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_RS27570 BWI76_RS27570 phosphotransferase system, fructose-specific IIC component
Query= TCDB::Q3JZE4 (367 letters) >FitnessBrowser__Koxy:BWI76_RS27570 Length = 363 Score = 228 bits (580), Expect = 3e-64 Identities = 124/347 (35%), Positives = 193/347 (55%), Gaps = 7/347 (2%) Query: 11 KGHLLTAISYLIPIVCGAGFLVAIGMAMGGRAQDALVIGNFSFWDTMATMGGKALGLLPV 70 K HLLT IS++IP++ AG +A+G +GG G + + +GG +GL+ Sbjct: 13 KKHLLTGISWMIPLIVAAGICIALGQVLGGTNVGEKT-GTIPWM--LNQIGGWGMGLIVP 69 Query: 71 IIATGIAFSIAGKPGIAPGFVVGLIANAISAGFIGGILGGYIAGFIALGILKNVKVPNWA 130 +I IA+SIA +PG APG +VG + I GFIGG+LGG++ G+ L + +++P Sbjct: 70 LICAAIAYSIADRPGFAPGLIVGFVCGQIHTGFIGGMLGGFLVGYTVLALKHYIRLPKSM 129 Query: 131 KGLMPTLIVPFFAALLSSLIMIYLIGGPISAFTGWLTDFLKSLGNTSNLVMGAVIGVLSG 190 +GLMP +++P + ++S L+M+ LIG PI+ L L+S+ S ++GA++G ++ Sbjct: 130 QGLMPIMVLPVLSTIISGLLMMTLIGKPIAWLQDALIHLLESMQGGSRFLLGAILGAMAT 189 Query: 191 VDLGGPLNKTVYAFVLTLQAEGVKEPLTALQLVNTATPVGFGLAYFIAKLFKKNIYTNDE 250 D GGP+NKT+ F L GV P + + P G L++ L ++ YT E Sbjct: 190 FDFGGPVNKTMSLFADGLLVSGVYGPEAVKFVGSIIPPFGITLSF----LLTRHKYTRAE 245 Query: 251 IETLKSAVPMGIVNIVEGVIPIVMNNLMPAILAIGVGGAVGGAVSMTMGADSAVPFGGIL 310 E LK+A PMGI I EGVIPI +L+ + + V AV G + MT G +S VP GG+ Sbjct: 246 REALKAAFPMGICMITEGVIPIAARDLLRVVGSCVVASAVAGGLIMTWGVESPVPHGGMF 305 Query: 311 MIPTMTRPIAGICGLLSNILVTGLVYSLAKKPVDRNEVTIVSAEDEE 357 ++P T P+ L ++ G++ SL KKPV + D++ Sbjct: 306 VVPLFTHPLLFCLSLAIGTVICGVMLSLWKKPVTERDEEFDELNDQK 352 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: 521 Number of extensions: 47 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: 367 Length of database: 363 Length adjustment: 30 Effective length of query: 337 Effective length of database: 333 Effective search space: 112221 Effective search space used: 112221 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: 49 (23.5 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