# List of top-scoring protein chains for t2k-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 1h6gA 256 6.49e-01 1h6gA a.24.9.1,a.24.9.1 60669,60670 1biqA 375 8.07e-01 1xikA a.25.1.2 16786 1ribA 375 1.24e+00 1xikA a.25.1.2 16788 2itbA 206 1.63e+00 1xikA 375 1.79e+00 1xikA a.25.1.2 16784 1mxrA 375 1.92e+00 a.25.1.2 85197 2f6hX 419 2.09e+00 1av8A 340 2.69e+00 1xikA a.25.1.2 16796 2vpzC 253 2.84e+00 1n97A 389 3.43e+00 a.104.1.1 80335 1krqA 167 3.51e+00 a.25.1.1 68855 1r03A 182 3.85e+00 a.25.1.1 104675 2h7oA 303 3.90e+00 1rp3A 239 4.10e+00 a.4.13.1,a.4.13.2,a.177.1.1 97678,97679,97680 3bqoA 211 4.27e+00 1jsdB 176 4.51e+00 h.3.1.1 63259 1w1wE 121 4.76e+00 a.4.5.57 114084 1h68A 239 5.47e+00 f.13.1.1 118486 1csh 435 5.51e+00 1csh 1cshA 435 5.51e+00 a.103.1.1 18880 1ymtA 246 5.54e+00 2yzrA 330 5.97e+00 1unlD 208 6.57e+00 a.74.1.1 113326 1uddA 226 6.62e+00 a.132.1.3 107776 1k0fA 277 6.78e+00 c.92.2.2 71974 1epwA 1290 7.07e+00 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1au1A 166 7.46e+00 1ifa a.26.1.3 16889 1h2sA 225 7.65e+00 f.13.1.1 76578 2c2jA 211 7.73e+00 1txdA 385 7.78e+00 a.87.1.1,b.55.1.1 107422,107423 1jgjA 217 9.09e+00 1c3wA f.13.1.1 62952 1wwmA 190 9.18e+00 a.132.1.3 121363 2or0A 414 9.23e+00 3caxA 369 9.66e+00 2pziA 681 9.94e+00 1v2aA 210 1.01e+01 a.45.1.1,c.47.1.5 100263,100264 1jpnA 296 1.09e+01 a.24.13.1,c.37.1.10 67039,67040 1qqtA 551 1.12e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 2b5dX 528 1.17e+01 a.8.3.3,c.6.2.4 127886,127887 3c6gA 479 1.17e+01 1p8cA 145 1.18e+01 a.152.1.2 94354 1oj7A 408 1.20e+01 e.22.1.2 103971 2rdzA 452 1.20e+01 1z21A 112 1.23e+01 a.243.1.2 124367 2o9gA 234 1.26e+01 1k0iA 394 1.40e+01 c.3.1.2,d.16.1.2 67942,67943 2uxwA 607 1.42e+01 1toaA 313 1.43e+01 1toaA c.92.2.2 35598 1tqyA 424 1.45e+01 c.95.1.1,c.95.1.1 107245,107246 1pfvA 551 1.46e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 3bg2A 444 1.50e+01 1gkzA 388 1.52e+01 a.29.5.1,d.122.1.4 65268,65269 2hi4A 495 1.53e+01 2q9fA 456 1.54e+01 3biqA 467 1.55e+01 1pbe 394 1.56e+01 1pbe 1pbeA 394 1.56e+01 c.3.1.2,d.16.1.2 30338,37869 1vkeA 133 1.56e+01 a.152.1.2 108650 2qzcA 214 1.65e+01 1q8cA 151 1.67e+01 a.79.1.2 96202 1dd5A 185 1.72e+01 1dd5A d.67.3.1 39564 1iw0A 215 1.74e+01 a.132.1.1 83720 1glqA 209 1.77e+01 1pgtA a.45.1.1,c.47.1.5 17588,32882 3b5oA 244 1.77e+01 1syyA 346 1.78e+01 a.25.1.2 106126 2h79A 269 1.85e+01 3c3rA 380 1.87e+01 1sw6A 327 1.89e+01 1sw6A d.211.1.1 19176 1wzdA 215 1.93e+01 a.132.1.1 121493 1cj3A 392 1.97e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1ls1A 295 1.98e+01 a.24.13.1,c.37.1.10 78170,78171 1ng1 294 2.01e+01 1ng1 1yisA 478 2.03e+01 2px6A 316 2.04e+01 1ps1A 337 2.13e+01 1ps1A a.128.1.4 19450 1d8cA 723 2.15e+01 1d8cA c.1.13.1 29325 1qkrA 188 2.16e+01 1qkrA a.24.9.1 16628 2givA 295 2.18e+01 d.108.1.1 