# List of top-scoring protein chains for t06-100-30-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 2ew8A 249 5.87e-03 1wmaA 276 1.48e-02 2ci1A 275 2.15e-02 1h1yA 228 8.67e-02 c.1.2.2 76506 2cwxA 430 1.09e-01 2d69A 430 1.15e-01 2fliA 220 1.22e-01 2bd0A 244 1.45e-01 1regX 122 1.89e-01 1regX d.58.27.1 39406 1g61A 228 2.40e-01 1g61A d.126.1.1 41126 1m93B 245 2.70e-01 7taa 478 2.81e-01 7taa b.71.1.1,c.1.8.1 27778,28765 1cjcA 460 2.91e-01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1t3gA 159 3.09e-01 1udxA 416 3.32e-01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 2b9dA 52 3.69e-01 1xg5A 279 4.57e-01 1iro 54 4.78e-01 1rb9 g.41.5.1 45223 1tqhA 247 5.33e-01 c.69.1.29 107225 2bgkA 278 6.52e-01 1v7rA 186 6.77e-01 c.51.4.1 100482 1jae 471 7.16e-01 1smd b.71.1.1,c.1.8.1 27773,28760 1zemA 262 7.51e-01 1muwA 386 7.63e-01 c.1.15.3 79495 1k7kA 221 8.74e-01 c.51.4.1 72104 1n40A 396 1.04e+00 a.104.1.1 79977 1zz1A 369 1.10e+00 2c07A 285 1.12e+00 1ve3A 227 1.23e+00 1ycdA 243 1.24e+00 1id0A 152 1.25e+00 d.122.1.3 66111 1mrzA 293 1.28e+00 b.43.5.1,c.26.1.3 91452,91453 1ht6A 405 1.58e+00 b.71.1.1,c.1.8.1 83629,83630 1eokA 290 1.63e+00 1eokA c.1.8.5 28991 1zwyA 185 1.74e+00 2cygA 312 1.76e+00 1t71A 281 1.80e+00 1uzmA 247 1.80e+00 1uanA 227 1.81e+00 c.134.1.1 99135 2c2aA 258 1.87e+00 1oz9A 150 2.07e+00 d.92.1.15 93808 1yk4A 52 2.07e+00 1vcvA 226 2.20e+00 1u5mA 73 2.29e+00 1kq6A 141 2.38e+00 d.189.1.1 91020 1oaa 259 2.44e+00 1oaa c.2.1.2 29829 2fqxA 318 2.48e+00 1tqjA 230 2.50e+00 c.1.2.2 107228 2ca6A 386 2.51e+00 1s2oA 244 2.63e+00 1xaoA 121 2.69e+00 1m3sA 186 2.74e+00 c.80.1.3 78573 8tlnE 316 2.80e+00 1hyt d.92.1.2 59075 1ihoA 283 2.85e+00 1ihoA c.26.1.4 62390 1wwjA 105 2.89e+00 1brfA 53 3.04e+00 1rb9 g.41.5.1 45236 1f8vA 355 3.08e+00 2bbvA b.121.4.4 23329 2erfA 209 3.09e+00 1kamA 194 3.13e+00 c.26.1.3 72254 1y7lA 316 3.22e+00 1rtqA 299 3.28e+00 c.56.5.4 97819 1ejbA 168 3.32e+00 1rvv1 c.16.1.1 59417 1zmtA 254 3.36e+00 1pwxA 254 3.39e+00 c.2.1.2 95262 1to2I 64 3.39e+00 1lba 146 3.58e+00 1lba d.118.1.1 41062 1e5mA 416 3.60e+00 1dd8A c.95.1.1,c.95.1.1 58973,58974 1rdg 53 3.68e+00 1rb9 g.41.5.1 45221 2bh1A 250 3.72e+00 6rxn 46 3.84e+00 1rb9 g.41.5.1 45222 1yljA 263 4.02e+00 2g2cA 167 4.03e+00 1nn5A 215 4.09e+00 c.37.1.1 85892 1gegA 256 4.14e+00 1ybvA c.2.1.2 29888 1v65A 64 4.20e+00 a.212.1.1 108393 1msk 331 4.42e+00 1msk d.173.1.1 42495 1j5pA 253 4.49e+00 d.81.1.3,c.2.1.3 71577,83092 1q9uA 130 4.59e+00 