# List of top-scoring protein chains for t2k-80-60-80-str2+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.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 1e54A 332 1.10e-12 1e54A f.4.3.1 59258 2fgqX 332 3.06e-12 f.4.3.1 133439 1hxxA 340 5.75e-11 2omf f.4.3.1 61385 2omf 340 6.74e-11 2omf 2j1nA 346 7.22e-11 2porA 301 2.24e-04 f.4.3.1 43759 2por 301 2.46e-04 2por 2o4vA 411 5.17e-03 3prnA 289 7.47e-03 f.4.3.1 43761 3prn 289 7.63e-03 3prn 1prn 289 7.99e-03 3prn 2bbdA 350 4.46e-01 1ex0A 731 9.15e-01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 2fauA 341 1.19e+00 1hx6A 394 1.43e+00 1cjdA b.121.2.1,b.121.2.1 58995,58996 1f1sA 814 2.28e+00 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1j5qA 437 2.34e+00 b.121.2.3,b.121.2.3 77084,77085 1evuA 731 2.99e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1h54A 754 3.23e+00 a.102.1.4,b.30.5.3 60634,60635 1t16A 427 3.33e+00 f.4.3.4 106242 1m3yA 413 3.36e+00 b.121.2.3,b.121.2.3 78579,78580 1f13A 731 3.39e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 2cqsA 842 3.76e+00 1p4tA 155 3.78e+00 f.4.1.1 87779 1wcdJ 441 4.17e+00 b.121.4.9 120887 1g0dA 695 4.34e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 2oitA 434 5.82e+00 2df7A 458 5.86e+00 b.121.4.9 131449 1mkfA 382 6.04e+00 b.116.1.1 79232 1yewA 382 6.10e+00 1vaxA 287 6.23e+00 d.96.1.4,d.96.1.4 119910,119911 2gagA 965 6.56e+00 1f60A 458 7.26e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1fieA 731 7.39e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21879,22167,22168,37109 2qt6A 498 7.47e+00 1fnhA 271 8.44e+00 1fnhA b.1.2.1,b.1.2.1,b.1.2.1 21976,21977,21978 2gu1A 361 8.68e+00 2h5uA 499 8.94e+00 1ne9A 335 9.05e+00 d.108.1.4,d.108.1.4 91839,91840 1uwvA 433 9.17e+00 b.40.4.12,c.66.1.40 100128,100129 1vjjA 692 9.20e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1cs0A 1073 9.35e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 2odjA 428 1.02e+01 1r17A 343 1.09e+01 b.2.3.4,b.2.3.4 96796,96797 2hb0A 369 1.14e+01 1k1xA 659 1.15e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1v10A 521 1.15e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1xruA 282 1.15e+01 b.82.1.13 122262 1alyA 146 1.17e+01 b.22.1.1 23856 1cb8A 678 1.18e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1w99A 558 1.19e+01 1f0lA 535 1.19e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 2axtO 247 1.20e+01 1kyaA 499 1.22e+01 b.6.1.3,b.6.1.3,b.6.1.3 73203,73204,73205 1c3oA 1073 1.29e+01 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 1n67A 359 1.36e+01 b.2.3.4,b.2.3.4 85354,85355 1zjkA 403 1.37e+01 b.47.1.2,g.18.1.1,g.18.1.1 125149,125150,125151 2qkiC 343 1.40e+01 2cjaA 522 1.40e+01 1q2wA 308 1.46e+01 b.47.1.4 88355 1jv2A 957 1.46e+01 b.1.15.1,b.1.15.1,b.1.15.1,b.69.8.1 67334,67335,67336,67337 1a9xA 1058 1.47e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1so7A 382 1.48e+01 b.68.1.1 112106 2h2zA 306 1.50e+01 1aly 146 1.51e+01 1aly 1gl4A 285 1.64e+01 d.22.1.2,g.3.11.5 65286,65287 2bf6A 449 1.65e+01 2a73B 991 1.66e+01 1bquA 215 