Align PTS system, fructose-specific, IIC component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)
Query= TCDB::Q3JZE4 (367 letters) >FitnessBrowser__Keio:14863 Length = 658 Score = 159 bits (403), Expect = 2e-43 Identities = 97/310 (31%), Positives = 161/310 (51%), Gaps = 10/310 (3%) Query: 7 KANFKGHLLTAISYLIPIVCGAGFLVAIGMAMGG--RAQDALVIGNFSFWDTMATMGGKA 64 K K LL+ IS+ +P++ G ++A+ + + QD N W +GG Sbjct: 303 KTELKQALLSGISFAVPLIVAGGTVLAVAVLLSQIFGLQDLFNEENSWLW-MYRKLGGGL 361 Query: 65 LGLLPV-IIATGIAFSIAGKPGIAPGFVVGLIANAISAGFIGGILGGYIAGFIALGILKN 123 LG+L V ++A A+S+A KP +APGF GL AN I +GF+G ++GG IAG++ + + Sbjct: 362 LGILMVPVLAAYTAYSLADKPALAPGFAAGLAANMIGSGFLGAVVGGLIAGYLMRWVKNH 421 Query: 124 VKVPNWAKGLMPTLIVPFFAALLSSLIMIYLIGGPISAFTGWLTDFLKSLGNTSNLVMGA 183 +++ + G + + P L + +M++++G P++ LT +L L ++ L++GA Sbjct: 422 LRLSSKFNGFLTFYLYPVLGTLGAGSLMLFVVGEPVAWINNSLTAWLNGLSGSNALLLGA 481 Query: 184 VIGVLSGVDLGGPLNKTVYAFVLTLQAEGVKEPLTALQLVNTATPVGFGLAYFIA-KLFK 242 ++G + DLGGP+NK YAF L A GV P V + + +A +LFK Sbjct: 482 ILGFMCSFDLGGPVNKAAYAFCLGAMANGVYGPYAIFASVKMVSAFTVTASTMLAPRLFK 541 Query: 243 KNIYTNDEIETLKSAVPMGIVNIVEGVIPIVMNNLMPAILAIGVGGAVGGAVSMTMGADS 302 + EIET KS +G+ I EG IP+ + + + I + +G V GA+ M Sbjct: 542 E-----FEIETGKSTWLLGLAGITEGAIPMAIEDPLRVIGSFVLGSMVTGAIVGAMNIGL 596 Query: 303 AVPFGGILMI 312 + P GI + Sbjct: 597 STPGAGIFSL 606 Lambda K H 0.323 0.143 0.415 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: 642 Number of extensions: 34 Number of successful extensions: 4 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: 367 Length of database: 658 Length adjustment: 34 Effective length of query: 333 Effective length of database: 624 Effective search space: 207792 Effective search space used: 207792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 52 (24.6 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