# List of top-scoring protein chains for t04-100-30-near-backbone-11-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 1vin 268 6.19e-35 1vin a.74.1.1,a.74.1.1 18354,18355 2cchB 260 1.15e-34 1w98B 283 7.02e-28 1kxu 333 5.89e-25 1jkw a.74.1.1,a.74.1.1 18358,18359 1aisB 200 7.34e-20 1aisB a.74.1.2,a.74.1.2 18384,18385 1f5qB 252 1.06e-18 1f5qB a.74.1.1,a.74.1.1 18362,18363 1lqaA 346 1.55e-01 c.1.7.1 84674 1r29A 127 1.92e-01 d.42.1.1 96856 1z7dA 433 3.23e-01 1guxB 152 6.52e-01 1guxB a.74.1.3 18389 1j1vA 94 8.70e-01 a.4.12.2 83981 1dl2A 511 9.54e-01 1dl2A a.102.2.1 18844 1z7yA 322 1.03e+00 1pbv 195 1.04e+00 1pbv a.118.3.1 19179 1ww8A 439 1.23e+00 1xd3A 230 1.37e+00 1t6sA 162 1.40e+00 1z7wA 322 1.40e+00 1uch 230 1.72e+00 1uch d.3.1.6 37129 1ujnA 348 1.82e+00 e.22.1.1 99460 1b43A 340 1.82e+00 1a76 a.60.7.1,c.120.1.2 18092,33362 1r8sE 203 1.82e+00 a.118.3.1 97248 1vpqA 273 2.00e+00 1ku3A 73 2.59e+00 a.4.13.2 73000 1xjeA 644 2.71e+00 1ojxA 263 2.75e+00 c.1.10.1 93164 1w8sA 263 2.84e+00 2c3nA 247 2.88e+00 2f57A 317 3.12e+00 1v9nA 360 3.37e+00 2g8yA 385 3.43e+00 1txoA 237 3.67e+00 1vk8A 106 3.68e+00 d.58.48.1 108636 1tr0A 108 3.71e+00 d.58.4.4 107261 1r8mE 203 3.76e+00 a.118.3.1 97242 1nhyA 219 3.78e+00 a.45.1.1,c.47.1.5 80520,80521 1auk 489 3.93e+00 1auk c.76.1.2 35030 1f5mA 180 4.01e+00 1f5mB d.110.2.1 40895 1q4rA 112 4.17e+00 d.58.4.4 95823 1ctt 294 4.36e+00 1ctt c.97.1.1,c.97.1.1 36022,36023 1mun 225 4.65e+00 1mun a.96.1.2 18744 2ax4A 198 4.93e+00 2gx9A 129 5.16e+00 1oz9A 150 5.17e+00 d.92.1.15 93808 1r59O 505 5.22e+00 1xjjA 644 5.24e+00 1oe4A 247 5.29e+00 c.18.1.3 86895 1hrhA 136 5.43e+00 1rthA c.55.3.1 33577 1uyrA 737 5.44e+00 c.14.1.4,c.14.1.4 100188,100189 1j0aA 325 6.26e+00 c.79.1.1 83871 2cwoA 197 6.42e+00 1e8yA 966 6.43e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1v2zA 111 6.47e+00 a.186.1.1 108300 1nxcA 478 6.53e+00 a.102.2.1 92293 1vmeA 410 6.91e+00 c.23.5.1,d.157.1.3 108893,108894 2b33A 140 7.17e+00 1w2xA 758 7.41e+00 c.14.1.4,c.14.1.4 109134,109135 1ls1A 295 7.44e+00 a.24.13.1,c.37.1.10 78170,78171 1oatA 439 7.54e+00 2dkb c.67.1.4 34461 3tmkA 216 7.64e+00 3tmkA c.37.1.1 31920 1vb3A 428 8.15e+00 1whnA 128 8.19e+00 1tbmA 326 8.23e+00 a.211.1.2 106744 1z0xA 220 8.25e+00 1o8uA 257 8.29e+00 c.14.1.3 81194 2byjA 439 8.44e+00 1wa5C 960 8.87e+00 1zrn 232 9.15e+00 1qq5A c.108.1.1 43323 1jfmA 174 9.33e+00 d.19.1.1 66640 1zz1A 369 9.56e+00 1ve1A 304 9.60e+00 1qlpA 394 9.95e+00 1ovaA e.1.1.1 42628 1iapA 211 1.01e+01 