# List of top-scoring protein chains for T0323.t06-w0.5 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 1ornA 226 1.10e-42 a.96.1.1 87342 1p59A 226 1.25e-42 a.96.1.1 87794 1kg6A 225 1.70e-41 a.96.1.2 77382 1kg2A 225 2.00e-41 a.96.1.2 77378 1kg5A 225 2.21e-41 a.96.1.2 77381 1weiA 225 2.48e-41 a.96.1.2 109339 1kg4A 225 3.87e-41 a.96.1.2 77380 1kg7A 225 5.12e-41 a.96.1.2 77383 1mun 225 1.71e-40 1mun a.96.1.2 18744 1kqjA 225 1.90e-40 a.96.1.2 72879 2abk 211 2.94e-40 2abk a.96.1.1 18743 1rrsA 369 1.63e-37 a.96.1.2,d.113.1.3 97800,97801 1rrqA 369 3.62e-37 a.96.1.2,d.113.1.3 97798,97799 1keaA 221 2.25e-32 a.96.1.2 68491 1ko9A 345 3.92e-29 a.96.1.3,d.129.1.2 68717,68718 1mpgA 282 4.69e-29 1mpgA a.96.1.3,d.129.1.2 18747,41296 1lwyA 324 6.86e-29 a.96.1.3,d.129.1.2 78285,78286 1fn7A 317 7.74e-29 1ebmA a.96.1.3,d.129.1.2 59892,59893 1ebmA 317 2.64e-28 1ebmA a.96.1.3,d.129.1.2 18751,41300 1yqkA 319 5.96e-28 1n3cA 317 6.94e-28 a.96.1.3,d.129.1.2 85293,85294 1m3qA 317 7.70e-28 a.96.1.3,d.129.1.2 91184,91185 1yqrA 319 2.06e-27 1n3aA 317 2.15e-27 a.96.1.3,d.129.1.2 85291,85292 1pu6A 218 6.41e-19 a.96.1.5 95123 1ngnA 155 1.88e-11 a.96.1.2 85697 2csbA 519 3.64e-03 1z00A 89 1.15e-01 2a1jB 91 1.57e-01 1n8iA 741 2.71e-01 c.1.13.1 80297 1y88A 199 2.80e-01 1cuk 203 4.89e-01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1hjp 203 5.58e-01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1y6iA 233 6.51e-01 1lmzA 187 6.52e-01 a.96.1.4 74037 1d8lA 149 7.04e-01 1hjp a.60.2.1,b.40.4.2 17948,25267 1nc5A 373 7.52e-01 a.102.1.6 85548 2bhnA 214 7.72e-01 1ynjA 314 8.25e-01 2bgwA 219 8.35e-01 1i6vA 314 8.36e-01 d.74.3.1,d.181.1.1 61852,61853 1xwiA 322 8.90e-01 1bvsA 203 1.47e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16280,17955,25274 1vicA 262 1.59e+00 c.68.1.13 100756 1vp8A 201 1.68e+00 1vddA 228 1.71e+00 e.49.1.1 108519 1g99A 408 2.07e+00 1g99A c.55.1.2,c.55.1.2 33457,33458 1tuuA 399 2.09e+00 1hqmA 313 2.43e+00 i.8.1.1 45972 1u2zA 433 2.79e+00 c.66.1.31 107626 1x2iA 75 2.92e+00 1qzxA 440 3.19e+00 a.24.13.1,a.36.1.1,c.37.1.10 96711,96712,96713 1gq2A 555 4.15e+00 c.2.1.7,c.58.1.3 70308,70309 1e3cP 489 4.26e+00 1auk c.76.1.2 59187 1e33P 489 4.29e+00 1auk c.76.1.2 59186 1e2sP 489 4.74e+00 1auk c.76.1.2 35031 1e1zP 489 4.77e+00 1auk c.76.1.2 59158 1b22A 114 4.89e+00 1b22A a.60.4.1 17969 1auk 489 4.99e+00 1auk c.76.1.2 35030 2sqcA 631 5.24e+00 2sqcA a.102.4.2,a.102.4.2 18854,18855 1z82A 335 5.47e+00 1umpA 631 5.69e+00 a.102.4.2,a.102.4.2 99619,99620 1ixrA 191 6.21e+00 a.60.2.1,b.40.4.2 76925,76926 3sqcA 631 6.37e+00 2sqcA a.102.4.2,a.102.4.2 18860,18861 2a6hA 315 7.12e+00 1jiqA 558 8.73e+00 c.80.1.2 71689 1iatA 557 8.82e+00 1dqrA c.80.1.2 62123 