# List of top-scoring protein chains for t04-100-30-alpha-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.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 3e8tA 220 4.94e-02 2h1tA 188 3.49e-01 b.178.1.1 147215 2ai4A 119 5.12e-01 b.6.1.7 126816 1cy5A 97 7.95e-01 1cy5A a.77.1.3 18430 1kcgC 178 9.49e-01 d.19.1.1 68440 3gkuA 225 1.14e+00 3lzjA 903 1.26e+00 3l8bA 906 1.59e+00 1ig9A 903 1.80e+00 1clqA c.55.3.5,e.8.1.1 62367,62368 2nxpA 156 1.93e+00 d.379.1.1 148504 2ox7A 155 1.93e+00 b.172.1.1 149054 1k0iA 394 2.02e+00 c.3.1.2,d.16.1.2 67942,67943 2vh1A 220 2.13e+00 1x12A 208 2.23e+00 3c3vA 510 2.31e+00 1ykjA 394 2.41e+00 c.3.1.2,d.16.1.2 145914,145915 1pbe 394 2.76e+00 1pbe 1pbeA 394 2.76e+00 c.3.1.2,d.16.1.2 30338,37869 3h5lA 419 2.98e+00 1x82A 190 3.10e+00 b.82.1.7 114955 2bbeA 108 3.17e+00 1qxrA 189 3.21e+00 b.82.1.7 96552 1r03A 182 3.24e+00 a.25.1.1 104675 2w2sA 202 3.38e+00 2cxxA 190 3.49e+00 c.37.1.8 131013 3c0qA 301 3.67e+00 3gwfA 540 3.71e+00 1u6rA 380 4.05e+00 a.83.1.1,d.128.1.2 119600,119601 1nn7A 105 4.20e+00 d.42.1.2 85894 1hd2A 161 4.44e+00 c.47.1.10 60962 1kit 757 5.09e+00 1kit 2gc1A 188 5.61e+00 b.82.1.7 134928 1ispA 181 6.06e+00 c.69.1.18 76778 3d2fA 675 6.23e+00 2hw2A 143 6.24e+00 1rsy 152 6.34e+00 1rsy 1rsyA 152 6.34e+00 b.7.1.2 23192 1cbgA 490 6.49e+00 c.1.8.4 28933 3ff1A 446 6.88e+00 3d37A 381 7.00e+00 b.106.1.1,b.106.1.1 157269,157270 3l57A 299 7.18e+00 1s1dA 331 7.37e+00 b.67.3.1 98344 1iu8A 206 7.52e+00 c.56.4.1 71436 1bob 320 7.72e+00 1bob 1bobA 320 7.72e+00 d.108.1.1 40816 1wtjA 343 7.72e+00 1wdaA 670 8.31e+00 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 1dk8A 147 8.51e+00 1agrE a.91.1.1 18548 2p14A 192 8.60e+00 3i0yA 140 8.62e+00 1v9cA 218 8.69e+00 c.23.17.1 100533 1j58A 385 8.92e+00 b.82.1.2 71531 2dexX 671 9.27e+00 b.2.9.1,b.6.1.6,d.126.1.5 131436,131437,131438 3f85A 463 9.28e+00 2qf3A 243 9.68e+00 b.47.1.1 150724 1hh1A 143 9.82e+00 1gefA c.52.1.18 61036 1mjnA 179 9.96e+00 c.62.1.1 79210 2imfA 203 1.01e+01 2j6vA 301 1.02e+01 1qn2A 100 1.02e+01 1ycc a.3.1.1 15882 2fqmA 75 1.05e+01 d.378.1.1 147042 3c1qA 123 1.05e+01 3l6tA 302 1.06e+01 2hy7A 406 1.08e+01 2bc4B 211 1.09e+01 2ivfB 352 1.14e+01 3cniA 156 1.14e+01 1qh4A 380 1.18e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 2eeyA 162 1.19e+01 1lfaA 187 1.20e+01 1ido c.62.1.1 34122 1i6wA 181 1.20e+01 1i6wA c.69.1.18 61859 3kxeC 88 1.23e+01 2v4cA 309 1.23e+01 1vrpA 381 1.23e+01 a.83.1.1,d.128.1.2 120473,120474 2w7qA 204 1.26e+01 3e8vA 82 1.27e+01 1x9nA 688 1.29e+01 a.235.1.1,b.40.4.6,d.142.2.1 115002,115003,115004 2fy7A 287 1.30e+01 2jf7A 532 1.37e+01 1hn4A 131 1.38e+01 a.133.1.2 65893 3hurA 395 1.42e+01 1o7dC 159 1.46e+01 b.30.5.6 86640 2qz7A 194 1.46e+01 3enbA 222 1.47e+01 c.55.3.14 158189 1ew4A 106 1.48e+01 