Bold face: keyword "prediction-based threading"
Effect: alignments with possible remote homologues (<25% sequence identity) are returned
Joe Sequencer, Department of Advanced Protein Research, National Univeristy, Timbuktu joe@amino.churn.edu prediction-based threading # incredulase from paracoccus dementiae, translated from cDNA KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKD WWKVEVNDRQGFVPAAYVKKLD
Bold face: keyword "prediction-based threading"
Effect: alignments with possible remote homologues (<25% sequence identity) are returned
Joe Sequencer, Department of Advanced Protein Research,
National Univeristy, Timbuktu
joe@amino.churn.edu
prediction-based threading
# COLUMN format , incredulase from paracoccus dementiae, translated from cDNA
AA PSEC PACC RI_SEC RI_ACC
M L o 9 3
Q L o 9 2
T L o 8 4
L H i 4 4
S H o 8 4
E H o 9 5
R H o 8 2
L H i 7 2
K H o 9 5
K H o 9 8
R H o 9 2
R H o 9 1
I H o 9 3
A H i 9 2
L H i 9 6
K H o 9 6
M H o 9 3
T H o 9 1
Q H i 9 1
T H o 9 4
E H o 9 4
L H i 9 3
A H i 9 9
T H o 9 5
K H o 9 8
A H o 4 6
G L o 8 4
V L o 9 4
K L o 3 7
Q H o 6 4
Q H o 9 1
S H i 9 7
I H i 9 5
Compulsory information: (1) sequence (AA) in one-letter code; (2) secondary structure (PSEC) in either of the states H=helix, E=strand, or L=rest; (3) relative accessibility (PACC) in the two states o=outside (>15% solvent accessible), or i=inside (<15% solvent accessible).
Optional: (1) reliability, or strength for secondary structure (RI_SEC) scaled from 0 (low) to 9 (high); (2) reliability, or strength for relative accessibility (RI_ACC) scaled from 0 (low) to 9 (high).