# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1z6nA 167 4.24e-01 1bjz 207 4.25e-01 2tct a.4.1.9,a.121.1.1 16065,19242 2tct 207 5.98e-01 2tct a.4.1.9,a.121.1.1 16063,19240 1zcbA 362 7.39e-01 2d1eA 248 1.06e+00 1zbmA 280 1.10e+00 1a6i 217 1.19e+00 2tct a.4.1.9,a.121.1.1 16066,19243 1p5zB 263 1.24e+00 c.37.1.1 87815 1e6cA 173 1.27e+00 1shkA c.37.1.2 59296 1whtA 256 1.52e+00 1ivyA c.69.1.5 34646 1utg 70 1.61e+00 1utg a.101.1.1 18813 2utgA 70 1.85e+00 1utg a.101.1.1 18814 1qjtA 99 2.12e+00 1eh2 a.39.1.6 17335 2f6hX 419 2.19e+00 1g97A 459 2.23e+00 1fwyA b.81.1.4,c.68.1.5 60394,60395 1uu1A 335 2.42e+00 c.67.1.1 99993 1rbp 182 2.57e+00 1aqb b.60.1.1 27085 1h2eA 207 3.05e+00 c.60.1.1 70857 1q3eA 207 3.32e+00 b.82.3.2 95669 1hm9A 468 4.01e+00 b.81.1.4,c.68.1.5 65866,65867 2f9fA 177 4.11e+00 1xklA 273 4.21e+00 1ad3A 452 4.62e+00 1ad3A c.82.1.1 35335 1ay7B 89 5.13e+00 1ay7B c.9.1.1 30836 1wlmA 151 5.20e+00 1r45A 204 5.42e+00 1whsA 255 5.61e+00 1ivyA c.69.1.5 34649 1bcsA 263 5.69e+00 1ivyA c.69.1.5 34647 1c3pA 375 5.94e+00 1c3pA c.42.1.2 32606 1brsD 89 6.37e+00 1ay7B c.9.1.1 30825 1b2sD 90 6.62e+00 1ay7B c.9.1.1 30837 1pzqA 60 7.08e+00 a.34.3.1 95466 1pjr 724 7.14e+00 1pjr c.37.1.19,c.37.1.19 32391,32392 1b27D 90 7.18e+00 1ay7B c.9.1.1 30840 1zwxA 301 7.18e+00 1dppA 507 7.46e+00 1dpe c.94.1.1 35800 1ebbA 202 7.69e+00 c.60.1.1 64900 1svr 114 8.17e+00 1svy d.109.1.1 40833 2cyeA 133 8.27e+00 2eboA 74 8.41e+00 2eboA h.3.2.1 45754 1wpbA 172 8.70e+00 1jvr 137 8.73e+00 1jvr a.61.1.2 18132 1ap4 89 8.78e+00 1ncx a.39.1.5 17253 1ka8A 100 9.20e+00 a.4.5.20 72241 1aj8A 371 9.71e+00 1aj8A a.103.1.1 18900 1svq 114 9.81e+00 1svy d.109.1.1 40832 1tag 324 1.11e+01 1cipA a.66.1.1,c.37.1.8 18197,32080 1xvjA 109 1.15e+01 1vgwA 231 1.19e+01 c.68.1.13 100612 1aj4 161 1.20e+01 1ncx a.39.1.5 17244 2gs8A 317 1.25e+01 1f0iA 504 1.30e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1tadA 324 1.39e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 2fz0A 149 1.40e+01 1a19A 90 1.41e+01 1ay7B c.9.1.1 30831 1rwyA 109 1.41e+01 a.39.1.4 98002 1wz7A 111 1.43e+01 1w9gA 104 1.43e+01 1w24A 182 1.47e+01 1jl3A 139 1.47e+01 c.44.1.1 66826 1pmzA 86 1.56e+01 a.39.1.10 104195 1i36A 264 1.59e+01 a.100.1.8,c.2.1.6 71108,71109 2bwkA 121 