# List of top-scoring protein chains for t04-100-30-str2-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 1hlvA 131 3.38e-01 a.4.1.7,a.4.1.7 65854,65855 1sedA 117 8.77e-01 a.219.1.1 105449 1huuA 90 8.83e-01 1huuA a.55.1.1 17897 1ywfA 296 1.06e+00 1s69A 124 1.06e+00 a.1.1.1 105305 1pyaB 228 1.37e+00 1pyaB 1whzA 70 1.53e+00 1a41 234 1.69e+00 1a41 d.163.1.2 42174 1zljA 78 1.78e+00 1b8zA 90 1.91e+00 1huuA a.55.1.1 17902 1ugjA 141 2.24e+00 b.41.1.3 107826 1z77A 200 2.74e+00 1w2yA 229 3.18e+00 a.204.1.1 109140 1ekeA 230 3.39e+00 1ekeA c.55.3.1 33572 2cg4A 152 3.46e+00 1u20A 212 3.64e+00 1rkbA 173 4.16e+00 1g5cA 170 4.17e+00 1g5cA c.53.2.1 60264 1ldg 316 4.62e+00 1ceqA c.2.1.5,d.162.1.1 30165,42132 2cfxA 144 4.75e+00 1aua 296 5.03e+00 1aua a.5.3.1,c.13.1.1 16290,30882 1y63A 184 5.17e+00 1pb6A 212 6.00e+00 a.4.1.9,a.121.1.1 88017,88018 1zbsA 291 6.08e+00 1pgjA 478 6.20e+00 2pgd a.100.1.1,c.2.1.6 18783,30195 2bjbA 462 6.85e+00 1s9jA 341 7.01e+00 1knvA 293 7.35e+00 c.52.1.7 68707 1zdc 35 7.49e+00 1fc2C k.13.1.1 46434 2fx0A 201 7.83e+00 1p7tA 731 8.11e+00 c.1.13.1 94319 1jnrA 643 8.30e+00 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1ffyA 917 8.32e+00 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1my6A 199 8.33e+00 a.2.11.1,d.44.1.1 85232,85233 2fjbA 643 8.49e+00 1d8cA 723 8.52e+00 1d8cA c.1.13.1 29325 1oqyA 368 8.90e+00 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1l9vA 317 9.16e+00 d.13.2.1,d.216.1.1 73760,73761 1l6xB 34 9.80e+00 k.13.1.1 73644 1l7vA 326 1.01e+01 f.22.1.1 73672 2ccmA 191 1.01e+01 1fvkA 189 1.02e+01 1fvkA c.47.1.13 90351 1acvA 189 1.04e+01 1fvkA c.47.1.13 90328 2a97A 439 1.04e+01 1ta3B 303 1.05e+01 c.1.8.3 106732 1kdgA 546 1.06e+01 c.3.1.2,d.16.1.1 77337,77338 1pveA 72 1.08e+01 a.189.1.1 104322 1t2dA 322 1.10e+01 c.2.1.5,d.162.1.1 99084,99085 1jf2A 195 1.14e+01 1ej3A a.39.1.5 62930 1kutA 230 1.19e+01 d.143.1.1 73017 1t3qA 168 1.21e+01 a.56.1.1,d.15.4.2 106367,106368 1ka2A 499 1.23e+01 d.92.1.5 77305 1pufA 77 1.24e+01 a.4.1.1 95131 1rtxA 123 1.29e+01 a.1.1.1 97827 1qgxA 357 1.31e+01 1qgxA e.7.1.1 42973 1u9lA 70 1.31e+01 a.60.4.2 107751 1fc3A 120 1.31e+01 1fc3A a.4.6.3 16237 1sup 275 1.31e+01 1gci c.41.1.1 32510 1keaA 221 1.39e+01 a.96.1.2 68491 1lw6E 281 1.42e+01 c.41.1.1 74293 1to2E 281 1.44e+01 1ydnA 295 1.47e+01 5eau 548 1.53e+01 5eat a.102.4.1,a.128.1.3 18851,19443 1ka1A 357 1.53e+01 e.7.1.1 68369 1g99A 408 1.55e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 2polA 366 1.56e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1ok7A 366 1.58e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1je8A 82 1.60e+01 a.4.6.2 77108 