1.70e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 2bazA 142 1.79e+01 1ospO 257 1.88e+01 1ospO b.76.1.1 27971 1fx5A 242 1.95e+01 1led b.29.1.1 24135 1hn0A 1021 1.96e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1olzA 663 1.96e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1s3rA 535 1.97e+01 1a0tP 413 1.98e+01 1a0tP f.4.3.2 43794 2z8rA 591 2.00e+01 1lj5A 379 2.12e+01 e.1.1.1 73928 2amdA 311 2.12e+01 1t3qB 788 2.14e+01 d.41.1.1,d.133.1.1 106369,106370 2tbvA 387 2.21e+01 2tbvA b.121.4.7 23302 2hkdA 320 2.25e+01 1zx5A 300 2.26e+01 b.82.1.3 125763 1yx2A 365 2.31e+01 2ismA 352 2.34e+01 2pgzA 230 2.34e+01 3blcA 330 2.39e+01 1cid 177 2.40e+01 1cid 1bdfA 235 2.42e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2in5A 207 2.51e+01 1vgyA 393 2.58e+01 c.56.5.4,d.58.19.1 100620,100621 1tjxA 159 2.63e+01 b.7.1.2 112465 1ndoB 194 2.64e+01 1ndoB d.17.4.4 38121 1cidA 177 2.64e+01 b.1.1.1,b.1.1.3 19740,21679 2qdrA 303 2.67e+01 2o62A 270 2.68e+01 1wsrA 375 2.69e+01 1pfoA 500 2.70e+01 f.9.1.1 43826 1pfo 500 2.70e+01 1pfo 1n7oA 721 2.76e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1yi9A 309 2.79e+01 b.121.1.2,b.121.1.2 123276,123277 2vfrA 422 2.84e+01 2j43A 219 2.88e+01 1rhi3 236 2.92e+01 1aym3 1c3hA 137 2.95e+01 b.22.1.1 90405 1yifA 533 2.97e+01 b.29.1.23,b.67.2.1 123283,123284 1a65A 504 3.01e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 2a9dA 372 3.08e+01 b.1.18.6,d.176.1.1 126431,126432 2bwrA 401 3.09e+01 2p52A 196 3.12e+01 2grvA 621 3.14e+01 1pk6C 129 3.15e+01 b.22.1.1 94803 1suuA 312 3.17e+01 b.68.10.1 99006 1p4uA 153 3.32e+01 b.1.10.2 87780 4aahA 571 3.34e+01 4aahA b.70.1.1 27678 2hyxA 352 3.37e+01 1phm 310 3.37e+01 1phm 2edmA 161 3.42e+01 1s0uA 408 3.45e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1ltlA 279 3.45e+01 b.40.4.11 84701 2bfgA 503 3.47e+01 b.71.1.2,c.1.8.3 128423,128424 1gycA 499 3.56e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1ei5A 520 3.63e+01 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 1tnrA 144 3.63e+01 2tnfA b.22.1.1 23867 2bw8A 227 3.74e+01 b.29.1.11 129324 1aozA 552 3.78e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 2jg9C 131 3.84e+01 1eg9B 194 3.86e+01 1ndoB d.17.4.4 38120 2qsvA 220 3.88e+01 1cov3 238 3.89e+01 1aym3 2petA 231 3.93e+01 2zaiA 497 3.97e+01 1y8qB 640 4.04e+01 2biqA 219 4.06e+01 2g8cO 251 4.06e+01 1vyoA 128 4.09e+01 1xnaA 183 4.10e+01 1xnaA b.18.1.8 23773 2iwvA 281 4.11e+01 2bklA 695 4.12e+01 2fxqA 264 4.22e+01 2oseA 234 4.26e+01 1soxA 466 4.30e+01 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 2de6A 392 4.35e+01 b.33.1.2,d.129.3.3 131415,131416 1zlqA 502 4.40e+01 c.94.1.1 125253 2i51A 195 4.40e+01 2awkA 228 4.47e+01 2o26U 290 4.57e+01 2bynA 227 4.58e+01 1se8A 301 4.61e+01 b.40.4.3 105448 2mprA 421 4.61e+01 2mprA f.4.3.2 43788 1af6A 421 4.64e+01 2mprA f.4.3.2 43772 2phlA 397 4.65e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1bkzA 135 4.70e+01 1a3k b.29.1.3 24202 1e1aA 314 4.70e+01 1e1aA b.68.6.1 59155 1ju3A 583 4.84e+01 b.18.1.13,c.69.1.21 67300,67301 1zpuA 534 4.85e+01 1o7nB 