Align PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized)
to candidate 17988 b3949 predicted enzyme IIC component of PTS (NCBI)
Query= SwissProt::P23355 (580 letters) >FitnessBrowser__Keio:17988 Length = 359 Score = 270 bits (690), Expect = 7e-77 Identities = 155/328 (47%), Positives = 204/328 (62%), Gaps = 5/328 (1%) Query: 245 KHLMTGVSFMLPFVTAGGLLIALAFALGGIYAGDDAHQGTLAWSLFQIGAKAGFTLMVPA 304 +HLMTGVS M+PFV +GG+L+A++ L G A DA LF IG AG TLMVP Sbjct: 13 QHLMTGVSHMIPFVVSGGILLAVSVMLYGKGAVPDAVADPNLKKLFDIGV-AGLTLMVPF 71 Query: 305 LAGYIAYSIADRPGIAPGMIGGLVAANLNAGFLGGIIAGFIAGYGVAALNRYIKLPRNLE 364 LA YI YSIA+R +AP IG V + AGF G +IAG I G V L + I + + L Sbjct: 72 LAAYIGYSIAERSALAPCAIGAWVGNSFGAGFFGALIAGIIGGIVVHYLKK-IPVHKVLR 130 Query: 365 GLKPVLILPVLGTLLVGLAMMYVFGQPVADLLAWLTAWLRGMQGSSALLLGLLLGGMMAF 424 + P+ I+P++GTL+ MM+ G+PV L LT WL+GMQ S ++L +++G M+AF Sbjct: 131 SVMPIFIIPIVGTLITAGIMMWGLGEPVGALTNSLTQWLQGMQQGSIVMLAVIMGLMLAF 190 Query: 425 DMGGPVNKAAYAFSTGLIASQVYTPMAAAMVAGMTPPLGIALATWVFRNRFTVEERGSAT 484 DMGGPVNK AYAF +A VYT +A A V PPLG+ LAT + R F+ EER + Sbjct: 191 DMGGPVNKVAYAFMLICVAQGVYTVVAIAAVGICIPPLGMGLATLIGRKNFSAEERETGK 250 Query: 485 AAGVLGLAFVTEGAIPYAARDPLRTIPALVIGSAVAGAISMTAGAELKAPHGGIFVLLIP 544 AA V+G VTEGAIP+AA DPLR IP++++GS + GA+ A GG+ VL + Sbjct: 251 AALVMGCVGVTEGAIPFAAADPLRVIPSIMVGSVCGAVTAALVGAQCYAGWGGLIVLPV- 309 Query: 545 NAVTHLLNYVLALVVGVVVTAVALRLLK 572 V L Y+ A+ VG VVTAV + +LK Sbjct: 310 --VEGKLGYIAAVAVGAVVTAVCVNVLK 335 Lambda K H 0.320 0.135 0.386 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: 451 Number of extensions: 17 Number of successful extensions: 3 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: 580 Length of database: 359 Length adjustment: 33 Effective length of query: 547 Effective length of database: 326 Effective search space: 178322 Effective search space used: 178322 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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