1jlhA 558 8.85e+00 c.80.1.2 77131 1ydhA 216 9.02e+00 1zlpA 318 9.03e+00 1rlr 761 9.09e+00 1rlr a.98.1.1,c.7.1.2 18753,30679 1ayzA 169 9.28e+00 1u9aA d.20.1.1 38326 1jm6A 407 9.35e+00 a.29.5.1,d.122.1.4 66876,66877 1pujA 282 1.05e+01 c.37.1.8 88294 6r1rA 761 1.08e+01 1rlr a.98.1.1,c.7.1.2 18760,30686 2r1rA 761 1.08e+01 1rlr a.98.1.1,c.7.1.2 18769,30695 7r1rA 761 1.08e+01 1rlr a.98.1.1,c.7.1.2 18763,30689 5r1rA 761 1.08e+01 1rlr a.98.1.1,c.7.1.2 18757,30683 4r1rA 761 1.08e+01 1rlr a.98.1.1,c.7.1.2 18772,30698 1n5xA 1331 1.12e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 85342,85343,85344,85345,85346,85347 1qrcA 559 1.13e+01 1tyv b.80.1.6 28045 1v97A 1332 1.13e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1tsp 559 1.13e+01 1tyv b.80.1.6 28044 1qrbA 559 1.13e+01 1tyv b.80.1.6 28042 1qq1A 559 1.13e+01 1tyv b.80.1.6 28041 1rf6A 427 1.25e+01 d.68.2.2 97366 1tjyA 316 1.32e+01 c.93.1.1 107062 1qa1A 554 1.33e+01 1tyv b.80.1.6 28047 1clwA 554 1.33e+01 1tyv b.80.1.6 28043 1qa3A 554 1.33e+01 1tyv b.80.1.6 28046 1tyv 554 1.33e+01 1tyv b.80.1.6 28038 1qa2A 554 1.33e+01 1tyv b.80.1.6 28048 2btzA 394 1.37e+01 1r1rA 761 1.39e+01 1rlr a.98.1.1,c.7.1.2 18754,30680 1p9bA 442 1.44e+01 c.37.1.10 94385 2asdA 360 1.46e+01 1vl8A 267 1.54e+01 c.2.1.2 108733 2aynA 404 1.81e+01 2bg9C 369 1.93e+01 1kwsA 261 1.98e+01 c.68.1.7 73083 1ho3A 326 1.99e+01 4pgaA c.88.1.1 61101 1vkyA 347 2.00e+01 e.53.1.1 108696 1pznA 349 2.02e+01 a.60.4.1,c.37.1.11 95456,95457 1j8mF 297 2.02e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1j8yF 297 2.02e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 2bp5M 435 2.04e+01 1gw5M 435 2.04e+01 b.2.7.1,d.110.4.2 70631,70632 1jm1A 204 2.05e+01 b.33.1.1 71745 1no1A 126 2.06e+01 a.179.1.1 85913 2agqA 341 2.08e+01 1ztmA 490 2.09e+01 1tjrA 261 2.20e+01 1dgsA 667 2.27e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1vk3A 615 2.32e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1rd5A 262 2.33e+01 1v8gA 329 2.41e+01 a.46.2.1,c.27.1.1 100505,100506 2bq3A 358 2.41e+01 1qhtA 775 2.48e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1szpA 321 2.50e+01 a.60.4.1,c.37.1.11 106176,106177 1v9pA 584 2.50e+01 a.60.2.2,b.40.4.6,d.142.2.2 100544,100545,100546 2fgcA 193 2.55e+01 1nnsA 326 2.63e+01 c.88.1.1 85910 1jazA 326 2.64e+01 c.88.1.1 90883 4ecaA 326 2.67e+01 4pgaA c.88.1.1 35550 1f6fA 199 2.77e+01 1f6fA a.26.1.1 16839 1jx4A 352 2.80e+01 d.240.1.1,e.8.1.7 90378,90379 3gcb 470 2.88e+01 3gcb d.3.1.1 37032 1a6r 471 2.95e+01 3gcb d.3.1.1 37033 1lq9A 112 2.95e+01 d.58.4.3 78129 2bl0B 145 2.97e+01 1diiA 521 3.06e+01 1qltA d.58.32.1,d.145.1.1 39481,41744 1wvfA 520 3.09e+01 2avyJ 103 3.15e+01 1xktA 289 3.20e+01 1zq1C 633 