d.129.7.1 96314 1bm8 99 4.64e+00 1bm8 d.34.1.1 38528 1w6uA 302 4.68e+00 1yhtA 367 4.68e+00 1s7zA 117 4.76e+00 a.159.3.1 98715 1qh8B 519 4.89e+00 1qguB c.92.2.3 35634 1xc3A 302 5.04e+00 1hc7A 477 5.29e+00 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1jixA 351 5.48e+00 1c3jA c.87.1.1 63081 1dpe 507 5.55e+00 1dpe c.94.1.1 35799 1f2vA 219 5.58e+00 1f2vA c.23.17.1 59627 1n4qB 377 5.60e+00 a.102.4.3 91636 1wy7A 207 5.76e+00 1h2bA 359 5.78e+00 b.35.1.2,c.2.1.1 90543,90544 1zo0A 126 5.85e+00 1z2wA 192 5.91e+00 1gxrA 337 5.91e+00 b.69.4.1 70722 1jjtA 228 6.00e+00 1a7tA d.157.1.1 63139 1k8kB 394 6.42e+00 c.55.1.1 68307 1g6hA 257 6.43e+00 1gajA c.37.1.12 60318 1rq2A 382 6.69e+00 c.32.1.1,d.79.2.1 105048,105049 1gntA 553 6.82e+00 e.26.1.1 70290 2end 138 6.88e+00 2end a.18.1.1 16400 1bdb 277 6.88e+00 1bdb c.2.1.2 29874 1w2wB 191 6.95e+00 1sc3A 178 7.13e+00 c.17.1.1 105416 1v76A 96 7.53e+00 2fa8A 105 7.58e+00 1ja9A 274 7.77e+00 c.2.1.2 62817 1z7xW 461 7.81e+00 1x1tA 260 7.90e+00 1bebA 162 8.54e+00 1bebA b.60.1.1 27115 1cbf 285 8.56e+00 1cbf c.90.1.1 35587 1sgwA 214 8.57e+00 c.37.1.12 105541 1wd7A 261 8.73e+00 3tgl 269 8.85e+00 3tgl c.69.1.17 34733 1i36A 264 8.89e+00 a.100.1.8,c.2.1.6 71108,71109 1tjyA 316 9.00e+00 c.93.1.1 107062 1spxA 278 9.05e+00 c.2.1.2 98958 2c1xA 456 9.05e+00 1jihA 531 9.09e+00 d.240.1.1,e.8.1.7 90374,90375 1js3A 486 9.15e+00 c.67.1.6 67215 1hrhA 136 9.22e+00 1rthA c.55.3.1 33577 1nffA 260 9.32e+00 c.2.1.2 80457 1yj7A 171 9.44e+00 1rb9 53 9.65e+00 1rb9 g.41.5.1 45214 1a8d 452 9.95e+00 1a8d b.29.1.6,b.42.4.2 24262,25607 2c36A 285 9.96e+00 1jdc 429 9.97e+00 1jdc b.71.1.1,c.1.8.1 27789,28776 1h3gA 601 9.99e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1uxoA 192 1.01e+01 c.69.1.31 108121 1i19A 561 1.02e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 2fi9A 128 1.02e+01 1gmxA 108 1.02e+01 c.46.1.3 65355 1jtvA 327 1.03e+01 c.2.1.2 84230 1w78A 422 1.05e+01 1xqaA 113 1.05e+01 1le6A 123 1.05e+01 a.133.1.2 73862 1iy8A 267 1.07e+01 c.2.1.2 83774 1evlA 401 1.08e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1u9cA 224 1.08e+01 1u14A 172 1.08e+01 c.51.4.3 107579 1rvkA 382 1.09e+01 c.1.11.2,d.54.1.1 97928,97929 2ah5A 210 1.09e+01 2f0aA 98 1.11e+01 1pufB 73 1.12e+01 a.4.1.1 95132 1ne9A 335 1.15e+01 d.108.1.4,d.108.1.4 91839,91840 1nzaA 103 1.17e+01 d.58.5.2 86444 2bzgA 232 1.19e+01 1j2jB 45 1.20e+01 a.7.8.1 84017 1lw7A 365 1.22e+01 c.26.1.3,c.37.1.1 74295,74296 1lfpA 249 1.22e+01 