# List of top-scoring protein chains for t2k.100-30-str 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.soe.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 2kl6A 114 2.12e-10 3iduA 127 2.23e-10 2kutA 122 1.47e-05 2x42A 721 4.47e-03 2x41A 721 4.74e-03 1ic1A 190 8.78e-03 1zxq b.1.1.3 21654 b.1.1.4 21690 1iamA 185 1.15e-02 b.1.1.3 21653 b.1.1.4 21689 1zxq 192 1.23e-02 1zxq 1zxqA 192 1.23e-02 b.1.1.3 21657 b.1.1.4 21693 3bn3B 196 1.51e-02 1v8hA 107 1.68e-02 b.1.18.19 119870 2w3jA 145 5.62e-02 1ktjA 129 6.70e-02 b.1.18.7 72974 2vsdA 105 7.11e-02 1yq2A 1024 1.06e-01 b.1.4.1 123843 b.1.4.1 123844 b.18.1.5 123845 b.30.5.1 123846 c.1.8.3 123847 1xwvA 129 1.13e-01 b.1.18.7 116134 3hrzB 252 1.22e-01 3hrzA 627 1.39e-01 1vcaA 202 1.40e-01 1vcaA b.1.1.3 21649 b.1.1.4 21685 3gc3A 385 2.06e-01 1uvqA 197 2.07e-01 b.1.1.2 100062 d.19.1.1 100063 1mq8A 291 2.20e-01 b.1.1.3 79405 b.1.1.4 79406 2wngA 327 2.22e-01 1g4mA 393 2.73e-01 b.1.18.11 65143 b.1.18.11 65144 2oxgA 108 3.18e-01 3a0eA 110 3.44e-01 3b9eA 584 3.63e-01 1w0nA 131 4.34e-01 b.18.1.28 114069 1xvsA 126 4.37e-01 b.1.23.1 116095 3isyA 120 5.07e-01 1f13A 731 5.35e-01 1f13A b.1.18.9 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1bx2B 191 5.44e-01 1iakB b.1.1.2 21610 d.19.1.1 38184 2qkiB 188 5.52e-01 1ti6B 274 5.61e-01 b.3.5.1 106976 d.58.1.5 106977 1cf1A 404 5.72e-01 1cf1A b.1.18.11 21907 b.1.18.11 21908 2bc4A 211 5.72e-01 1vjjA 692 5.78e-01 b.1.18.9 100814 b.1.5.1 100815 b.1.5.1 100816 d.3.1.4 100817 2vzsA 1032 6.61e-01 b.1.4.1 153727 b.1.4.1 153728 b.1.4.1 153729 b.18.1.5 153730 c.1.8.3 153731 1w8oA 601 6.79e-01 b.1.18.2 114374 b.18.1.1 114375 b.68.1.1 114376 2a74B 188 6.84e-01 1yq5A 144 6.86e-01 1hdmA 201 6.88e-01 1iakA b.1.1.2 21583 d.19.1.1 38157 1cqkA 101 6.92e-01 1cqkA b.1.1.2 21547 1nepA 130 7.34e-01 b.1.18.7 80440 2qmwA 267 7.49e-01 c.94.1.1 150899 d.58.18.3 150900 1ex0A 731 7.59e-01 b.1.18.9 90465 b.1.5.1 90466 b.1.5.1 90467 d.3.1.4 90468 2zzjA 238 7.73e-01 1wcqA 601 7.93e-01 b.1.18.2 120894 b.18.1.1 120895 b.68.1.1 120896 1ymmB 198 8.07e-01 b.1.1.2 123703 d.19.1.1 123704 2a73B 991 8.42e-01 1iakB 185 8.55e-01 1iakB b.1.1.2 21626 d.19.1.1 38200 2p9rA 102 8.95e-01 2r5oA 188 9.06e-01 2w5fA 540 9.82e-01 1ayrA 368 1.00e+00 1cf1A b.1.18.11 21915 b.1.18.11 21916 1eut 605 1.08e+00 1eut 1d0hA 469 1.12e+00 1a8d b.29.1.6 24265 b.42.4.2 25610 1fieA 731 1.22e+00 1f13A b.1.18.9 21879 b.1.5.1 22167 b.1.5.1 22168 d.3.1.4 37109 1tzaA 134 1.26e+00 