3.23e+01 2az4A 429 3.43e+01 2tbvA 387 3.47e+01 2tbvA b.121.4.7 23302 1yv9A 264 3.48e+01 1v3vA 333 3.67e+01 b.35.1.2,c.2.1.1 108345,108346 3pcdM 238 3.68e+01 3pchM b.3.6.1 22778 1jtaA 361 3.71e+01 b.80.1.1 71859 1pe9A 361 3.71e+01 b.80.1.1 94595 1ng1 294 3.72e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 1ls1A 295 3.74e+01 a.24.13.1,c.37.1.10 78170,78171 1fxiA 96 3.74e+01 1awd d.15.4.1 37664 1jpnA 296 3.75e+01 a.24.13.1,c.37.1.10 67039,67040 1o87A 297 3.77e+01 a.24.13.1,c.37.1.10 92640,92641 3pcgM 238 3.82e+01 3pchM b.3.6.1 22742 1j31A 262 3.89e+01 d.160.1.2 90808 1x2gA 337 3.93e+01 1qs1A 462 3.94e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1zs3A 182 3.95e+01 1qqcA 773 3.97e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1ykkB 238 4.07e+01 1nyaA 176 4.11e+01 a.39.1.5 92335 1qs2A 401 4.15e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 1uxc 65 4.18e+01 1uxc a.35.1.5 17119 1gcb 454 4.18e+01 3gcb d.3.1.1 37034 1h9dB 134 4.49e+01 2jhbA b.54.1.1 60822 1qfjA 232 4.54e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1u0fA 564 4.58e+01 1wcnA 70 4.76e+01 1zhhA 344 4.78e+01 1jx6A 342 4.82e+01 c.93.1.1 67406 1g5cA 170 4.94e+01 1g5cA c.53.2.1 60264 1bgxT 832 4.97e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18083,33353,33699,42992 2jhbA 143 5.02e+01 2jhbA b.54.1.1 26950 2cxnA 557 5.03e+01 1zmzA 98 5.03e+01 1gzdA 557 5.04e+01 c.80.1.2 70804 1taq 832 5.04e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1w79A 489 5.09e+01 1io4D 141 5.10e+01 2jhbA b.54.1.1 62617 1mx3A 347 5.22e+01 c.2.1.4,c.23.12.1 79638,79639 1doqA 69 5.24e+01 1coo a.60.3.1 17968 1cl3A 138 5.30e+01 2jhbA b.54.1.1 26949 1d5aA 733 5.35e+01 1tgoA c.55.3.5,e.8.1.1 33723,43012 1tcvA 287 5.37e+01 1doi 128 5.37e+01 1awd d.15.4.1 37676 1wxcB 134 5.42e+01 1md8A 329 5.50e+01 b.47.1.2,g.18.1.1 91245,91246 1xoyA 161 5.52e+01 1huxA 270 5.53e+01 1huxA c.55.1.5 61278 1ykpB 238 5.55e+01 1h8fB 350 5.56e+01 d.144.1.7 65734 1h8fA 352 5.56e+01 d.144.1.7 65733 1ugsA 203 5.61e+01 d.149.1.1 107837 2a19A 175 5.64e+01 1brwA 433 5.65e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1q46A 175 5.75e+01 b.40.4.5 95782 1eupA 403 5.79e+01 1rom a.104.1.1 18967 1qasA 622 5.88e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17340,23157,29585 1djxA 624 5.97e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17342,23159,29587 1pqvS 309 5.98e+01 i.8.1.1 95040 1gpjA 404 6.09e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1jctA 446 6.11e+01 c.1.11.2,d.54.1.1 62882,62883 1wsaA 330 6.21e+01 4pgaA c.88.1.1 35558 1md7A 328 6.32e+01 b.47.1.2,g.18.1.1 91243,91244 1fiqC 763 6.47e+01 1fiqC d.41.1.1,d.133.1.1 38588,41418 2ffhA 425 6.48e+01 1ng1 a.24.13.1,a.36.1.1,c.37.1.10 