a.91.1.1 62119 1e8gA 560 1.01e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1tzjA 338 1.02e+01 1ynpA 317 1.03e+01 1qqfA 277 1.04e+01 1c3d a.102.4.4 18875 2oatA 439 1.05e+01 2dkb c.67.1.4 34452 1rfmA 344 1.05e+01 c.122.1.1 97385 2bg5A 324 1.05e+01 1hw1A 239 1.16e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1g5hA 454 1.17e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1w1kA 560 1.17e+01 d.58.32.1,d.145.1.1 109059,109060 1vhnA 318 1.18e+01 c.1.4.1 100693 1ymiA 334 1.21e+01 2aheA 267 1.21e+01 1r3cA 366 1.24e+01 d.144.1.7 96906 2b1eA 564 1.25e+01 1nu7D 282 1.27e+01 a.8.6.1,a.8.6.1 92191,92192 1dqpA 230 1.28e+01 1dqnA c.61.1.1 34069 2bryA 497 1.28e+01 1ld8A 382 1.28e+01 a.118.6.1 73838 1szoA 257 1.29e+01 c.14.1.3 106164 1c3pA 375 1.30e+01 1c3pA c.42.1.2 32606 1lxnA 99 1.30e+01 d.58.48.1 84737 1jd1A 129 1.33e+01 1qu9A d.79.1.1 62890 1e7uA 961 1.34e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1atlA 202 1.35e+01 1atlA d.92.1.9 40322 1d8dA 377 1.35e+01 1ft1A a.118.6.1 19185 1r5lA 262 1.36e+01 a.5.3.1,c.13.1.1 97099,97100 1mmsA 140 1.36e+01 1mmsA a.4.7.1,d.47.1.1 16247,38766 1ngnA 155 1.36e+01 a.96.1.2 85697 1blxA 326 1.37e+01 1hcl d.144.1.7 41596 2ct8A 497 1.38e+01 1wbsA 360 1.38e+01 1lnzA 342 1.40e+01 b.117.1.1,c.37.1.8 78112,78113 1v5iB 76 1.40e+01 1eqfA 280 1.41e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 1wzuA 300 1.42e+01 1zzlA 351 1.43e+01 1mkmA 249 1.44e+01 a.4.5.33,d.110.2.2 79242,79243 1dqnA 230 1.45e+01 1dqnA c.61.1.1 34067 1hl2A 297 1.49e+01 c.1.10.1 83581 1y14A 187 1.51e+01 2bylA 439 1.54e+01 1dk0A 188 1.57e+01 1b2vA d.35.1.1 38530 1s6cA 183 1.57e+01 a.39.1.5 98594 2aw5A 541 1.58e+01 1o4uA 285 1.58e+01 c.1.17.1,d.41.2.1 86624,86625 1u7lA 392 1.59e+01 1rkbA 173 1.61e+01 1m12A 84 1.65e+01 a.64.1.1 84745 2d2mB 142 1.69e+01 1cb0A 283 1.73e+01 1cb0A c.56.2.1 33790 1j1bA 420 1.81e+01 d.144.1.7 90758 1esmA 316 1.82e+01 1esmA c.37.1.6 31953 1us5A 314 1.82e+01 c.94.1.1 99856 1tn6A 382 1.84e+01 1vixA 420 1.86e+01 c.56.5.4,d.58.19.1 100777,100778 1ngr 85 1.88e+01 1ngr a.77.1.2 18422 1vljA 407 1.89e+01 e.22.1.2 108832 1o58A 303 1.91e+01 c.79.1.1 92491 1y13A 181 1.93e+01 2gfsA 372 1.95e+01 2cxcA 144 1.99e+01 1orjA 130 2.00e+01 a.24.19.1 93456 1m4lA 307 2.02e+01 c.56.5.1 78604 1vlwA 217 2.02e+01 c.1.10.1 108868 2bhoA 130 2.02e+01 1fnoA 417 2.03e+01 d.58.19.1,c.56.5.4 70145,75841 1vjyA 303 2.03e+01 d.144.1.7 108633 1sq5A 308 2.06e+01 c.37.1.6 105882 1yadA 221 2.07e+01 1kr4A 125 2.09e+01 