1ew4A d.82.2.1 40023 3hihA 223 1.49e+01 1iyeA 309 1.50e+01 e.17.1.1 83786 3gj0A 221 1.55e+01 1rtwA 220 1.59e+01 a.132.1.3 97823 2cihA 183 1.59e+01 3fz3A 531 1.61e+01 2x53S 298 1.63e+01 2x54S 298 1.63e+01 3dodA 448 1.68e+01 1urmA 172 1.70e+01 c.47.1.10 113413 2qycA 103 1.73e+01 1umwA 237 1.76e+01 d.223.1.2,d.223.1.2 99631,99632 3brcA 156 1.78e+01 2gagA 965 1.81e+01 2b06A 155 1.83e+01 d.113.1.1 127624 2arzA 247 1.84e+01 b.45.1.1 127225 2cxhA 217 1.85e+01 c.51.1.2 131005 2hfxA 260 1.89e+01 2r3uA 211 1.91e+01 b.47.1.1 151558 1l4dB 122 1.94e+01 d.15.5.1 77684 1vr3A 191 1.96e+01 b.82.1.6 120431 1otkA 249 1.97e+01 a.25.1.2 93521 1w0pA 781 1.97e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 2fha 183 2.02e+01 2fha 2a1fA 247 2.06e+01 c.73.1.3 125991 2wjrA 214 2.07e+01 2nqcA 138 2.08e+01 b.1.18.10 148344 3fqgA 360 2.09e+01 1qg4A 216 2.11e+01 1byuA c.37.1.8 32035 3l60A 250 2.11e+01 3f04A 143 2.18e+01 1wchA 315 2.19e+01 c.45.1.2 114508 1nmmB 286 2.20e+01 c.68.1.2 80662 2qxlA 658 2.25e+01 3hikA 237 2.26e+01 2wozA 318 2.33e+01 2obdA 476 2.33e+01 1yroB 286 2.34e+01 c.68.1.2 123932 3kasA 640 2.37e+01 3hhyA 280 2.38e+01 3k28A 429 2.40e+01 3cp5A 124 2.40e+01 1ug8A 87 2.41e+01 d.68.7.1 107825 1yaxA 153 2.41e+01 1ut1A 148 2.42e+01 b.2.3.6 108014 2uubR 88 2.46e+01 a.4.8.1 139949 1xahA 354 2.48e+01 3fvhA 237 2.53e+01 3eeyA 197 2.54e+01 1w36C 1122 2.54e+01 c.37.1.19,c.37.1.19,c.52.1.25 114125,114126,114127 1g1xC 88 2.55e+01 1fjfR a.4.8.1 16249 1bd8 156 2.57e+01 1bd8 1bd8A 156 2.57e+01 d.211.1.1 19157 2vqeR 88 2.59e+01 a.4.8.1 153442 1uayA 242 2.59e+01 c.2.1.2 88390 2dbnA 461 2.63e+01 2wmkA 606 2.64e+01 2w02A 620 2.65e+01 3b50A 310 2.71e+01 2j49A 148 2.72e+01 d.379.1.1 147870 2bneA 241 2.74e+01 c.73.1.3 128824 3i3wA 443 2.76e+01 1ukxA 137 2.88e+01 d.20.1.3 107919 2vk3A 142 2.93e+01 3a4yA 431 2.94e+01 1zgsA 447 2.95e+01 1uc2A 481 2.98e+01 d.261.1.1 99161 2cw8A 537 3.00e+01 2pkpA 170 3.01e+01 3ie0A 431 3.01e+01 1h49A 512 3.07e+01 c.1.8.4 83477 1aisB 200 3.14e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 3ibwA 88 3.20e+01 3hczA 148 3.21e+01 3dktA 265 3.24e+01 1de4C 640 3.24e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1k8tA 510 3.24e+01 e.41.1.1 68316 1fgxA 288 3.27e+01 1fgxA c.68.1.2 34508 2wmiA 606 3.28e+01 2bv9A 290 3.30e+01 c.1.8.3 129242 2zh7A 436 3.31e+01 a.160.1.3,d.218.1.7,d.58.16.2 154451,154452,154453 2v3gA 283 3.32e+01 c.1.8.3 152457 2bszA 278 3.35e+01 d.3.1.5 129131 3kreA 263 3.36e+01 2btuA 346 3.37e+01 3isqA 393 3.38e+01 1fljA 260 3.39e+01 2cba b.74.1.1 27954 1ydyA 356 3.41e+01 c.1.18.3 123006 1q7fA 286 3.45e+01 b.68.9.1 96036 2wmiB 606 3.47e+01 1q40B 219 3.47e+01 d.17.4.2 95771 1d5rA 324 3.47e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 1z2iA 358 3.50e+01 2v78A 313 3.52e+01 3i4rA 277 