************************************************************ This is an example of the output when linked fragments are requested. The header contains keywords and result values. Most of these are self-explanatory. The keyword "KEY" shows the order of the columns in the output "&" lines: Seq = sequence number Res = residue label (if any. usually the same as sequence number If negative, no structure data was available.) aa = one-letter amino-acid code phi, psi, omega = predicted backbone torsion angles. range=(-180,180) cf(phi), cf(psi) = confidence for the predicted phi or psi(omega) rel = PHD reliability index, if PHD predictions were used. ss = PHD secondary structure prediction if used, otherwise the secondary structure from the I-sites fragment is reported. clustID = I-sites cluster identifier, this can be used to idientify the sequence motif from the table on the web page: http://isites.bio.rpi.edu/Isites/ISL_table.html pos = position within the cluster, starting from 0. For example, "7312 0" indicates the column (3) matched the first column of cluster 7312, identified on the web page as an "Aspartate beta-bend". ************************************************************ PROGRAM ISLlink VERSION 18-JUL-97 DATE Thu Jul 24 17:29:29 1997 REFERENCE C.Bystroff & D.Baker NSB (submitted) NOTE This program carries out "Algorithm 4" NOTE (the last part) from the above reference. PREDICTION_LIST /mnt/rz2a/users/isites/tmp/isl.sort.bystroff.86979 TARGET_PROFILES /mnt/rz2a/users/isites/tmp/isl.drct.bystroff.86979 DATABASE /usr3/users/bystroff/motif/VALL/vall16.drct ANGLES_OUTPUT /mnt/rz2a/users/isites/tmp/isl.ang.bystroff.869790 STATS_OUTPUT this file LOWEST_CONFIDENCE_ALLOWED 0.250 MDA_ALLOWED_FOR_LINKING 60.000 DEVIATION_USED_FOR_STATS 60.000 OVERHANGS 0 UNDERCUTTING no METHOD I-sites predictions only DATABASE_SIZE_IN_COLUMNS 126232 DATABASE_NUMBER_OF_SEQUENCE_FAMILIES 471 #INPUT_SEQUENCE ALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVH AMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGG LTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPRE GLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVM RTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGH GDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIE AFELGAAAHFKVTGEWNDDLMTSVLAPSGT ## SEQUENCE_LENGTH 330 NUMBER_OF_CHAINS 1 KNOWN_ANGLES 0 ***Blind prediction*** SUMMARY of this run:::::::::::::: UNDERCUTS 0 Opportunities. 0 undercuts to N. 0 undercuts to C. PHD_PREDICTIONS 329 present, 0 used. KEY Seq Res aa phi psi omega cf(phi) cf(psi) rel ss clustID pos & 1 -1 A -75.0 -15.0 180.0 0.00 0.00 5 L 0 0 & 2 -2 L -75.0 -15.0 180.0 0.00 0.00 5 L 0 0 & 3 -3 P -75.0 44.4 176.0 0.00 0.29 5 L 7312 0 & 4 -4 R -75.6 115.1 179.4 0.29 0.36 5 E 7312 1 & 5 -5 Q -113.4 92.6 -172.0 0.36 0.50 5 E 5097 1 & 6 -6 K -98.2 115.1 179.4 0.50 0.50 5 E 3260 1 & 7 -7 V -113.4 118.0 179.5 0.50 0.55 5 E 5097 1 & 8 -8 E -107.9 119.7 180.0 0.55 0.55 5 E 4190 1 & 9 -9 L -101.5 123.9 178.0 0.55 0.55 5 E 4190 2 & 10 -10 V -127.5 109.7 -175.1 0.55 0.41 5 E 6488 4 & 11 -11 D -108.4 119.0 -178.4 0.41 0.38 5 E 6355 1 & 12 -12 P -107.9 129.3 -174.4 0.38 0.62 5 E 6355 2 & 13 -13 P -124.8 132.3 -177.1 0.62 0.62 5 E 6139 1 & 14 -14 F -135.5 113.9 165.3 0.62 0.62 5 E 6139 2 & 15 -15 V -96.6 111.0 179.8 0.62 0.62 5 E 6139 3 & 16 -16 H -167.8 154.8 179.4 0.62 0.62 5 L 6139 4 & 17 -17 A -74.8 75.3 170.4 0.62 0.43 5 L 3162 1 & 18 -18 H -82.9 -51.9 -179.1 0.43 0.34 5 H 4137 1 & 19 -19 S -60.0 -47.9 179.3 0.34 0.34 5 H 4137 2 & 20 -20 Q -62.9 118.0 179.5 0.00 0.35 5 H 4137 3 & 21 -21 V -107.9 119.7 180.0 0.35 0.35 5 E 4190 1 & 22 -22 A -101.5 123.9 178.0 0.35 0.35 5 E 4190 2 & 23 -23 E -127.5 125.0 177.3 0.35 0.25 5 E 5097 3 & 24 -24 G -94.2 -15.0 180.0 0.25 0.00 5 E 5097 4 & 25 -25 G -75.0 103.1 -175.7 0.00 0.30 5 L 3162 0 & 26 -26 P -80.3 115.1 179.4 0.30 0.36 5 L 3162 1 & 27 -27 K -113.4 118.0 179.5 0.36 0.39 5 E 5097 1 & 28 -28 V -107.9 115.1 179.4 0.39 0.58 5 E 4190 1 & 29 -29 V -113.4 92.6 -172.0 0.58 0.73 5 E 5097 1 & 30 -30 E -98.2 108.9 175.4 0.73 0.73 5 E 3260 1 & 31 -31 F -95.4 141.7 177.7 0.73 0.68 5 E 6488 1 & 32 -32 T -107.9 119.7 180.0 0.69 0.69 5 E 4190 1 & 33 -33 M -101.5 123.9 178.0 0.69 0.69 5 E 4190 2 & 34 -34 V -127.5 109.7 -175.1 0.69 0.68 5 E 6488 4 & 35 -35 I -108.4 123.9 178.0 0.68 0.60 5 E 4190 2 & 36 -36 E -127.5 119.7 180.0 0.60 0.40 5 E 4190 1 & 37 -37 E -101.5 123.9 178.0 0.40 0.40 5 E 4190 2 & 38 -38 K -100.4 107.2 -179.6 0.38 0.55 5 E 6288 1 & 39 -39 K -100.4 115.1 179.4 0.55 0.68 5 E 7428 1 & 40 -40 I -113.4 118.0 179.5 0.68 0.69 5 E 5097 1 & 41 -41 V -107.9 119.7 180.0 0.69 0.69 5 E 4190 1 & 42 -42 I -101.5 123.9 178.0 0.69 0.69 5 E 4190 2 & 43 -43 D -127.5 109.7 -175.1 0.69 0.62 5 E 6488 4 & 44 -44 D -108.4 101.0 175.5 0.62 0.45 5 E 6355 4 & 45 -45 A -94.3 111.0 179.8 0.45 0.33 5 E 7428 5 & 46 -46 G -108.4 8.3 -179.9 0.00 0.36 5 E 6488 5 & 47 -47 T -90.0 92.6 -172.0 0.36 0.64 5 L 7410 1 & 48 -48 E -98.2 108.9 175.4 0.64 0.64 5 E 3260 1 & 49 -49 V -95.4 123.9 178.0 0.64 0.47 5 E 4190 2 & 50 -50 H -98.2 108.9 175.4 0.52 0.52 5 E 3260 1 ... & 330 -330 T -75.0 -15.0 180.0 0.00 0.00 5 L 0 0