e.39.1.1 73885 2b9eA 303 1.25e+01 1f02T 66 1.26e+01 1f02T j.67.1.1 46360 1v3vA 333 1.28e+01 b.35.1.2,c.2.1.1 108345,108346 1vhxA 150 1.31e+01 c.55.3.8 100712 1smd 496 1.31e+01 1smd b.71.1.1,c.1.8.1 27768,28755 1s98A 107 1.31e+01 b.124.1.1 105377 1cs1A 386 1.31e+01 1ibjA c.67.1.3 34399 2g03A 194 1.31e+01 1n6jG 35 1.32e+01 1puiA 210 1.36e+01 c.37.1.8 88292 1ey4A 149 1.37e+01 1snc b.40.1.1 24815 2aq5A 402 1.38e+01 1u69A 163 1.39e+01 d.32.1.7 107699 1du3A 130 1.42e+01 1d4vA g.24.1.1,g.24.1.1,g.24.1.1 44927,44928,44929 1t0iA 191 1.44e+01 c.23.5.4 106209 1hdoA 206 1.46e+01 1he2A c.2.1.2 60965 2an1A 292 1.50e+01 1y7bA 542 1.50e+01 1qlpA 394 1.53e+01 1ovaA e.1.1.1 42628 1cy5A 97 1.53e+01 1cy5A a.77.1.3 18430 1bgvA 449 1.54e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 2csgA 424 1.54e+01 1ocsA 162 1.55e+01 d.189.1.1 92776 2azeC 46 1.55e+01 2cs3A 93 1.56e+01 1gcyA 527 1.57e+01 1jdc b.71.1.1,c.1.8.1 27788,28775 1o57A 291 1.58e+01 a.4.5.40,c.61.1.1 92483,92484 1yr1A 119 1.58e+01 1wdeA 294 1.60e+01 1e5dA 402 1.60e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1rf6A 427 1.63e+01 d.68.2.2 97366 1naqA 112 1.63e+01 d.58.5.2 91761 2abqA 306 1.67e+01 1c0pA 363 1.70e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1fexA 59 1.70e+01 a.4.1.3 59803 1l3iA 192 1.70e+01 c.66.1.22 77676 2gk4A 232 1.71e+01 2ae2A 260 1.71e+01 1bdb c.2.1.2 29945 1cozA 129 1.72e+01 1cozA c.26.1.2 31598 1qreA 247 1.72e+01 1qreA b.81.1.5 28066 1sq5A 308 1.75e+01 c.37.1.6 105882 1qzzA 374 1.80e+01 a.4.5.29,c.66.1.12 96719,96720 1izoA 417 1.80e+01 a.104.1.1 83851 1j1iA 296 1.80e+01 c.69.1.10 83977 1d4oA 184 1.81e+01 1d4oA c.31.1.4 31748 2d83A 363 1.82e+01 2eutA 294 1.83e+01 2f9dA 125 1.84e+01 1buoA 121 1.87e+01 1buoA d.42.1.1 38631 1e4yA 214 1.91e+01 1zin c.37.1.1,g.41.2.1 31901,45181 16vpA 366 1.92e+01 16vpA d.180.1.1 42601 1wdyA 285 1.93e+01 2dexX 671 1.94e+01 1nbaA 264 1.97e+01 1nbaA c.33.1.3 31753 1eceA 358 1.98e+01 1eceA c.1.8.3 28813 1orvA 728 1.98e+01 b.70.3.1,c.69.1.24 87354,87355 1bsg 266 1.98e+01 1btl e.3.1.1 42729 1weyA 104 2.01e+01 1kllA 130 2.03e+01 d.32.1.2 72720 1ej2A 181 2.03e+01 1f9aA c.26.1.3 59414 1zymA 258 2.05e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1fvpA 231 2.10e+01 1nfp c.1.16.2 29556 1lgpA 116 2.11e+01 b.26.1.2 73890 1sazA 381 2.11e+01 1geqA 248 2.12e+01 2tysA c.1.2.4 28589 1nwaA 203 2.15e+01 d.58.28.1 86295 1geeA 261 2.15e+01 c.2.1.2 90509 1hxhA 253 2.17e+01 c.2.1.2 76725 1ooeA 236 2.18e+01 