAMPVFTDAPALYYRKDLLEKYKKPVPKTWDEMAATAKEIQDGERAAGNKS 177 Query: 181 IWGFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAP 240 I+G+VFQ NAYEGLTCNALEW+KSSGGGQI+E DGTIS+NN AA A+++ K WI TI+P Sbjct: 178 IYGYVFQANAYEGLTCNALEWVKSSGGGQIVEADGTISINNPDAAVAIDRAKGWIDTISP 237 Query: 241 KGVLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSS 300 KGVLAY EEE+RG+WQTGN+VFMRNWPYAYAL DDS +KGKF+VAPLP+ +G ++ Sbjct: 238 KGVLAYTEEEARGIWQTGNSVFMRNWPYAYALAGSDDSTIKGKFDVAPLPSGKEGQNSAA 297 Query: 301 TLGGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPF 360 TLGGWN+AVSKYS E AI FL SA+ QK RA+ +++PTI +LYDD ++AAAQP Sbjct: 298 TLGGWNVAVSKYSKSPEEAIKLALFLSSADEQKARALSQASMPTIKSLYDDKDIAAAQPL 357 Query: 361 MPHWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKG 420 +P+WKP+F+++VPRPSA KVKYNEVS+ FWSAVH+TLSGNGTAA+NLELLE +LTEL+G Sbjct: 358 IPNWKPVFENSVPRPSAPTKVKYNEVSNMFWSAVHDTLSGNGTAADNLELLEAKLTELQG 417 Query: 421 DAW 423 +W Sbjct: 418 GSW 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: 603 Number of extensions: 16 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