b.1.23.1 107468 1g0dA 695 1.30e+00 1f13A b.1.18.9 60166 b.1.5.1 60167 b.1.5.1 60168 d.3.1.4 60169 1a8d 452 1.36e+00 1a8d 1a8dA 452 1.36e+00 b.29.1.6 24262 b.42.4.2 25607 3hmyA 450 1.41e+00 1fngA 192 1.41e+00 1iakA b.1.1.2 59904 d.19.1.1 59905 1xd5A 112 1.42e+00 b.78.1.1 115155 1ciy 590 1.47e+00 1ciy 1ciyA 590 1.47e+00 b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 2q3zA 687 1.63e+00 b.1.18.9 150037 b.1.5.1 150038 b.1.5.1 150039 d.3.1.4 150040 2vmhA 151 1.65e+00 b.18.1.33 153327 3gqqA 195 1.76e+00 3i26A 384 1.79e+00 1q48A 134 1.81e+00 d.224.1.2 95783 1diwA 441 1.85e+00 1a8d b.29.1.6 24264 b.42.4.2 25609 1kjvB 100 1.86e+00 b.1.1.2 77423 1d5mB 192 1.87e+00 1iakB b.1.1.2 21618 d.19.1.1 38192 1bglA 1023 1.92e+00 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.5.1 24358 c.1.8.3 28857 1o91A 178 1.98e+00 b.22.1.1 92656 1kjlA 146 2.00e+00 b.29.1.3 118689 1k5nB 100 2.03e+00 b.1.1.2 77268 1agdB 99 2.08e+00 1agdB b.1.1.2 20742 1uzvA 114 2.11e+00 b.115.1.1 113461 2zxqA 1376 2.13e+00 1t5rA 284 2.18e+00 f.6.1.1 106465 1n4xH 120 2.21e+00 b.1.1.1 85324 1ao7B 100 2.23e+00 1agdB b.1.1.2 20697 1uvqB 198 2.28e+00 b.1.1.2 100064 d.19.1.1 100065 1k2dB 189 2.30e+00 b.1.1.2 84293 d.19.1.1 84294 2nn8A 138 2.32e+00 b.29.1.3 138392 3c5jB 190 2.40e+00 1k12A 158 2.40e+00 b.18.1.15 71978 1kbvA 327 2.41e+00 b.6.1.3 68395 b.6.1.3 68396 1ieaA 192 2.44e+00 1iakA b.1.1.2 21631 d.19.1.1 38205 1ri6A 343 2.49e+00 b.69.11.1 97503 3kw7A 502 2.50e+00 2qq2A 193 2.53e+00 3fcgA 90 2.54e+00 1iakA 199 2.61e+00 1iakA b.1.1.2 21625 d.19.1.1 38199 1jk8B 190 2.66e+00 1iakB b.1.1.2 63147 d.19.1.1 63148 1tg7A 971 2.69e+00 b.149.1.1 112418 b.18.1.27 112419 b.18.1.27 112420 b.71.1.5 112421 c.1.8.14 112422 1a3k 137 2.70e+00 1a3k 3butA 136 2.71e+00 3h9iA 407 2.75e+00 1l6xA 207 2.81e+00 b.1.1.2 73642 b.1.1.2 73643 1ieaB 228 2.85e+00 1iakB b.1.1.2 21632 d.19.1.1 38206 3gblA 97 2.85e+00 3hxlA 446 2.99e+00 1fc2D 224 3.03e+00 1igtB b.1.1.2 21516 b.1.1.2 21517 3dj9A 107 3.22e+00 b.1.1.2 157755 1dyoA 160 3.25e+00 1dyoA b.18.1.7 23771 1z4rA 168 3.28e+00 d.108.1.1 124444 2q0zX 339 3.28e+00 a.289.1.1 149993 b.1.18.22 149994 1igtD 444 3.31e+00 1igtB b.1.1.1 19767 b.1.1.2 20871 b.1.1.2 20872 b.1.1.2 20873 3im1A 328 3.37e+00 1igtB 444 3.40e+00 1igtB b.1.1.1 19765 b.1.1.2 20867 b.1.1.2 20868 b.1.1.2 20869 2q1fA 1022 3.57e+00 2qxvA 361 3.68e+00 1aqdB 198 3.80e+00 1iakB b.1.1.2 21586 d.19.1.1 38160 1sv6A 269 3.82e+00 d.177.1.1 106043 2bvyA 475 