c.2.1.2 87196 1r1hA 696 2.18e+01 d.92.1.4 104756 1vjqA 79 2.19e+01 k.43.1.1 100830 1div 149 2.19e+01 1div d.99.1.1,d.100.1.1 40692,40693 1qzmA 94 2.19e+01 c.37.1.20 96651 1knvA 293 2.20e+01 c.52.1.7 68707 1ko3A 230 2.20e+01 d.157.1.1 90974 2fb0A 94 2.22e+01 1wkbA 810 2.23e+01 1fvgA 199 2.23e+01 1fvaA d.58.28.1 39408 1kr4A 125 2.23e+01 d.58.5.2 72889 2bywA 418 2.24e+01 2cdcA 366 2.25e+01 1bt3A 345 2.25e+01 1bt3A a.86.1.2 18507 2f1kA 279 2.26e+01 1egpA 45 2.28e+01 1egpA d.40.1.1 38561 1xw3A 110 2.28e+01 1t5iA 172 2.29e+01 c.37.1.19 106450 1dozA 309 2.29e+01 1ak1 c.92.1.1 35592 1wkcA 184 2.30e+01 1udzA 182 2.32e+01 b.51.1.1 99239 1dbqA 289 2.35e+01 1qpzA c.93.1.1 35666 1drw 273 2.36e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1u7iA 136 2.36e+01 d.32.1.7 107724 1tqxA 227 2.38e+01 1qyiA 384 2.41e+01 c.108.1.13 96595 1fo8A 343 2.44e+01 1foaA c.68.1.10 59927 1xk7A 408 2.45e+01 1o26A 232 2.46e+01 d.207.1.1 86566 1r3sA 367 2.48e+01 c.1.22.1 96963 1x9iA 302 2.50e+01 1t15A 214 2.50e+01 c.15.1.3,c.15.1.3 99067,99068 2aneA 125 2.51e+01 1ufyA 122 2.51e+01 d.79.1.2 88489 1n7kA 234 2.52e+01 c.1.10.1 85374 1pa4A 116 2.55e+01 d.52.7.1 94409 1vqoV 71 2.56e+01 1m1cA 680 2.57e+01 e.42.1.1 78395 2ez9A 603 2.57e+01 1m8jA 181 2.57e+01 c.26.1.3 84875 1zosA 230 2.57e+01 1z90A 469 2.58e+01 1i0dA 332 2.59e+01 1pscA c.1.9.3 61487 1uf3A 228 2.60e+01 d.159.1.6 99317 1gxjA 186 2.63e+01 d.215.1.1 70707 1qgoA 264 2.63e+01 1qgoA c.92.1.2 35596 1vg0A 650 2.64e+01 c.3.1.3,d.16.1.6 108596,108597 2fjbA 643 2.64e+01 1jnrA 643 2.65e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1h70A 255 2.65e+01 1h70A d.126.1.3 60711 1qsgA 265 2.66e+01 1eny c.2.1.2 29935 1nrzA 164 2.66e+01 c.38.1.1 86131 1nu0A 138 2.67e+01 c.55.3.8 92165 2bwnA 401 2.67e+01 1tqzA 133 2.69e+01 1wf3A 301 2.71e+01 1n7hA 381 2.72e+01 c.2.1.2 80250 1jflA 228 2.72e+01 c.78.2.1,c.78.2.1 71656,71657 1vjyA 303 2.74e+01 d.144.1.7 108633 1afwA 393 2.75e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 1t77A 414 2.75e+01 1gtkA 313 2.77e+01 c.94.1.1,d.50.2.1 76346,76347 1lriA 98 2.77e+01 a.134.1.1 74223 2a2pA 129 2.77e+01 1shfA 59 2.77e+01 1bbzA b.34.2.1 24462 1yzsA 121 2.79e+01 1mwwA 128 2.82e+01 d.80.1.4 91483 1otgA 125 2.83e+01 1otgA d.80.1.2 39831 1dd9A 338 2.84e+01 1dd9A e.13.1.1 43254 2g2dA 193 2.84e+01 1qtoA 122 2.85e+01 1bylA d.32.1.2 38494 1ur1A 378 2.85e+01 c.1.8.3 99804 1vhwA 253 2.87e+01 c.56.2.1 100706 4uagA 437 2.89e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1zk4A 