16965,17122,32276 1c0eA 157 6.50e+01 1dg9A c.44.1.1 32638 1mijA 152 6.56e+01 a.4.1.1 79150 1d7qA 143 6.63e+01 1d7qA b.40.4.5 25331 1vh1A 256 6.64e+01 c.68.1.13 100632 1k4wA 252 6.65e+01 a.123.1.1 72068 1ec7A 446 6.68e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1hnnA 282 6.71e+01 c.66.1.15 65895 1nq7A 244 6.72e+01 a.123.1.1 92047 1yknB 238 6.73e+01 2an3A 289 6.79e+01 1rj9B 300 6.81e+01 a.24.13.1,c.37.1.10 97555,97556 2ng1 293 6.82e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1dxlA 470 6.83e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30585,30586,40214 1ffh 294 6.84e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1sf8A 126 6.84e+01 d.271.1.1 105472 2f7tA 227 6.97e+01 1ko7A 314 6.99e+01 c.98.2.1,c.91.1.2 72797,72798 1tgoA 773 7.03e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1u7iA 136 7.05e+01 d.32.1.7 107724 1emsA 440 7.10e+01 1emsA d.13.1.1,d.160.1.1 37520,42086 1bg1A 596 7.12e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17767,22461,40527 2bs4C 256 7.27e+01 1uv5A 350 7.29e+01 d.144.1.7 100029 1byeA 213 7.29e+01 1gnwA a.45.1.1,c.47.1.5 17732,33026 1w5bA 364 7.31e+01 1jdfA 446 7.31e+01 c.1.11.2,d.54.1.1 62897,62898 1eg5A 384 7.32e+01 1ecxA c.67.1.3 34429 2aplA 157 7.39e+01 1txgA 335 7.49e+01 1ltdA 506 7.50e+01 1gox c.1.4.1,d.120.1.1 28618,41086 1cg2A 393 7.51e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1i7kA 179 7.58e+01 1u9aA d.20.1.1 61889 1n4hA 259 7.66e+01 a.123.1.1 91618 1axdA 209 7.69e+01 1gnwA a.45.1.1,c.47.1.5 17730,33024 1n8tA 557 7.78e+01 c.80.1.2 85454 1xpxA 163 7.82e+01 1yizA 429 7.88e+01 1hm5A 558 7.91e+01 c.80.1.2 76717 1kojA 557 7.98e+01 c.80.1.2 72821 1w6gA 646 8.00e+01 1w4nA 646 8.00e+01 1zy4A 303 8.04e+01 1zwwA 256 8.10e+01 1szfA 511 8.15e+01 c.1.4.1 106153 1szeA 511 8.17e+01 c.1.4.1 106151 1fsz 372 8.20e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1dj3A 442 8.21e+01 1adeA c.37.1.10 32239 2gw6A 123 8.22e+01 1tlyA 278 8.37e+01 f.4.6.1 107143 1ireA 204 8.38e+01 d.149.1.1 76769 1kbiA 511 8.40e+01 c.1.4.1,d.120.1.1 72277,72278 1iqyA 638 8.42e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1ui7A 638 8.43e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1y5oA 115 8.43e+01 1ivvA 638 8.43e+01 b.30.2.1,d.17.2.1,d.17.2.1 71450,71451,71452 2cwtA 638 8.46e+01 2d1wA 638 8.47e+01 1lkvX 232 8.47e+01 a.118.14.1 73980 1ugpA 203 8.59e+01 d.149.1.1 107831 1lcoA 511 8.59e+01 1gox c.1.4.1,d.120.1.1 28624,41088 1hdr 244 8.63e+01 1dhr c.2.1.2 29837 1yr2A 741 8.63e+01 1j1iA 296 8.67e+01 c.69.1.10 83977 1ui8A 638 8.74e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1xvlA 321 8.81e+01 1yirA 408 8.87e+01 1q41A 424 8.89e+01 d.144.1.7 95774 2gfqA 298 8.92e+01