3.53e+01 2citA 282 3.56e+01 c.1.8.3 130499 1g5hA 454 3.57e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 3licA 274 3.58e+01 3idzA 431 3.59e+01 3d7nA 193 3.62e+01 1lugA 259 3.65e+01 b.74.1.1 91127 2p0wA 324 3.65e+01 1uw4B 248 3.65e+01 a.118.1.14 100072 2r6fA 972 3.66e+01 1nwbA 124 3.68e+01 b.124.1.1 86296 2drwA 363 3.71e+01 e.3.1.1 131674 2zv3A 115 3.72e+01 3blnA 143 3.74e+01 2r7hA 177 3.75e+01 1lc0A 294 3.80e+01 c.2.1.3,d.81.1.4 73823,73824 3bjoA 103 3.82e+01 2rb9A 334 3.83e+01 2p0sA 143 3.87e+01 c.94.1.3 149140 2whnA 116 3.90e+01 1sotA 320 3.92e+01 b.36.1.4,b.47.1.1 105852,105853 2z0uA 155 3.99e+01 2p6yA 142 4.01e+01 3ks3A 260 4.02e+01 3bkrA 126 4.09e+01 3lfmA 495 4.14e+01 1b0uA 262 4.18e+01 1b0uA c.37.1.12 32370 1prn 289 4.18e+01 3prn 2cdcA 366 4.20e+01 2i4lA 458 4.22e+01 3lhnA 126 4.22e+01 2o5aA 125 4.31e+01 d.218.1.12 148593 3mc4A 287 4.36e+01 2do1A 55 4.40e+01 a.140.2.1 131595 1jmmA 377 4.42e+01 b.30.6.1 71749 1snzA 344 4.44e+01 b.30.5.4 98930 2f5xA 312 4.46e+01 2gzxA 265 4.47e+01 1te0A 318 4.48e+01 b.36.1.4,b.47.1.1 112400,112401 3ioxA 497 4.53e+01 2ozeA 298 4.55e+01 2p5qA 170 4.55e+01 3ie1A 431 4.64e+01 2b1mA 246 4.66e+01 1b56A 135 4.67e+01 b.60.1.2 27183 1qhtA 775 4.67e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1e8gA 560 4.68e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1v8hA 107 4.69e+01 b.1.18.19 119870 1f60A 458 4.72e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 3ge9A 255 4.73e+01 2cw3A 280 4.75e+01 3kq5A 393 4.75e+01 2izpA 303 4.78e+01 a.250.1.1 137826 1oixA 191 4.78e+01 c.37.1.8 118710 2dkfA 431 4.79e+01 d.157.1.10 146536 3cuqC 176 4.83e+01 2dkjA 407 4.84e+01 3h9eA 346 4.85e+01 2wnwA 447 4.85e+01 3k5rA 218 4.86e+01 1e5pA 151 4.90e+01 1bj7 b.60.1.1 59272 1oh0A 131 4.99e+01 d.17.4.3 87004 1hroA 106 5.00e+01 1ycc a.3.1.1 15897 1yixA 265 5.02e+01 c.1.9.12 123371 3lacA 215 5.03e+01 3g91A 265 5.05e+01 3a68A 212 5.06e+01 1s12A 94 5.07e+01 d.64.2.1 112003 1h09A 338 5.14e+01 b.109.1.1,c.1.8.8 83420,83421 1dkzA 219 5.19e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 2ceyA 306 5.24e+01 1opy 131 5.25e+01 1opy 2qg3A 208 5.28e+01 2a1iA 146 5.28e+01 c.52.1.20 125999 1tljA 213 5.30e+01 d.282.1.1 107126 2iwaA 266 5.31e+01 1pztA 286 5.45e+01 c.68.1.2 95470 2j8gA 339 5.46e+01 b.109.1.1,c.1.8.8 147915,147916 2d5fA 493 5.46e+01 2bsnA 145 5.47e+01 2w6kA 145 5.47e+01 c.151.1.1 153740 3hbuP 462 5.47e+01 3gfcA 425 5.50e+01 1czaN 917 5.55e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1lu4A 136 5.57e+01 c.47.1.10 91124 1gai 472 5.65e+01 1ayx 1gaiA 472 5.65e+01 a.102.1.1 18819 3ho1A 685 5.67e+01 1yd9A 193 5.68e+01 c.50.1.2 122976 2o7tA 199 5.69e+01 a.4.1.9,a.121.1.1 148670,148671 1ym0A 238 5.71e+01 1w1kA 560 5.72e+01 d.58.32.1,d.145.1.1 109059,109060 1j96A 323 5.73e+01 c.1.7.1 