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 BWI76_RS19725 BWI76_RS19725 PTS fructose transporter subunit EIIBC
Query= TCDB::Q3JZE4 (367 letters) >FitnessBrowser__Koxy:BWI76_RS19725 Length = 558 Score = 216 bits (551), Expect = 9e-61 Identities = 124/338 (36%), Positives = 194/338 (57%), Gaps = 20/338 (5%) Query: 13 HLLTAISYLIPIVCGAGFLVAIGMAMGGRAQDALVIGNFSFWDTMATM-----GGKALGL 67 HLLT +SY++P+V G +A+ A G +A F DT+A GG A L Sbjct: 228 HLLTGVSYMLPMVVAGGLCIALSFAFGIKA--------FEVKDTLAAALMQIGGGSAFAL 279 Query: 68 LPVIIATGIAFSIAGKPGIAPGFVVGLIANAISAGFIGGILGGYIAGFIALGILKNVKVP 127 + ++A IAFSIA +PG+ PG + G++A + +GFIGGI+ G++AG++A I +K+P Sbjct: 280 MVPVLAGFIAFSIADRPGLTPGLIGGMLAVSTGSGFIGGIIAGFLAGYVAKAISTKLKLP 339 Query: 128 NWAKGLMPTLIVPFFAALLSSLIMIYLIGGPISAFTGWLTDFLKSLGNTSNLVMGAVIGV 187 + L P LI+P ++L+ L MIYLIG P++ LT +L+++G + +++GA++G Sbjct: 340 QSMEALKPILIIPLVSSLIVGLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGG 399 Query: 188 LSGVDLGGPLNKTVYAFVLTLQAEGVKEPLTALQLVNTATPVGFGLAYFIAKLFKKNIYT 247 + D+GGP+NK YAF + L + P+ A+ P+ GLA IA+ KK + Sbjct: 400 MMCTDMGGPVNKAAYAFGVGLLSTQTYAPMAAIMAAGMVPPLALGLATLIAR--KK--FD 455 Query: 248 NDEIETLKSAVPMGIVNIVEGVIPIVMNNLMPAILAIGVGGAVGGAVSMTMGADSAVPFG 307 + E K+A+ +G+ I EG IP + M + VGGAV GA+SM +GA P G Sbjct: 456 KAQQEGGKAALVLGLCFITEGAIPFAARDPMRVLPCCIVGGAVTGAMSMWVGAKLMAPHG 515 Query: 308 G--ILMIPTMTRPIAG-ICGLLSNILVTGLVYSLAKKP 342 G +L+IP P+ G + ++ LV GL Y++ K+P Sbjct: 516 GLFVLLIPGAITPVLGYLMAIVVGTLVAGLSYAVLKRP 553 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: 679 Number of extensions: 53 Number of successful extensions: 7 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: 558 Length adjustment: 33 Effective length of query: 334 Effective length of database: 525 Effective search space: 175350 Effective search space used: 175350 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: 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