251 2.90e+01 2ccjA 205 2.91e+01 1hx0A 496 2.91e+01 b.71.1.1,c.1.8.1 61346,61347 2dri 271 2.92e+01 2dri c.93.1.1 35637 1q02A 52 2.94e+01 a.5.2.1 95490 1tr9A 341 3.01e+01 2f6kA 307 3.03e+01 2cxkA 95 3.03e+01 1ob8A 135 3.04e+01 2cbiA 594 3.07e+01 1i3zA 103 3.07e+01 d.93.1.1 83667 1no5A 114 3.11e+01 d.218.1.5 92014 1yqeA 282 3.13e+01 1ufzA 83 3.14e+01 a.5.9.1 107821 1kdgA 546 3.14e+01 c.3.1.2,d.16.1.1 77337,77338 1h4vB 421 3.15e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1hqkA 154 3.15e+01 c.16.1.1 65902 1dg9A 157 3.16e+01 1dg9A c.44.1.1 32637 1unlD 208 3.17e+01 2d4pA 141 3.18e+01 1xq6A 253 3.19e+01 1wnaA 131 3.21e+01 1xwwA 157 3.23e+01 1tzyA 129 3.25e+01 a.22.1.1 107530 1ijyA 130 3.30e+01 1ijxA a.141.1.1 62517 1vc1A 110 3.31e+01 c.13.2.1 108493 1p4oA 322 3.31e+01 d.144.1.7 87775 1lj5A 379 3.31e+01 e.1.1.1 73928 1l0wA 580 3.36e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1g5tA 196 3.39e+01 1g5rA c.37.1.11 32366 1wr2A 238 3.41e+01 1fv5A 36 3.43e+01 1fv5A g.37.1.2 45075 1j77A 209 3.45e+01 1j77A a.132.1.2 62674 1ro7A 259 3.52e+01 c.130.1.1 97667 1i8kA 107 3.54e+01 b.1.1.1 71130 1g60A 260 3.54e+01 c.66.1.11 70151 2fwtA 125 3.58e+01 1xhkA 187 3.61e+01 1ahsA 126 3.61e+01 1ahsA b.19.1.1 23794 1ycoA 279 3.63e+01 1mzbA 136 3.65e+01 a.4.5.42 91497 1x9gA 200 3.67e+01 c.33.1.3 109527 1rp3B 88 3.68e+01 a.137.11.1 97681 1uc2A 481 3.71e+01 d.261.1.1 99161 1im8A 244 3.75e+01 c.66.1.14 66212 1snyA 267 3.81e+01 c.2.1.2 105833 2aibA 98 3.83e+01 1nulA 152 3.85e+01 1nulA c.61.1.1 34011 1i5gA 144 3.87e+01 1ewxA c.47.1.10 61784 1eq2A 310 3.87e+01 1eq2A c.2.1.2 29814 1d2fA 390 3.87e+01 1d2fA c.67.1.3 34411 1wcwA 261 3.88e+01 1n9lA 109 3.92e+01 d.110.3.6 85468 1j9lA 247 3.95e+01 c.106.1.1 62762 1ja1A 622 3.98e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1xdnA 277 3.98e+01 2bb6A 414 3.98e+01 1a3aA 148 3.99e+01 1a3aA d.112.1.1 40917 1lssA 140 4.00e+01 c.2.1.9 74246 2f06A 144 4.03e+01 1qopB 396 4.05e+01 2tysB c.79.1.1 35270 1v3wA 173 4.07e+01 b.81.1.5 100291 1q0rA 298 4.11e+01 c.69.1.28 95508 1bgk 37 4.14e+01 1bgk g.19.1.1 44875 1g26A 31 4.16e+01 1g26A g.3.16.1 44381 1ud9A 245 4.17e+01 d.131.1.2,d.131.1.2 107768,107769 1wt9B 123 4.22e+01 2f2hA 773 4.24e+01 2bhuA 602 4.25e+01 1pmmA 466 4.29e+01 c.67.1.6 94901 1j4aA 333 4.29e+01 c.2.1.4,c.23.12.1 71502,71503 1e58A 249 4.32e+01 1qhfA c.60.1.1 59262 1bbzA 58 4.32e+01 1bbzA b.34.2.1 24477 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