1.59e+01 1q5nA 454 1.63e+01 a.127.1.1 95901 1ab7 89 1.67e+01 1ay7B c.9.1.1 30835 1ah7 245 1.68e+01 1ah7 a.124.1.1 19339 1jvwA 167 1.78e+01 d.26.1.1 71907 1qhhC 115 1.81e+01 1pjr 1rvgA 305 1.85e+01 c.1.10.2 97920 1jfvA 131 1.87e+01 c.44.1.1 66654 1x8dA 104 1.88e+01 1g33A 73 1.93e+01 a.39.1.4 65121 1jf8A 131 2.00e+01 c.44.1.1 66621 1z1dA 103 2.01e+01 1gmpA 96 2.02e+01 1rgeA d.1.1.2 36036 1rgeA 96 2.06e+01 1rgeA d.1.1.2 36028 1i8vA 96 2.07e+01 d.1.1.2 61985 1lniA 96 2.11e+01 d.1.1.2 74046 1alvA 173 2.14e+01 1alvA a.39.1.8 17370 1b7qA 130 2.21e+01 3lzt d.2.1.2 36549 1u09A 476 2.24e+01 e.8.1.4 107545 1kfuS 184 2.25e+01 a.39.1.8 68574 1f3yA 165 2.26e+01 d.113.1.1 59635 1dp4A 435 2.29e+01 1dp4A c.93.1.1 35710 1k6iA 352 2.32e+01 c.2.1.2 68223 1ycdA 243 2.34e+01 1fxrA 64 2.34e+01 1fxd d.58.1.4 38993 1oaiA 59 2.36e+01 a.5.2.3 81255 1u53A 196 2.48e+01 1z2aA 168 2.50e+01 1xgkA 352 2.51e+01 1b3sD 90 2.55e+01 1ay7B c.9.1.1 30846 1n6aA 259 2.55e+01 b.76.2.1,b.85.7.1 80121,80122 1eh2 106 2.60e+01 1eh2 a.39.1.6 17339 1zr5A 214 2.63e+01 1k6xA 352 2.69e+01 c.2.1.2 68238 1n6jG 35 2.69e+01 1aq0A 306 2.72e+01 1aq0A c.1.8.3 28842 1w41A 101 2.73e+01 1ghr 306 2.74e+01 1aq0A c.1.8.3 28844 5pal 109 2.75e+01 1a75A a.39.1.4 17215 1np8A 159 2.79e+01 a.39.1.8 92022 1bjx 110 2.82e+01 1bjx c.47.1.2 32774 2bjxA 110 2.82e+01 1bjx c.47.1.2 32776 2gar 212 2.83e+01 2gar c.65.1.1 34161 2f6kA 307 2.85e+01 1z4eA 153 2.96e+01 1h7mA 102 2.97e+01 d.79.3.1 83485 1yobA 179 2.97e+01 1dpuA 99 2.97e+01 1dpuA a.4.5.16 16150 1y1xA 191 3.04e+01 2fvtA 135 3.06e+01 1id3B 102 3.11e+01 a.22.1.1 66113 2fi9A 128 3.12e+01 1atzA 189 3.18e+01 1atzA c.62.1.1 34132 1b2uD 90 3.20e+01 1ay7B c.9.1.1 30843 1atzB 189 3.21e+01 1atzA c.62.1.1 34133 1irqA 71 3.21e+01 a.43.1.4 66297 1reqD 637 3.22e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 2es9A 115 3.22e+01 1xahA 354 3.24e+01 1chmA 401 3.26e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1svy 114 3.27e+01 1svy d.109.1.1 40831 2tmdA 729 3.34e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1reqB 637 3.35e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1djqA 729 3.39e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 7reqB 637 3.39e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1jkxA 