d.58.5.2 72889 1k4nA 192 2.09e+01 d.32.1.5 72059 1up6A 416 2.10e+01 c.2.1.5,d.162.1.2 107976,107977 1fmjA 351 2.10e+01 c.37.1.5 59879 1kuuA 202 2.11e+01 d.153.2.1 73019 1wmaA 276 2.12e+01 1fvzA 271 2.16e+01 1fvzA 1o3uA 135 2.18e+01 a.24.16.3 86615 1ysjA 404 2.21e+01 1wa3A 205 2.21e+01 1n25A 368 2.24e+01 c.37.1.20 85264 1wqsA 173 2.27e+01 1opjA 293 2.28e+01 d.144.1.7 87230 1q79A 514 2.29e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1iomA 377 2.30e+01 a.103.1.1 83698 2bfgA 503 2.36e+01 1r31A 428 2.37e+01 d.58.20.1,d.179.1.1 96897,96898 1t7lA 766 2.40e+01 1h5uA 842 2.42e+01 1a8i c.87.1.4 60655 2abwA 227 2.42e+01 2c6cA 707 2.42e+01 1mvcA 240 2.42e+01 a.123.1.1 79499 1s1eA 224 2.42e+01 3kvt 115 2.43e+01 1t1dA d.42.1.2 38642 2ctc 307 2.43e+01 1aye c.56.5.1 33802 1ekqA 272 2.43e+01 1c3qA c.72.1.2 34941 1zz2A 360 2.46e+01 1h4lD 147 2.46e+01 a.74.1.1 70873 1tkiA 321 2.50e+01 1tkiA d.144.1.7 41638 2ca6A 386 2.50e+01 1winA 143 2.51e+01 1vkwA 218 2.51e+01 d.90.1.2 108695 1ls6A 295 2.52e+01 c.37.1.5 91115 1wqaA 455 2.54e+01 1cd31 152 2.57e+01 1cd31 2ng1 293 2.57e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1f80D 81 2.58e+01 1acp a.28.1.1 59686 1wz7A 111 2.59e+01 1jdlA 121 2.66e+01 a.3.1.1 66557 1oniA 137 2.68e+01 d.79.1.1 87144 1zs3A 182 2.68e+01 1i45A 248 2.71e+01 1amk c.1.1.1 61665 1go3F 107 2.72e+01 a.60.8.2 65407 1odkA 235 2.75e+01 c.56.2.1 86863 1h6kZ 98 2.76e+01 d.58.7.1 60686 1xfkA 336 2.82e+01 2bmeA 186 2.85e+01 1kjnA 157 2.88e+01 c.115.1.1 72614 1b65A 375 2.89e+01 1b65A d.154.1.1 42020 1womA 271 2.89e+01 1wvqA 167 2.99e+01 1hf8A 289 3.00e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1yrgA 385 3.02e+01 1yrgA c.10.1.2 30854 1hw5A 210 3.07e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1qwkA 317 3.09e+01 c.1.7.1 96482 1r2jA 366 3.10e+01 a.29.3.1,e.6.1.1 96869,96870 1unlD 208 3.11e+01 1t8xA 267 3.12e+01 2ffjA 300 3.22e+01 2dfkA 402 3.24e+01 1b72B 87 3.29e+01 1akhA a.4.1.1 16001 2f5tX 233 3.29e+01 1h1wA 289 3.31e+01 d.144.1.7 83460 1jpaA 312 3.32e+01 d.144.1.7 67011 1bouB 302 3.37e+01 1bouB c.56.6.1 33859 1r9lA 309 3.39e+01 c.94.1.1 97262 1s7oA 113 3.39e+01 a.4.13.3 105354 1rqjA 299 3.40e+01 a.128.1.1 97744 1ywrA 360 3.41e+01 1bw0A 416 3.41e+01 1bw0A c.67.1.1 34385 1yi9A 309 3.42e+01 1qahA 136 3.42e+01 d.79.1.1 96338 1ars 396 3.45e+01 1ajsA c.67.1.1 34287 2bnlA 136 3.45e+01 1a8i 842 3.46e+01 1a8i c.87.1.4 35490 2bs9A 503 3.51e+01 1t3lA 337 3.52e+01 b.34.2.1,c.37.1.1 106358,106359 1hekA 131 3.53e+01 