1wkaA 147 1.64e+01 1el4A 195 1.66e+01 1ej3A a.39.1.5 59453 1sd4A 126 1.72e+01 a.4.5.39 105428 1s5jA 847 1.74e+01 1mmiA 366 1.74e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1nrvA 105 1.75e+01 d.93.1.1 86126 2gfnA 209 1.75e+01 1tca 317 1.79e+01 1tca c.69.1.17 34726 1m3kA 392 1.83e+01 c.95.1.1,c.95.1.1 78565,78566 1u3aA 189 1.84e+01 1io2A 213 1.91e+01 1ekeA c.55.3.1 62612 1iv3A 152 1.92e+01 d.79.5.1 76828 1mdc 133 1.99e+01 1hmt b.60.1.2 27198 1lxa 262 2.06e+01 1lxa b.81.1.1 28052 1qflA 389 2.06e+01 1afwA c.95.1.1,c.95.1.1 35908,35909 1p49A 562 2.10e+01 c.76.1.2 94089 3tmkA 216 2.11e+01 3tmkA c.37.1.1 31920 1l8nA 679 2.13e+01 c.1.8.10,d.92.2.2 84564,84565 1ji8A 111 2.20e+01 d.203.1.1 66733 1zv1A 65 2.20e+01 1ukz 203 2.26e+01 1zin c.37.1.1 31840 2c30A 321 2.27e+01 1rlzA 369 2.28e+01 c.31.1.1 104989 1m4tA 392 2.28e+01 c.95.1.1,c.95.1.1 78617,78618 1i88A 389 2.31e+01 c.95.1.2,c.95.1.2 66070,66071 1uz5A 402 2.32e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1ci4A 89 2.36e+01 1qckA a.60.5.1 17970 1bi5A 389 2.37e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1ax4A 467 2.37e+01 1ax4A c.67.1.2 34391 1fjlA 81 2.42e+01 2hddA a.4.1.1 16017 1q0pA 223 2.42e+01 c.62.1.1 95507 1j55A 95 2.46e+01 a.39.1.2 77078 1nktA 922 2.48e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 85830,85831,85832,85833 1pmzA 86 2.55e+01 a.39.1.10 104195 1tg7A 971 2.58e+01 1v32A 101 2.62e+01 a.42.1.1 100277 1v7nV 163 2.64e+01 a.26.1.2 100476 1rx0A 393 2.65e+01 a.29.3.1,e.6.1.1 98007,98008 1jt6A 188 2.68e+01 a.4.1.9,a.121.1.1 67247,67248 2ahyA 110 2.68e+01 1gu9A 177 2.69e+01 a.152.1.1 65540 2atxA 194 2.74e+01 1o4sA 389 2.74e+01 c.67.1.1 86620 1lw1A 177 2.75e+01 a.152.1.1 74290 2cfaA 217 2.80e+01 1ui5A 215 2.81e+01 a.4.1.9,a.121.1.1 107856,107857 1yxmA 303 2.82e+01 1cjgA 62 2.85e+01 1pru a.35.1.5 17112 1li5A 461 2.87e+01 a.27.1.1,c.26.1.1 73912,73913 1dhs 344 2.93e+01 1dhs c.31.1.1 31727 1ve4A 206 2.94e+01 1so2A 420 2.95e+01 a.211.1.2 98936 1qc7A 101 2.98e+01 1qc7A a.118.14.1 18456 1d5yA 292 3.11e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1f1eA 154 3.14e+01 a.22.1.2 64927 1a04A 215 3.15e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1neeA 138 3.15e+01 d.241.1.1,g.59.1.1 91841,91842 1cs1A 386 3.15e+01 1ibjA c.67.1.3 34399 1d8bA 81 3.23e+01 1d8bA a.60.8.1 18094 1p5hA 428 3.27e+01 c.123.1.1 87802 2fexA 188 3.32e+01 1u7kA 131 3.33e+01 1oaoA 674 3.40e+01 e.26.1.2 86744 1ri7A 171 3.45e+01 a.4.5.32,d.58.4.2 97504,97505 2g7gA 213 3.56e+01 1sur 215 3.61e+01 1sur c.26.2.2 31620 1adjA 421 3.64e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1tv8A 340 3.66e+01 c.1.28.3 107352 1alu 