4.10e+00 b.1.18.2 129301 c.1.8.3 129302 2eisA 133 4.13e+00 1k9tA 540 4.14e+00 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1edqA 540 4.14e+00 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 3bevB 99 4.16e+00 1d2oA 187 4.17e+00 1d2oA b.3.5.1 22625 b.3.5.1 22626 3do3A 212 4.20e+00 3grwA 241 4.21e+00 2chhA 114 4.26e+00 b.115.1.1 130471 2p24B 259 4.29e+00 2bc4B 211 4.31e+00 1vj2A 126 4.34e+00 b.82.1.10 100796 2q2bA 179 4.40e+00 1o7iA 119 4.43e+00 b.40.4.3 86642 1ds6B 180 4.56e+00 1rhoA b.1.18.8 21898 1uxxX 133 4.58e+00 b.18.1.10 100169 1tjxA 159 4.60e+00 b.7.1.2 112465 1uqxA 113 4.66e+00 b.115.1.1 99801 3hibA 318 4.67e+00 1ic7H 114 4.82e+00 1f3rB b.1.1.1 62258 2j1vA 151 4.86e+00 2zaiA 497 4.91e+00 3b93A 133 4.91e+00 b.22.1.1 154987 1h6yA 170 4.92e+00 b.18.1.7 70904 1ctn 540 4.98e+00 1ctn 2wk2A 540 4.98e+00 2wlzA 548 4.98e+00 1a6pA 94 5.00e+00 1cdcA b.1.1.1 19748 1zpuA 534 5.15e+00 1qpxA 218 5.26e+00 1qpxA b.1.11.1 22318 b.7.2.1 23200 1d2pA 373 5.33e+00 1d2oA b.3.5.1 22629 b.3.5.1 22630 b.3.5.1 22631 b.3.5.1 22632 1f9zA 135 5.34e+00 1qipA d.32.1.1 38484 2fytA 340 5.46e+00 c.66.1.6 134391 3iiwA 365 5.49e+00 3jybA 145 5.51e+00 1fa8A 135 5.56e+00 1qipA d.32.1.1 38486 2q1mA 130 5.61e+00 b.22.1.1 149998 1nkqA 259 5.73e+00 d.177.1.1 103862 1uacH 114 5.74e+00 b.1.1.1 99132 2v24A 208 5.76e+00 1kj1D 109 5.78e+00 b.78.1.1 68639 3k26A 366 5.80e+00 3c5jA 181 5.81e+00 3kwuA 150 5.82e+00 1kl9A 182 5.83e+00 a.60.14.1 111574 b.40.4.5 111575 1a64A 97 5.90e+00 1cdcA b.1.1.1 19750 2oz4A 265 5.96e+00 b.1.1.3 149099 b.1.1.4 149100 b.1.1.4 149101 1evuA 731 5.97e+00 1f13A b.1.18.9 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 2iaaA 390 5.98e+00 1fhgA 154 6.13e+00 1tlk b.1.1.4 21706 2hrgA 496 6.16e+00 1tlk 154 6.16e+00 1tlk 1ofzA 312 6.21e+00 b.68.8.1 86978 1bkzA 135 6.23e+00 1a3k b.29.1.3 24202 2dtqA 223 6.25e+00 b.1.1.2 131725 b.1.1.2 131726 1vpmA 169 6.31e+00 d.38.1.1 113967 1yc7A 124 6.35e+00 2volA 207 6.38e+00 2a6vA 226 6.50e+00 b.29.1.13 126312 1aqdA 192 6.56e+00 1iakA b.1.1.2 21585 d.19.1.1 38159 1nslA 184 6.56e+00 d.108.1.1 86137 2j2zA 218 6.61e+00 b.1.11.1 137974 b.7.2.1 137975 3cjjA 219 6.61e+00 3cjyA 259 6.65e+00 2w07A 218 6.69e+00 2c78A 405 6.70e+00 b.43.3.1 130037 b.44.1.1 130038 c.37.1.8 130039 2yv5A 302 6.70e+00 2qguA 211 6.71e+00 1n0lA 224 6.72e+00 b.1.11.1 79744 b.7.2.1 79745 2j42A 721 6.73e+00 2wo1A 185 6.79e+00 1dqqB 210 6.88e+00 1igtB b.1.1.1 20421 b.1.1.2 21391 1aipA 405 6.89e+00 