135253 1ykjA 394 2.19e+01 2pq8A 278 2.19e+01 1h21A 247 2.24e+01 a.138.1.3 76510 2zfoD 155 2.31e+01 2qf9A 179 2.31e+01 1tm0A 350 2.37e+01 d.21.1.3 107147 2ntoA 201 2.38e+01 2ouwA 138 2.39e+01 1i5pA 633 2.41e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 2a6tA 271 2.42e+01 a.242.1.1,d.113.1.7 126309,126310 1v4aA 440 2.46e+01 a.24.16.4,d.218.1.9 108350,108351 1fcyA 236 2.47e+01 2lbd a.123.1.1 19282 1c8bA 371 2.49e+01 1c8bA c.56.1.2 59082 2yqyA 169 2.54e+01 2ehgA 149 2.58e+01 2oltA 227 2.71e+01 1s2xA 206 2.76e+01 a.47.3.1 105229 1b5l 172 2.85e+01 1b5l 1b5lA 172 2.85e+01 a.26.1.3 16900 1p7tA 731 2.87e+01 c.1.13.1 94319 2pg0A 385 2.89e+01 2p6vA 114 2.89e+01 2paqA 201 2.91e+01 a.211.1.1 139643 2j3xA 431 2.95e+01 2pvqA 201 2.98e+01 1f4lA 551 3.03e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 2ax9A 256 3.04e+01 a.123.1.1 127481 2veqA 565 3.05e+01 1keyA 235 3.05e+01 a.118.16.1 72389 1uedA 406 3.11e+01 a.104.1.1 99256 2ojqA 348 3.14e+01 1vf1A 229 3.35e+01 2bdwA 362 3.35e+01 3ck6A 252 3.37e+01 1bbhA 131 3.37e+01 1bbhA a.24.3.2 16546 2parA 201 3.46e+01 1sedA 117 3.50e+01 a.219.1.1 105449 1p7gA 222 3.54e+01 a.2.11.1,d.44.1.1 94223,94224 2d2mA 140 3.54e+01 1ehkA 562 3.62e+01 1ehkA f.24.1.1 43624 2ax8A 256 3.62e+01 1hz4A 373 3.72e+01 a.118.8.2 65960 1aorA 605 3.73e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1iybA 208 3.79e+01 d.124.1.1 90720 2aelA 374 3.81e+01 2oewA 380 3.81e+01 17gsA 210 3.81e+01 1pgtA a.45.1.1,c.47.1.5 17524,32818 1zs3A 182 3.83e+01 a.25.1.1 125573 1kktA 511 3.88e+01 a.102.2.1 68687 1pjcA 361 3.89e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 2b1eA 564 3.91e+01 1sayA 361 3.93e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 2ngrB 234 3.95e+01 1tx4A a.116.1.1 19105 2rfpA 171 3.96e+01 2ax6A 256 4.01e+01 a.123.1.1 127479 1t7rA 269 4.03e+01 a.123.1.1 106635 2bnxA 386 4.05e+01 a.118.1.23 128861 2aaxA 275 4.07e+01 2z8aA 146 4.08e+01 2avkA 136 4.27e+01 2a2rA 210 4.39e+01 a.45.1.1,c.47.1.5 126058,126059 1xwrA 97 4.44e+01 a.35.1.9 122406 2pmzA 880 4.44e+01 1jfgA 374 4.49e+01 a.128.1.5 66636 1bvp1 349 4.56e+01 1bvp1 2lbd 267 4.56e+01 2lbd 1qusA 322 4.60e+01 1ltm d.2.1.6 36991 1pgtA 210 4.64e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 3ctzA 623 4.68e+01 1ra6A 461 4.72e+01 e.8.1.4 104879 1qu7A 227 4.81e+01 1qu7A h.4.5.1 45789 2hk0A 309 4.85e+01 2nsfA 261 4.88e+01 2a19B 284 4.95e+01 3d9nA 145 4.98e+01 1yyqA 374 5.06e+01 1ltm 320 5.08e+01 1ltm 2fm9A 215 5.09e+01 a.257.1.1 133770 2oexA 351 5.11e+01 1h99A 224 5.12e+01 a.142.1.1,a.142.1.1 60814,60815 3c1jA 424 5.13e+01 2e9xA 149 5.14e+01 1cpcA 162 5.16e+01 1cpcA a.1.1.3 15643 2qkmB 266 5.20e+01 1v9mA 323 5.29e+01 f.40.1.1 100543 2aplA 157 5.40e+01 a.258.1.1 127132 2dvmA 439 5.42e+01 2ph5A 480 5.42e+01 1smbA 154 5.51e+01 d.111.1.1 105756 2pbxA 203 5.54e+01 