a.61.1.5 65818 1fpzA 212 3.53e+01 1fpzA c.45.1.1 59976 1fwsA 267 3.54e+01 1d9eA c.1.10.4 60063 1ur3M 319 3.59e+01 c.1.7.1 99806 1l2tA 235 3.63e+01 c.37.1.12 73514 1neyA 247 3.63e+01 c.1.1.1 80449 1h3nA 878 3.69e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1uluA 261 3.70e+01 1r1dA 247 3.71e+01 c.69.1.29 96813 1nq7A 244 3.72e+01 a.123.1.1 92047 1yruB 74 3.74e+01 1km4A 247 3.74e+01 c.1.2.3 72740 1y82A 157 3.76e+01 2fuvA 549 3.77e+01 1vhwA 253 3.78e+01 c.56.2.1 100706 1tqhA 247 3.78e+01 c.69.1.29 107225 1l9xA 315 3.78e+01 c.23.16.1 73762 1xdpA 687 3.79e+01 2ahqA 76 3.80e+01 1ka2A 499 3.83e+01 d.92.1.5 77305 2a61A 145 3.83e+01 1ej0A 180 3.83e+01 1ej0A c.66.1.2 34179 1frb 315 3.86e+01 1frb c.1.7.1 28665 1is1A 185 3.90e+01 d.67.3.1 83704 1urjA 1136 3.91e+01 1j8uA 325 3.91e+01 d.178.1.1 71611 2a19A 175 3.92e+01 1nal1 297 3.95e+01 1nal3 1nqkA 381 3.95e+01 c.1.16.4 92050 1yakA 263 3.98e+01 1nlnA 204 4.01e+01 d.3.1.7 91962 1px5A 349 4.03e+01 a.160.1.2,d.218.1.6 95277,95278 1ni5A 433 4.11e+01 c.26.2.5,d.229.1.1 80533,80534 1ahxA 396 4.13e+01 1ajsA c.67.1.1 34293 1ornA 226 4.14e+01 a.96.1.1 87342 1o86A 589 4.18e+01 d.92.1.5 81177 1mrzA 293 4.18e+01 b.43.5.1,c.26.1.3 91452,91453 2a5dA 175 4.23e+01 1wtjA 343 4.27e+01 1p5jA 372 4.27e+01 c.79.1.1 104067 1ibrB 462 4.30e+01 1qgrA a.118.1.1 19120 1nmeA 146 4.31e+01 c.17.1.1 85874 1i27A 73 4.31e+01 1i27A a.4.5.30 61555 1dbhA 354 4.33e+01 1awe a.87.1.1,b.55.1.1 18514,26967 2bsjA 133 4.35e+01 1rtu 114 4.36e+01 9rnt d.1.1.4 36139 1zl0A 311 4.37e+01 2fq3A 104 4.38e+01 1pzxA 289 4.39e+01 c.119.1.1 95484 1fr2A 86 4.45e+01 a.28.2.1 83256 1c3jA 351 4.45e+01 1c3jA c.87.1.1 35459 1ef8A 261 4.47e+01 1ef8A c.14.1.3 30921 1avpA 204 4.47e+01 1avpA d.3.1.7 37132 1pq4A 291 4.48e+01 c.92.2.2 94995 1gdeA 389 4.48e+01 c.67.1.1 60456 1yhtA 367 4.48e+01 1mp9A 198 4.50e+01 d.129.1.1,d.129.1.1 91385,91386 1xahA 354 4.53e+01 1sfjA 238 4.54e+01 2awiA 317 4.54e+01 1q42A 201 4.59e+01 d.17.4.2 95776 1z7mA 344 4.62e+01 1ta9A 450 4.62e+01 1vk4A 298 4.63e+01 c.72.1.1 100850 1zhaA 267 4.68e+01 1c75A 71 4.68e+01 451c a.3.1.1 15796 1n2zA 245 4.69e+01 c.92.2.2 79865 2bshA 125 4.71e+01 1qrvA 73 4.74e+01 1cktA a.21.1.1 16425 1je8A 82 4.76e+01 a.4.6.2 77108 1zq4A 693 4.80e+01 1jcxA 267 4.84e+01 c.1.10.4 66510 1aj8A 371 4.85e+01 1aj8A a.103.1.1 18900 1pcxA 810 4.94e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 1gsoA 431 5.02e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1fvrA 327 5.04e+01 d.144.1.7 60047 