1efcA b.43.3.1 25697 b.44.1.1 25737 c.37.1.8 32132 2nsqA 155 6.91e+00 2v8lA 106 6.95e+00 1q46A 175 6.99e+00 a.60.14.1 111594 b.40.4.5 111595 1qppA 218 7.00e+00 1qpxA b.1.11.1 22320 b.7.2.1 23202 2qt6A 498 7.00e+00 3fvqA 359 7.09e+00 1exmA 405 7.13e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1g291 372 7.21e+00 1g291 3dnkA 212 7.40e+00 1nwpA 128 7.44e+00 1nwpA b.6.1.1 23011 2kdgA 100 7.60e+00 2rr3A 130 7.63e+00 1hdmB 193 7.63e+00 1hdmB b.1.1.2 21584 d.19.1.1 38158 2w2aA 194 7.71e+00 3immA 201 7.72e+00 2vq4A 106 7.76e+00 1j1xH 114 7.78e+00 b.1.1.1 77063 2cu9A 161 7.80e+00 b.1.22.1 146430 3ld7A 101 7.97e+00 1ollA 188 7.99e+00 b.1.1.4 93313 b.1.1.4 93314 2oiwA 136 8.00e+00 d.38.1.1 148794 3fncA 163 8.15e+00 3c26A 266 8.17e+00 1ewjA 126 8.19e+00 1ecsA d.32.1.2 59526 2a74A 643 8.19e+00 3cfuA 159 8.25e+00 1sy6A 204 8.29e+00 b.1.1.4 106111 b.1.1.4 106112 2vzpA 127 8.29e+00 3etpA 187 8.30e+00 2wnxA 170 8.39e+00 1y7mA 164 8.55e+00 b.160.1.1 122696 d.7.1.1 122697 1o4yA 288 8.61e+00 b.29.1.2 92473 1a0qL 212 8.62e+00 8fabA b.1.1.1 20286 b.1.1.2 21278 2vu9A 444 8.66e+00 3govA 155 8.70e+00 2yyoA 171 8.74e+00 3bqxA 150 8.76e+00 1qznA 173 8.77e+00 b.2.2.2 104669 1gycA 499 8.78e+00 b.6.1.3 70748 b.6.1.3 70749 b.6.1.3 70750 1s14A 194 8.86e+00 d.122.1.2 98329 1fnlA 175 8.91e+00 2fcbA b.1.1.4 21783 b.1.1.4 21784 2kbnA 109 8.94e+00 2gc9A 179 9.05e+00 b.60.1.6 134972 1uxzA 131 9.06e+00 b.18.1.10 100170 2zxrA 666 9.11e+00 1od3A 168 9.12e+00 b.18.1.10 86825 1ca1 370 9.15e+00 1ca1 1ca1A 370 9.15e+00 a.124.1.1 19340 b.12.1.3 23648 3fc0A 139 9.28e+00 2yv8A 164 9.29e+00 2zooA 442 9.34e+00 2iadB 205 9.41e+00 1iakB b.1.1.2 21640 d.19.1.1 38214 2q8oA 136 9.54e+00 b.22.1.1 150129 1lk2B 99 9.95e+00 b.1.1.2 91058 3bgaA 1010 1.03e+01 3dgtA 280 1.03e+01 3g5wA 318 1.04e+01 1cdcA 99 1.05e+01 1cdcA b.1.1.1 19746 1gr3A 160 1.05e+01 b.22.1.1 65476 3bnvA 152 1.05e+01 1qhqA 140 1.06e+01 1qhqA b.6.1.1 63326 1zbsA 291 1.06e+01 c.55.1.5 124870 c.55.1.5 124871 1psuA 140 1.06e+01 d.38.1.5 88285 1khoA 370 1.06e+01 a.124.1.1 72489 b.12.1.3 72490 2wy3A 319 1.06e+01 1ju3A 583 1.08e+01 b.18.1.13 67300 c.69.1.21 67301 3idaA 587 1.09e+01 1a5fH 217 1.10e+01 1igtB b.1.1.1 20303 b.1.1.2 21295 2fs2A 151 1.11e+01 d.38.1.5 134003 1k5wA 152 1.11e+01 b.7.1.2 68212 1gttA 429 1.12e+01 d.177.1.1 70529 d.177.1.1 70530 1ymmA 191 1.12e+01 b.1.1.2 123701 d.19.1.1 123702 3gbwA 164 1.13e+01 2r15A 212 1.13e+01 2fp8A 322 1.14e+01 3c12A 138 1.14e+01 1a65A 504 