194 4.88e+01 d.17.4.4 81164 3bs6A 280 4.90e+01 2czrA 226 5.00e+01 1m9sA 605 5.01e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 2cy9A 140 5.03e+01 d.38.1.5 131019 2dd7A 216 5.04e+01 1qexA 288 5.05e+01 1qexA b.32.1.1 24425 1qz8A 113 5.11e+01 b.140.1.1 96619 1n6eA 1071 5.16e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1elvA 333 5.17e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 2vesA 299 5.18e+01 2jqyA 280 5.22e+01 1h0bA 256 5.22e+01 b.29.1.11 83422 2f01A 127 5.25e+01 b.61.1.1 132647 2q6kA 283 5.28e+01 2omlA 189 5.29e+01 1qnxA 209 5.31e+01 1qnxA d.111.1.1 40914 2e8yA 718 5.38e+01 1b9cA 236 5.42e+01 1ema d.22.1.1 38358 1hfuA 503 5.45e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1uv6A 210 5.49e+01 b.96.1.1 100030 2hrgA 496 5.56e+01 1vq0A 302 5.59e+01 d.193.1.1,g.81.1.1 114000,114001 3b9cA 144 5.65e+01 2e4tA 519 5.67e+01 1i7dA 659 5.68e+01 1d6mA e.10.1.1 61886 2bcmA 165 5.69e+01 1fiqC 763 5.69e+01 1fiqC d.41.1.1,d.133.1.1 38588,41418 1bob 320 5.71e+01 1bob 1bobA 320 5.71e+01 d.108.1.1 40816 2re9A 181 5.72e+01 1ty9A 222 5.79e+01 b.45.1.1 112827 1hr6B 443 5.86e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 2v6oA 596 5.97e+01 1pk6B 132 5.98e+01 b.22.1.1 94802 1o91A 178 5.99e+01 b.22.1.1 92656 1uiuA 502 6.00e+01 c.94.1.1 99434 2cfmA 561 6.04e+01 1tupA 219 6.04e+01 1tupA b.2.5.2 22434 1zxiB 809 6.06e+01 d.41.1.1,d.133.1.1 125774,125775 1h7zA 194 6.08e+01 1qhvA b.21.1.1 60733 3b9jC 763 6.11e+01 2rb8A 104 6.17e+01 1q5hA 147 6.18e+01 b.85.4.1 95893 1xocA 520 6.18e+01 c.94.1.1 122201 1ema 236 6.19e+01 1ema 1luqA 127 6.24e+01 b.61.1.1 91128 1m8uA 173 6.35e+01 b.11.1.1,b.11.1.1 91233,91234 1nijA 318 6.42e+01 c.37.1.10,d.237.1.1 85741,85742 2madH 373 6.52e+01 2bbkH b.69.2.1 27639 1jroB 777 6.53e+01 d.41.1.1,d.133.1.1 67141,67142 1jnyA 435 6.55e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2q7nA 488 6.56e+01 1p2zA 968 6.67e+01 b.121.2.2,b.121.2.2 93962,93963 1z02A 446 6.69e+01 2hhpA 530 6.72e+01 a.160.1.1,d.218.1.3,d.58.16.1 136503,136504,136505 2aqmA 154 6.76e+01 1w24A 182 6.78e+01 d.159.1.7 120579 1hzgA 295 6.79e+01 1hzgA d.194.1.1 61436 2olrA 540 6.83e+01 c.91.1.1,c.109.1.1 139140,139141 3butA 136 6.96e+01 2oajA 902 6.97e+01 1gttA 429 7.00e+01 d.177.1.1,d.177.1.1 70529,70530 2fpnA 216 7.09e+01 d.129.10.1 133908 1yllA 200 7.10e+01 b.82.1.17 123653 2hbtA 247 7.18e+01 1zdyA 307 7.22e+01 d.313.1.1 124961 1efcA 393 7.29e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1ux2A 212 7.32e+01 b.96.1.1 100132 2ac0A 200 7.34e+01 b.2.5.2 126539 1pg4A 652 7.39e+01 e.23.1.1 88067 1uw6A 211 7.48e+01 b.96.1.1 100079 2qxlA 658 7.54e+01 1dpeA 507 7.56e+01 c.94.1.1 35799 1pvc3 238 7.76e+01 1aym3 2q5iA 691 7.79e+01 2yr5A 721 7.86e+01 1fa0B 537 7.87e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 1pmnA 364 7.89e+01 d.144.1.7 94907 1kypA 237 7.89e+01 d.22.1.1 73280 2q3zA 687 7.89e+01 1swuA 127 7.90e+01 1swuA b.61.1.1 27230 1mkaA 171 7.94e+01 1mkaA d.38.1.2 38543 1t8hA 277 7.96e+01 d.194.1.2 106664 1neu 124 7.99e+01 1neu 1neuA 124 7.99e+01 b.1.1.1 19704