212 3.40e+01 c.65.1.1 66813 1dmwA 307 3.41e+01 4pah d.178.1.1 42580 1djnA 729 3.41e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 4pah 308 3.42e+01 4pah d.178.1.1 42576 1pah 308 3.42e+01 4pah d.178.1.1 42578 1t46A 313 3.43e+01 d.144.1.7 106397 1j8uA 325 3.49e+01 d.178.1.1 71611 1tq4A 413 3.49e+01 c.37.1.8 107201 1yovA 537 3.51e+01 1garA 212 3.51e+01 2gar c.65.1.1 34162 1fhoA 119 3.61e+01 1fhoA b.55.1.1 26982 1mxiA 160 3.63e+01 c.116.1.1 79646 1pylA 97 3.66e+01 d.1.1.2 104391 1q32A 544 3.66e+01 d.136.1.3,d.136.1.3 104507,104508 1b5uA 130 3.68e+01 3lzt d.2.1.2 36453 1jtdB 273 3.76e+01 b.69.5.2 67265 1ou0A 207 3.77e+01 c.23.17.1 93536 1gz0A 253 3.80e+01 c.116.1.1,d.79.3.3 76391,76392 1b8gA 429 3.84e+01 1b8gA c.67.1.4 34499 1m7yA 435 3.85e+01 c.67.1.4 78761 1ywnA 316 3.94e+01 1hsr 344 3.98e+01 1arv a.93.1.1 18592 2bleA 367 3.98e+01 1e8yA 966 4.03e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1hl8A 449 4.07e+01 b.71.1.3,c.1.8.11 90646,90647 1b7lA 130 4.07e+01 3lzt d.2.1.2 36515 1hl9A 449 4.09e+01 b.71.1.3,c.1.8.11 90650,90651 1fmk 452 4.21e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1aj5A 173 4.21e+01 1alvA a.39.1.8 17367 1lucA 355 4.37e+01 1lucA c.1.16.1 29547 1tns 76 4.38e+01 1qpmA a.6.1.7 16228 1o0xA 262 4.40e+01 d.127.1.1 80755 1ynuA 473 4.45e+01 1l7vA 326 4.56e+01 f.22.1.1 73672 2gfoA 396 4.61e+01 1nz6A 101 4.73e+01 a.2.3.1 86441 1arv 344 4.73e+01 1arv a.93.1.1 18590 1aru 344 4.76e+01 1arv a.93.1.1 18589 1v37A 177 4.77e+01 2c1vA 338 4.78e+01 1v54C 261 4.82e+01 f.25.1.1 100324 2occC 261 4.85e+01 1ocrC f.25.1.1 43520 1b4uB 302 4.89e+01 1bouB c.56.6.1 33861 1u7eB 154 4.90e+01 1smxA 96 4.97e+01 b.40.4.5 105772 1kpgA 287 4.98e+01 c.66.1.18 68735 2blrA 206 5.04e+01 1brlA 355 5.04e+01 1lucA c.1.16.1 29553 1txoA 237 5.04e+01 1kwnA 207 5.04e+01 b.25.1.1 77568 1rqwA 207 5.06e+01 b.25.1.1 97781 1thw 207 5.08e+01 1thv b.25.1.1 23903 1jw2A 72 5.17e+01 a.23.5.1 67372 1e5pA 151 5.17e+01 1bj7 b.60.1.1 59272 1b1eA 123 5.22e+01 7rsa d.5.1.1 37300 1o2dA 371 5.23e+01 e.22.1.2 86591 1yzhA 214 5.24e+01 2aaa 484 5.25e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1shkA 173 5.25e+01 1shkA c.37.1.2 31932 1g1eB 89 5.31e+01 1g1eB a.59.1.1 17931 1a8q 274 5.32e+01 1brt c.69.1.12 34702 1b1jA 123 