1.15e+01 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1zatA 250 1.17e+01 b.160.1.1 124845 d.335.1.1 124846 2ac1A 541 1.17e+01 1c1lA 136 1.17e+01 1c1lA b.29.1.3 24219 1u1zA 168 1.17e+01 d.38.1.6 107602 1hfuA 503 1.18e+01 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 3hnpA 353 1.18e+01 2z5wA 136 1.18e+01 2d3vA 196 1.18e+01 1ecsA 126 1.19e+01 1ecsA d.32.1.2 59407 2b8mA 117 1.19e+01 b.82.1.18 128092 2uurA 245 1.20e+01 3g12A 128 1.21e+01 1sazA 381 1.24e+01 c.55.1.2 118925 c.55.1.2 118926 3fpxA 499 1.24e+01 1zv9A 172 1.24e+01 b.2.2.2 125700 3ec4A 228 1.25e+01 3c7fA 487 1.26e+01 1mexL 213 1.26e+01 b.1.1.1 91259 b.1.1.2 91260 3a57A 165 1.26e+01 3b9cA 144 1.26e+01 2w68A 195 1.28e+01 1rwiA 270 1.28e+01 b.68.9.1 97987 3h8nA 195 1.28e+01 1ospL 214 1.29e+01 32c2A b.1.1.1 20116 b.1.1.2 21146 3d37A 381 1.29e+01 b.106.1.1 157269 b.106.1.1 157270 1hdkA 141 1.30e+01 b.29.1.3 65807 1shwB 181 1.31e+01 b.18.1.4 105563 1lpbB 449 1.32e+01 1gpl b.12.1.2 23643 c.69.1.19 34791 2qv8A 159 1.32e+01 2wxuA 370 1.32e+01 3bwzA 181 1.33e+01 1yreA 197 1.33e+01 d.108.1.1 123919 1kyaA 499 1.35e+01 b.6.1.3 73203 b.6.1.3 73204 b.6.1.3 73205 1bia 321 1.37e+01 1bia 1biaA 321 1.37e+01 a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1adqA 206 1.37e+01 1igtB b.1.1.2 21518 b.1.1.2 21519 3iv4A 112 1.38e+01 1wckA 220 1.39e+01 3ecqA 1531 1.39e+01 1cczA 171 1.40e+01 1cczA b.1.1.1 19758 b.1.1.3 21683 3bbjA 272 1.40e+01 3ecbB 100 1.41e+01 3bexA 249 1.42e+01 c.55.1.13 155198 c.55.1.13 155199 3e0gA 483 1.42e+01 1w9sA 142 1.43e+01 b.18.1.10 114416 3brcA 156 1.46e+01 2gtdA 251 1.49e+01 c.55.1.13 135634 c.55.1.13 135635 2aabL 218 1.50e+01 b.1.1.1 144795 b.1.1.2 144796 2jjsC 127 1.51e+01 2gwnA 452 1.51e+01 2o26U 290 1.52e+01 3ibmA 167 1.53e+01 1a6aB 187 1.53e+01 1iakB b.1.1.2 21616 d.19.1.1 38190 2op6A 152 1.54e+01 2okxA 956 1.55e+01 2odiA 238 1.56e+01 1lcl 142 1.57e+01 1lcl 2zwnA 339 1.57e+01 3fswA 128 1.58e+01 1q9rA 219 1.58e+01 b.1.1.1 96305 b.1.1.2 96306 2q7eA 291 1.59e+01 3ft0A 129 1.59e+01 3hntL 214 1.60e+01 1o75A 415 1.63e+01 b.1.20.1 81117 b.1.20.1 81118 b.120.1.1 81119 1osyA 115 1.63e+01 b.1.21.1 93502 32c2A 217 1.63e+01 32c2A b.1.1.1 20438 b.1.1.2 21404 2a9mH 126 1.63e+01 2ccwA 129 1.63e+01 b.6.1.1 130259 1ncwH 222 1.64e+01 b.1.1.1 85555 b.1.1.2 85556 3es6B 118 1.67e+01 b.1.18.23 158195 1yrrA 382 1.67e+01 b.92.1.5 123935 c.1.9.10 123936 3hn9A 123 1.67e+01 3ejjX 289 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