2hr3A 147 5.55e+01 a.4.5.28 136678 2ps5A 374 5.58e+01 1iweA 457 5.59e+01 c.37.1.10 71486 1fouA 309 5.60e+01 1fouA e.27.1.1 43364 2j1oA 268 5.61e+01 2azjA 289 5.62e+01 1kwgA 645 5.62e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 2nx4A 194 5.63e+01 2bptA 861 5.77e+01 a.118.1.1 128951 1rh5B 74 5.79e+01 f.23.28.1 97465 1x9mA 698 5.89e+01 c.55.3.5,e.8.1.1 114999,115000 3bilA 348 5.93e+01 1aqwA 209 5.95e+01 1pgtA a.45.1.1,c.47.1.5 17517,32811 1e4mM 501 5.96e+01 1e70M c.1.8.4 59226 2p67A 341 5.96e+01 2zfoA 140 6.03e+01 1yoyA 175 6.03e+01 a.211.1.1 123795 2o57A 297 6.04e+01 2arkA 188 6.06e+01 c.23.5.8 127202 2np5A 203 6.10e+01 a.4.1.9,a.121.1.1 138424,138425 1tx4A 198 6.10e+01 1tx4A a.116.1.1 19098 2ew8A 249 6.10e+01 c.2.1.2 132447 1e70M 501 6.13e+01 1e70M c.1.8.4 28926 1ya0A 497 6.20e+01 a.118.8.1 122785 1t7pA 698 6.22e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 1nrlA 316 6.23e+01 a.123.1.1 92091 1a6dA 545 6.32e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 1ybxA 143 6.34e+01 2qr7A 342 6.38e+01 1uzeA 589 6.53e+01 d.92.1.5 108174 1lbkA 208 6.57e+01 a.45.1.1,c.47.1.5 73809,73810 1pu6A 218 6.62e+01 a.96.1.5 95123 1cfr 285 6.63e+01 1cfr 1cfrA 285 6.63e+01 c.52.1.7 33312 1brwA 433 6.67e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1m4rA 151 6.73e+01 a.26.1.3 84799 1v54A 514 6.81e+01 f.24.1.1 100321 2jdiG 273 6.81e+01 c.49.2.1 138272 3sdhA 146 6.82e+01 3sdhA a.1.1.2 14984 3bhcA 249 6.96e+01 2r6aC 143 6.99e+01 1em2A 229 7.03e+01 1em2A d.129.3.2 41321 2oqpA 134 7.06e+01 1nf1A 333 7.07e+01 1nf1A a.116.1.2 19110 2c0wA 50 7.11e+01 2r40D 266 7.13e+01 1twfB 1224 7.15e+01 e.29.1.1 112726 1nq7A 244 7.18e+01 a.123.1.1 92047 1h2sB 60 7.26e+01 f.13.1.1 76579 1ldjA 760 7.36e+01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1t2bA 397 7.36e+01 3b96A 587 7.39e+01 2occA 514 7.44e+01 2occA f.24.1.1 43518 1mj3A 260 7.46e+01 c.14.1.3 79183 1x4tA 92 7.46e+01 a.2.15.1 121698 1gjwA 637 7.49e+01 b.71.1.1,c.1.8.1 60582,60583 1y2mA 716 7.50e+01 2d0tA 406 7.53e+01 a.266.1.2 131093 1iuqA 367 7.53e+01 c.112.1.1 90703 1hn0A 1021 7.54e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 2qizA 982 7.55e+01 1h8eA 510 7.56e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1x9fB 145 7.61e+01 a.1.1.2 114984 2qsfX 171 7.61e+01 2a5vA 213 7.62e+01 1k4wA 252 7.62e+01 a.123.1.1 72068 2jg1A 330 7.64e+01 2pbeA 294 7.71e+01 1maz 221 7.73e+01 1maz 1otvA 259 7.73e+01 a.132.1.4 93526 2ct8A 497 7.78e+01 1ki1B 352 7.78e+01 a.87.1.1,b.55.1.1 72497,72498 1k30A 368 7.79e+01 c.112.1.1 68067 2d1lA 253 7.80e+01 1fkmA 396 7.84e+01 1fkmA a.69.2.1,a.69.2.1 18315,18316 1jm0A 50 7.86e+01 k.8.1.1 66870 1a75A 108 7.88e+01 1a75A a.39.1.4 17216 2fdvA 476 7.90e+01 2ck3G 272 7.95e+01 c.49.2.1 130562 2qwtA 196 7.95e+01 1b1bA 140 7.99e+01 1bi0 a.4.5.24,a.76.1.1 16215,18421