5.33e+01 7rsa d.5.1.1 37298 1v9jA 113 5.40e+01 d.52.6.1 100542 1ont 22 5.45e+01 j.31.1.2 46232 2az4A 429 5.49e+01 2shkA 173 5.59e+01 1shkA c.37.1.2 31934 1jqSB 32 5.61e+01 1jqsB 32 5.61e+01 i.1.1.1 63238 1jfiA 98 5.70e+01 1jfiA a.22.1.3 62936 1ntyA 311 5.75e+01 a.87.1.1,b.55.1.1 103873,103874 1vokA 200 5.76e+01 1ytbA d.129.1.1,d.129.1.1 41242,41243 1tahA 318 5.76e+01 1cvl c.69.1.18 34775 1qnaA 200 5.80e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1yd9A 193 5.81e+01 1fgkA 310 5.85e+01 1fgkA d.144.1.7 41693 1go5A 69 5.88e+01 a.5.2.3 65410 1u7gA 385 5.88e+01 f.44.1.1 107723 1hbyA 123 5.96e+01 7rsa d.5.1.1 60936 1a80 277 6.00e+01 1frb c.1.7.1 28700 1e0aB 46 6.10e+01 1e0aB j.65.1.1 46357 2ew2A 316 6.10e+01 1uekA 275 6.12e+01 d.14.1.5,d.58.26.5 88483,88484 1zoqC 47 6.16e+01 1fe8A 196 6.20e+01 1atzA c.62.1.1 59783 1wveC 80 6.24e+01 1d8bA 81 6.24e+01 1d8bA a.60.8.1 18094 1ur1A 378 6.26e+01 c.1.8.3 99804 1ao3A 187 6.27e+01 1atzA c.62.1.1 34134 1hqz1 141 6.31e+01 1wdeA 294 6.31e+01 1el5A 389 6.31e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1l9fA 389 6.32e+01 c.3.1.2,d.16.1.3 73716,73717 1h3oB 76 6.35e+01 a.22.1.3 76645 1o82A 70 6.38e+01 a.64.2.1 92630 1c4rA 182 6.46e+01 1c4rA b.29.1.4 24229 1b7oA 130 6.46e+01 3lzt d.2.1.2 36491 1z67A 135 6.56e+01 1yub 245 6.58e+01 2ercA c.66.1.24 34219 1b3mA 389 6.60e+01 1b3mA 1pp7U 131 6.64e+01 a.4.5.44 94973 1cpcA 162 6.65e+01 1cpcA a.1.1.3 15643 2g84A 197 6.67e+01 2fx2 147 6.67e+01 1rcf c.23.5.1 31158 1bouB 302 6.67e+01 1bouB c.56.6.1 33859 1lk5A 229 6.69e+01 c.124.1.4,d.58.40.1 73960,73961 1b1iA 123 6.69e+01 7rsa d.5.1.1 37295 1xbbA 291 6.70e+01 1tsm 316 6.73e+01 1bkpA d.117.1.1 41024 1e7uA 961 6.75e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1b7nA 130 6.75e+01 3lzt d.2.1.2 36468 1f4pA 147 6.78e+01 5nul c.23.5.1 59651 1f3mA 80 6.79e+01 1f3mA j.66.1.1 46358 1k59A 123 6.79e+01 d.5.1.1 72073 2c07A 285 6.80e+01 1ctdA 36 6.81e+01 1ctdA a.39.1.5 17230 1f1mA 164 6.84e+01 1ggqA a.24.12.1 59598 1akr 147 6.87e+01 1rcf c.23.5.1 31152 1lfo 128 6.91e+01 1hmt b.60.1.2 27223 1bu5A 147 6.95e+01 5nul c.23.5.1 31155 1j9eA 147 6.96e+01 c.23.5.1 62756 1kp9B 287 7.03e+01 c.66.1.18 68734 1akw 147 7.06e+01 5nul c.23.5.1 31153 1lyxA 248 7.09e+01 c.1.1.1 78304 1cydA 244 