1sflA 238 5.09e+01 1bv1 159 5.11e+01 1bv1 d.129.3.1 41313 1vzoA 355 5.13e+01 d.144.1.7 108971 2cq8A 110 5.15e+01 1j1iA 296 5.16e+01 c.69.1.10 83977 1pfvA 551 5.17e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1w9gA 104 5.20e+01 1cr1A 296 5.21e+01 1cr1A c.37.1.11 32286 1woyA 500 5.22e+01 1o08A 221 5.29e+01 c.108.1.6 86525 1rcwA 231 5.30e+01 a.132.1.4 97299 1l5xA 280 5.32e+01 c.106.1.1 77718 1fgkA 310 5.33e+01 1fgkA d.144.1.7 41693 1r3sA 367 5.33e+01 c.1.22.1 96963 1kjwA 295 5.35e+01 b.34.2.1,c.37.1.1 68643,68644 1jixA 351 5.36e+01 1c3jA c.87.1.1 63081 1r5eA 115 5.37e+01 4crxA 322 5.37e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 2d1yA 256 5.38e+01 1q32A 544 5.41e+01 d.136.1.3,d.136.1.3 104507,104508 1eiwA 111 5.42e+01 1eiwA c.23.3.1 31130 2fpoA 202 5.46e+01 1hu4A 288 5.48e+01 1hu4A 1f4lA 551 5.49e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1uehA 253 5.50e+01 c.101.1.1 99259 1z2iA 358 5.50e+01 1ej6D 418 5.51e+01 i.7.1.1 45970 1j0dA 341 5.55e+01 c.79.1.1 83902 2ezk 99 5.66e+01 2ezk a.4.1.2 16027 1hgxA 183 5.69e+01 1tc1A c.61.1.1 34027 1w0mA 226 5.70e+01 c.1.1.1 109027 1a8h 500 5.72e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1cjbA 231 5.72e+01 1qk3A c.61.1.1 34079 2d1eA 248 5.73e+01 2aucA 126 5.83e+01 1i6xA 209 5.84e+01 a.4.5.4,b.82.3.2 83673,83674 1yx1A 264 5.86e+01 1xngA 268 5.86e+01 1qy5A 269 5.90e+01 d.122.1.1 96573 1pe1A 267 5.90e+01 c.1.10.4 94591 2cg4A 152 5.91e+01 1owlA 484 5.93e+01 a.99.1.1,c.28.1.1 93647,93648 1fus 106 5.98e+01 9rnt d.1.1.4 36050 1v7pC 200 5.99e+01 c.62.1.1 108408 2fflA 756 6.00e+01 1uroA 367 6.02e+01 1uroA c.1.22.1 29675 2aebA 322 6.08e+01 1fdr 248 6.12e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 2ag5A 246 6.13e+01 1n5dA 288 6.13e+01 c.2.1.2 80030 1t3qA 168 6.16e+01 a.56.1.1,d.15.4.2 106367,106368 2kfnA 605 6.25e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1eswA 500 6.25e+01 1cwyA c.1.8.1 59500 1esiA 262 6.25e+01 1skf e.3.1.1 42682 1k4mA 213 6.28e+01 c.26.1.3 77258 1hssA 124 6.29e+01 1bea a.52.1.2 17819 1e5rA 290 6.30e+01 1e5rA b.82.2.4 59276 2f94F 350 6.33e+01 1r9kA 172 6.33e+01 a.168.1.1 104869 2a13A 166 6.34e+01 1d8cA 723 6.35e+01 1d8cA c.1.13.1 29325 1phnA 162 6.38e+01 1cpcA a.1.1.3 15641 2ew0A 192 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366 8.87e+01 1zrsA 317 8.89e+01 1elqA 390 8.91e+01 1elqA c.67.1.3 34436 1lucA 355 8.93e+01 1lucA c.1.16.1 29547 1f0kA 364 8.95e+01 1f0kA c.87.1.2 35465 1mdc 133 8.97e+01 1hmt b.60.1.2 27198