186 3.70e+01 1alu a.26.1.1 16826 5pal 109 3.72e+01 1a75A a.39.1.4 17215 1kp8A 547 3.73e+01 a.129.1.1,c.8.5.1,d.56.1.1 84414,84415,84416 1z2iA 358 3.78e+01 1y01A 102 3.81e+01 1x42A 232 3.82e+01 1li5B 461 3.84e+01 a.27.1.1,c.26.1.1 73914,73915 1pjjA 271 3.86e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1s6cA 183 3.90e+01 a.39.1.5 98594 2vhbA 146 3.94e+01 2vhbA a.1.1.2 15629 1vi0A 206 3.99e+01 a.4.1.9,a.121.1.1 100720,100721 1wy9A 147 4.00e+01 1y8oA 419 4.02e+01 1phnB 172 4.04e+01 1qgwC a.1.1.3 15642 1bed 181 4.06e+01 1fvkA c.47.1.13 90330 1res 43 4.06e+01 1ret a.4.1.2 16023 1nnjA 271 4.08e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1wviA 257 4.08e+01 1h4vB 421 4.11e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 2g8lA 299 4.14e+01 2gaiA 633 4.19e+01 1a8b 318 4.23e+01 1avc a.65.1.1 18171 2fnuA 375 4.23e+01 1qz9A 416 4.25e+01 c.67.1.3 96621 1yemA 179 4.31e+01 1tdzA 272 4.32e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1sfxA 109 4.38e+01 a.4.5.50 105505 2cchB 260 4.40e+01 2fd5A 180 4.42e+01 2c4nA 250 4.50e+01 2guhA 214 4.50e+01 1bqbA 301 4.58e+01 1hyt d.92.1.2 58962 1wovA 250 4.62e+01 1jq5A 370 4.64e+01 e.22.1.2 67084 2bjcA 62 4.65e+01 1ve3A 227 4.66e+01 1hruA 188 4.68e+01 1hruA d.115.1.1 40926 1eexB 224 4.70e+01 1dioB c.51.3.1 33213 1h3qA 140 4.71e+01 d.110.4.3 76652 1pufB 73 4.71e+01 a.4.1.1 95132 1yl31 118 4.71e+01 1vdlA 80 4.73e+01 a.5.2.1 108528 1j1vA 94 4.75e+01 a.4.12.2 83981 1vljA 407 4.76e+01 e.22.1.2 108832 1vj7A 393 4.80e+01 a.211.1.1,d.218.1.8 100801,100802 3kvt 115 4.90e+01 1t1dA d.42.1.2 38642 1y88A 199 4.97e+01 2fp4B 395 5.09e+01 1szhA 161 5.11e+01 a.226.1.1 106157 1m1nA 491 5.15e+01 c.92.2.3 78417 1s28A 132 5.17e+01 d.198.1.1 105223 1khyA 148 5.17e+01 a.174.1.1 77410 1m7yA 435 5.19e+01 c.67.1.4 78761 2au5A 139 5.22e+01 1j6wA 175 5.24e+01 1j98A d.185.1.2 62663 1zuhA 168 5.24e+01 2aeuA 374 5.25e+01 1v3yA 192 5.26e+01 1wzdA 215 5.33e+01 2hddA 61 5.33e+01 2hddA a.4.1.1 15971 1b8gA 429 5.34e+01 1b8gA c.67.1.4 34499 1rktA 205 5.36e+01 a.4.1.9,a.121.1.1 97623,97624 2bvaA 292 5.37e+01 1u0jA 267 5.42e+01 c.37.1.20 107546 1cojA 212 5.42e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1x3lA 440 5.43e+01 1qusA 322 5.44e+01 1ltm d.2.1.6 36991 1iz0A 302 5.46e+01 b.35.1.2,c.2.1.1 83821,83822 1eudB 396 5.51e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1iomA 377 5.57e+01 a.103.1.1 83698 2gh1A 301 5.57e+01 1bg4 302 5.58e+01 1taxA c.1.8.3 28806 1qh3A 260 5.60e+01 1qh5A d.157.1.2 42059 1qh5A 260 5.62e+01 1qh5A d.157.1.2 42057 1mba 147 5.63e+01 2fal a.1.1.2 15149 1xmxA 385 5.65e+01 2ran 316 5.73e+01 1avc a.65.1.1 18170 2c5rA 67 5.73e+01 