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 GFF3783 HP15_3725 PTS system, fructose-specific IIBC component
Query= TCDB::Q3JZE4 (367 letters) >FitnessBrowser__Marino:GFF3783 Length = 587 Score = 195 bits (496), Expect = 2e-54 Identities = 118/345 (34%), Positives = 190/345 (55%), Gaps = 23/345 (6%) Query: 6 KKANFKGHLLTAISYLIPIVCGAGFLVAIGMAMGGRAQDALVIGNFSFWDTMATM----- 60 KK +K HLLT +S+++P+V G L+A+ G A F T+A Sbjct: 245 KKGPYK-HLLTGVSFMLPMVVAGGLLIALSFVFGIEA--------FQEEGTLAAALMQIG 295 Query: 61 GGKALGLLPVIIATGIAFSIAGKPGIAPGFVVGLIANAISAGFIGGILGGYIAGFIALGI 120 GG A L+ ++A IA+SIA +PG+APG + G +A + AGF+GGI+ G++AG++A I Sbjct: 296 GGTAFKLMIPLLAGYIAWSIADRPGLAPGMIGGFLAGELGAGFLGGIVAGFLAGYVARFI 355 Query: 121 LKNVKVPNWAKGLMPTLIVPFFAALLSSLIMIYLIGGPISAFTGWLTDFLKSLGNTSNLV 180 + + +P + L P LI+P A+L++ L MIY+IG P++A G LT FL+ +G T+ ++ Sbjct: 356 SQKLPMPESIESLKPILIIPLLASLVTGLGMIYVIGEPMAAIMGALTGFLEGMGTTNAIL 415 Query: 181 MGAVIGVLSGVDLGGPLNKTVYAFVLTLQAEGV--KEPLTALQLVNTATPVGFGLAYFIA 238 +G ++G + DLGGP+NK Y F + L +EG P+ A+ +G G+A FIA Sbjct: 416 LGGILGAMMCFDLGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMAAGMVPAIGMGVASFIA 475 Query: 239 KLFKKNIYTNDEIETLKSAVPMGIVNIVEGVIPIVMNNLMPAILAIGVGGAVGGAVSMTM 298 + + E + +++ +G+ I EG IP + + + I +GGA+ GA+SM Sbjct: 476 ----RRKFAEAERQAGRASFVLGLCFISEGAIPFMAKDPLRVIPVCMIGGAITGALSMLF 531 Query: 299 GADSAVPFGG--ILMIP-TMTRPIAGICGLLSNILVTGLVYSLAK 340 P GG +L IP ++ + + + LV G Y+L K Sbjct: 532 TVKLMAPHGGLFVLAIPNAVSAVLPYLIAIAVGSLVIGFGYALLK 576 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: 721 Number of extensions: 50 Number of successful extensions: 8 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: 587 Length adjustment: 33 Effective length of query: 334 Effective length of database: 554 Effective search space: 185036 Effective search space used: 185036 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