7.09e+01 1cydA c.2.1.2 29825 1o94A 729 7.13e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1ghsA 306 7.30e+01 1aq0A c.1.8.3 28840 1r8sE 203 7.31e+01 a.118.3.1 97248 1tahB 318 7.32e+01 1cvl c.69.1.18 34774 1b5wA 130 7.34e+01 3lzt d.2.1.2 36557 2bj7A 138 7.34e+01 1azl 147 7.35e+01 5nul c.23.5.1 31154 1jsf 130 7.35e+01 3lzt d.2.1.2 36410 1lz1 130 7.35e+01 3lzt d.2.1.2 36415 2cujA 108 7.39e+01 1b7rA 130 7.41e+01 3lzt d.2.1.2 36436 1b5xA 130 7.41e+01 3lzt d.2.1.2 36550 1b5zA 130 7.42e+01 3lzt d.2.1.2 36567 1b7s 130 7.43e+01 3lzt d.2.1.2 36571 1akt 147 7.43e+01 5nul c.23.5.1 31157 1b5vA 130 7.45e+01 3lzt d.2.1.2 36563 2cygA 312 7.47e+01 133l 130 7.50e+01 3lzt d.2.1.2 36524 1owcA 427 7.54e+01 a.103.1.1 104039 1b7pA 130 7.58e+01 3lzt d.2.1.2 36551 134l 130 7.64e+01 3lzt d.2.1.2 36505 1lmt 136 7.65e+01 3lzt d.2.1.2 36416 2c5uA 375 7.66e+01 2bapC 56 7.68e+01 1whzA 70 7.69e+01 1diiC 80 7.69e+01 1diiC a.3.1.1 15925 1wmmA 145 7.70e+01 1z2wA 192 7.71e+01 1f93A 104 7.73e+01 1dcpA d.74.1.1 39688 1n9lA 109 7.74e+01 d.110.3.6 85468 1h0cA 392 7.76e+01 c.67.1.3 83424 1hq3D 103 7.79e+01 1aoiB a.22.1.1 16464 1tzyD 103 7.79e+01 a.22.1.1 107533 1pvaA 110 7.79e+01 1a75A a.39.1.4 17207 1cipA 353 7.81e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1aoiB 87 7.82e+01 1aoiB a.22.1.1 16470 1xhlA 297 7.84e+01 c.2.1.2 109591 2cxxA 190 7.85e+01 1bxyA 60 7.86e+01 1bxyA d.59.1.1 39525 1cb8A 678 7.90e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1xo7A 166 7.95e+01 1ggwA 140 7.95e+01 1ggwA a.39.1.5 60490 1aoiF 87 8.01e+01 1aoiB a.22.1.1 16471 1bb4A 130 8.02e+01 3lzt d.2.1.2 36583 1un3A 123 8.07e+01 d.5.1.1 99646 1b7mA 130 8.08e+01 3lzt d.2.1.2 36569 1dfoA 417 8.24e+01 1bj4A c.67.1.4 34480 1s69A 124 8.37e+01 a.1.1.1 105305 1bc6 77 8.47e+01 1a6l d.58.1.2 38986 1hqz9 141 8.50e+01 1pbv 195 8.52e+01 1pbv a.118.3.1 19179 1dpe 507 8.55e+01 1dpe c.94.1.1 35799 1lycA 343 8.60e+01 a.93.1.1 74344 1thv 207 8.65e+01 1thv b.25.1.1 23904 2bk7B 222 8.72e+01 2bo9B 222 8.72e+01 1hg3A 225 8.75e+01 1hg3A c.1.1.1 61025 1kcxA 518 8.79e+01 b.92.1.3,c.1.9.6 90953,90954 1hm2A 700 8.81e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 61083,61084,61085 1r8mE 203 8.95e+01 a.118.3.1 97242 1pn2A 280 8.98e+01 d.38.1.4,d.38.1.4 94930,94931