1v96A 149 5.76e+01 1ukxA 137 5.78e+01 d.20.1.3 107919 1m6eX 359 5.79e+01 c.66.1.35 91188 1yh2A 175 5.80e+01 2cobA 70 5.81e+01 2fw2A 260 5.87e+01 1p0yA 444 5.88e+01 a.166.1.1,b.85.7.3 87654,87655 2cu3A 64 5.94e+01 1enh 54 5.99e+01 2hddA a.4.1.1 15973 2a8aA 439 6.03e+01 1k8uA 90 6.08e+01 a.39.1.2 72181 1cc1L 498 6.29e+01 1h2rL e.18.1.1 43301 2g7uA 257 6.33e+01 2a11A 242 6.38e+01 2fifB 70 6.39e+01 1z8uA 102 6.40e+01 1w0dA 337 6.47e+01 2h21A 440 6.49e+01 1b74A 254 6.51e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1u5tC 202 6.54e+01 a.4.5.54,a.4.5.54 107688,107689 1hm6A 346 6.55e+01 1avc a.65.1.1 18147 1vjxA 157 6.55e+01 a.25.1.1 100837 1yu6A 275 6.55e+01 2bmjA 178 6.56e+01 1yozA 116 6.58e+01 1r0rE 274 6.60e+01 c.41.1.1 96735 1oyiA 82 6.65e+01 a.4.5.19 93729 1xk7A 408 6.65e+01 1xa3A 437 6.68e+01 1ox3A 109 6.69e+01 h.1.17.1 93668 1x58A 62 6.70e+01 3thiA 371 6.82e+01 2thiA c.94.1.1 35792 1c3wA 222 6.83e+01 1c3wA f.13.1.1 43405 2dbbA 151 6.84e+01 1hqsA 423 6.90e+01 1iso c.77.1.1 61154 1o65A 246 6.91e+01 b.58.1.2 92544 1yzbA 182 6.98e+01 1u14A 172 6.98e+01 c.51.4.3 107579 1igrA 478 7.18e+01 1igrA c.10.2.5,c.10.2.5,g.3.9.1 30877,30878,44188 1tc3C 51 7.27e+01 1tc3C a.4.1.2 16025 1twfB 1224 7.32e+01 1wh5A 80 7.51e+01 1q1hA 110 7.56e+01 a.4.5.41 95580 2ah5A 210 7.57e+01 3grs 478 7.65e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1w36B 1180 7.65e+01 1ow1A 195 7.78e+01 b.131.1.3 93625 1i74A 309 7.92e+01 1i74A c.107.1.1 61867 1rfmA 344 7.99e+01 c.122.1.1 97385 1n1fA 159 8.00e+01 a.26.1.3 79803 1o8rA 94 8.02e+01 d.234.1.1 86677 1j54A 186 8.04e+01 c.55.3.5 77077 1qb2A 109 8.09e+01 1qb2A a.36.1.1 17125 1no4A 97 8.09e+01 h.1.24.1 85918 1zy4A 303 8.09e+01 2gtsA 86 8.10e+01 2bnkA 67 8.14e+01 1m5yA 408 8.15e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 2a6cA 83 8.16e+01 1xuuA 349 8.16e+01 1t9bA 677 8.18e+01 2aw4Q 117 8.19e+01 1jggA 60 8.20e+01 2hddA a.4.1.1 62950 2h0uA 217 8.26e+01 2c7nA 74 8.28e+01 1mh1 186 8.33e+01 1eesA c.37.1.8 32002 1o6uA 403 8.37e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1aisB 200 8.41e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1gv3A 248 8.43e+01 a.2.11.1,d.44.1.1 70585,70586 2cmxA 118 8.43e+01 1v4sA 455 8.46e+01 c.55.1.3,c.55.1.3 100309,100310 1h6pA 203 8.66e+01 a.146.1.1 60690 1sh0A 510 8.66e+01 e.8.1.4 98876 1t6fA 37 8.70e+01 h.1.28.1 106565 1wu4A 396 8.75e+01 1tgrA 52 8.78e+01 2c2hA 192 8.79e+01 1k3pA 426 8.83e+01 a.103.1.1 77237 1m0kA 262 8.84e+01 f.13.1.1 78344 2ga1A 106 8.89e+01 1olmA 403 8.94e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1dm5A 315 8.94e+01 1avc a.65.1.1 18186 1vkeA 133 8.99e+01 a.152.1.2 108650