71616 3g3lA 327 5.74e+01 2pm7A 399 5.77e+01 2i8dA 123 5.83e+01 d.198.4.1 147561 2eyqA 1151 5.84e+01 b.34.18.1,c.37.1.19,c.37.1.19,c.37.1.19,c.37.1.19,d.315.1.1 132590,132591,132592,132593,132594,132595 1oivA 191 5.88e+01 c.37.1.8 93076 1mppA 361 5.94e+01 b.50.1.2 26856 2id4A 503 5.95e+01 b.18.1.20,c.41.1.1 137265,137266 1b8zA 90 5.95e+01 1huuA a.55.1.1 17902 3dqgA 151 5.98e+01 1co6A 107 6.06e+01 1ycc a.3.1.1 15894 2zfuA 215 6.09e+01 3h1tA 590 6.09e+01 2w2gA 264 6.10e+01 3hbvP 462 6.12e+01 3b7nA 320 6.12e+01 3i33A 404 6.14e+01 2bdeA 470 6.15e+01 c.108.1.23 128335 1a7j 290 6.17e+01 1a7j 1a7jA 290 6.17e+01 c.37.1.6 31952 2cunA 410 6.18e+01 3hbcA 320 6.18e+01 1q2lA 939 6.19e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 1r5bA 467 6.21e+01 b.43.3.1,b.44.1.1,c.37.1.8 104803,104804,104805 1h0hB 214 6.24e+01 d.58.1.5 76437 2pbnA 313 6.30e+01 2aamA 309 6.33e+01 c.1.8.15 126489 1go7P 462 6.35e+01 b.80.7.1,d.92.1.6 76245,76246 1nhp 447 6.35e+01 1nhp 1nhpA 447 6.35e+01 c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1viuA 203 6.36e+01 d.113.1.1 100771 3cqcA 270 6.37e+01 3prn 289 6.40e+01 3prn 3prnA 289 6.40e+01 f.4.3.1 43761 2o1xA 629 6.45e+01 3ie2A 431 6.51e+01 1vioA 243 6.52e+01 d.265.1.3,d.66.1.5 100762,100763 1nhsA 447 6.54e+01 c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 3ic9A 492 6.54e+01 1bupA 386 6.58e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 3mtiA 185 6.64e+01 1xyzA 347 6.71e+01 1taxA c.1.8.3 28804 2z6cA 129 6.72e+01 1g7dA 106 6.73e+01 1g7dA a.71.1.1 18318 1k7iA 479 6.76e+01 b.80.7.1,d.92.1.6 77281,77282 1ji0A 240 6.78e+01 c.37.1.12 71665 1tqmA 282 6.79e+01 a.4.5.56,d.144.1.9 107236,107237 3ehcA 128 6.80e+01 2jzbB 74 6.86e+01 2dcnA 311 6.87e+01 c.72.1.1 131374 2z1eA 342 6.91e+01 d.79.4.1,d.139.1.1 153932,153933 1r1hA 696 7.01e+01 d.92.1.4 104756 2wm8A 187 7.05e+01 1pu1A 94 7.06e+01 d.266.1.1 104307 1gpqA 135 7.06e+01 d.233.1.1 83295 3ipkA 497 7.08e+01 1fs0E 138 7.12e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 2vpuA 354 7.15e+01 2j97A 109 7.16e+01 3fblA 82 7.20e+01 3dmcA 134 7.26e+01 d.17.4.10 157805 1g8kA 825 7.33e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 2wmhA 581 7.38e+01 1prxA 224 7.39e+01 1prxA c.47.1.10 33076 2zj8A 720 7.54e+01 2o5hA 136 7.54e+01 d.363.1.1 148599 2pstX 74 7.56e+01 d.100.2.1 149829 1zm0A 114 7.57e+01 b.55.1.1 125276 2wmfA 581 7.58e+01 3i4kA 383 7.64e+01 3fzhA 381 7.69e+01 3mbjA 291 7.78e+01 2zxyA 87 7.80e+01 1lk5A 229 7.80e+01 c.124.1.4,d.58.40.1 73960,73961 2nvmA 126 7.82e+01 d.326.1.1 138631 2p91A 285 7.82e+01 1thjA 214 7.85e+01 1qreA b.81.1.5 28072 1dfoA 417 7.88e+01 1bj4A c.67.1.4 34480 2k4qA 156 7.89e+01 2yvlA 248 7.89e+01 1lb3A 182 7.89e+01 a.25.1.1 77873 2nlvA 112 7.92e+01 d.326.1.1 138362 1k2xA 177 8.00e+01 d.153.1.5 90929