Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate Synpcc7942_0950 Synpcc7942_0950 putative multiple sugar transport system substrate-binding protein
Query= TCDB::Q9R9Q7 (423 letters) >FitnessBrowser__SynE:Synpcc7942_0950 Length = 438 Score = 179 bits (454), Expect = 1e-49 Identities = 133/431 (30%), Positives = 211/431 (48%), Gaps = 29/431 (6%) Query: 1 MNVKPFVRTLISCAAIAGAIDLAAAAELSMAANSTGKNLSFL--------RDQIARFEKE 52 + + P + TL A+ G L + S AA+ST + L + IARF E Sbjct: 14 LRLLPLLLTLFIVLALGG---LGTGTQRSAAADSTVVLRALLPAPFREAMQPAIARFTAE 70 Query: 53 TGH-KVNLVTMPASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQL--AEQFVDLTEAT- 108 ++ LV P +S Y GN D+ DV W P+ A +DL++ Sbjct: 71 HPEIQLELVAGPNDTSLVSDLYTTAFLLGNAPYDLVFLDVTWLPKFVAAGWLLDLSDRVL 130 Query: 109 KDVVGEHFPSIIQSQTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKE 168 ++ E P+ + +L LP LYYR+DL+ + PP+T+ EL +++ Sbjct: 131 PEIQAEFLPAALNGSFYRDRLYRLPLNAAVGLLYYRQDLMPE----PPQTFTELVQRSQQ 186 Query: 169 VQDKERAAGSADIWGFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAV 228 +Q A WG+V+QG YEGL CN LE + GG I G + +++ +A AA Sbjct: 187 LQ-----AQGVVPWGYVWQGKQYEGLVCNFLEVLAGFGGYWIDPQTGEVGLDHPEAIAAA 241 Query: 229 EKVKEWI-GTIAPKGVLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVA 287 + + I I+P GV +QE E+ +++TG + FMRNWPYA L +SAV+GK +A Sbjct: 242 DWLHSTITDQISPAGVSTFQENEALKLFETGQSAFMRNWPYAEMLLERPESAVRGKVGIA 301 Query: 288 PLPAATDGDQPSSTLGGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAA 347 P+ A G ++T G W + +++ ++ EAA+ + L AE+Q++ ++ + +PT +A Sbjct: 302 PMVHA-PGQTSAATQGTWGVGIAQQTEHPEAALTALLALTDAESQRLISLGSNYIPTRSA 360 Query: 348 LYDDPEVAAAQPFMPHWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAEN 407 LY DPE+ A PF PI +S V R A +++ + SA +SG A Sbjct: 361 LYQDPELLARYPFYATLPPILESTVLRSPLPAYDALSDILQRHLSA---AISGQTPVAIA 417 Query: 408 LELLEVELTEL 418 L+ E +L Sbjct: 418 LQQAARESRQL 428 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: 428 Number of extensions: 23 Number of successful extensions: 5 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: 438 Length adjustment: 32 Effective length of query: 391 Effective length of database: 406 Effective search space: 158746 Effective search space used: 158746 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