# 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.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 1u1wA 298 8.06e-04 1xubA 298 1.91e-03 1t6kA 278 2.93e-03 1tm0A 350 2.18e-02 d.21.1.3 107147 1gqyA 475 7.74e-02 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1w61A 414 9.34e-02 1p3dA 475 1.11e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2gkeA 274 1.32e-01 1o0pA 104 1.33e-01 d.58.7.1 86535 1ym5A 300 1.51e-01 1mxmA 254 3.04e-01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1gqzA 274 3.38e-01 d.21.1.1,d.21.1.1 83311,83312 2b3nA 159 4.28e-01 2azpA 318 8.62e-01 1bwzA 274 9.24e-01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1yqfA 203 1.06e+00 2pcfB 250 1.63e+00 1hcz i.4.1.1 45911 1dp4A 435 1.77e+00 1dp4A c.93.1.1 35710 1qx4A 274 1.93e+00 b.43.4.2,c.25.1.1 104624,104625 1oe4A 247 1.99e+00 c.18.1.3 86895 1vdkA 466 3.03e+00 a.127.1.1 100561 1ewqA 765 3.20e+00 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1c0aA 585 3.25e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 2cxcA 144 3.32e+00 1xttA 216 4.53e+00 1sr8A 298 4.73e+00 e.54.1.1 105959 1vh5A 148 4.75e+00 d.38.1.5 100642 1gtzA 156 4.92e+00 c.23.13.1 70539 3uagA 437 5.29e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1tafB 70 5.36e+00 1tafB a.22.1.3 16482 1evhA 112 5.37e+00 1evhA b.55.1.4 26997 1d0iA 156 5.39e+00 2dhqA c.23.13.1 31383 1hcz 252 5.80e+00 1hcz b.2.6.1,b.84.2.2 22464,28250 1ycoA 279 5.81e+00 1jc9A 269 6.02e+00 d.171.1.1 66490 1g5cA 170 6.81e+00 1g5cA c.53.2.1 60264 1b3bA 415 7.63e+00 1hwyA c.2.1.7,c.58.1.1 30244,33892 1umkA 275 7.65e+00 1pfsA 78 7.72e+00 1pfsA b.40.4.7 25391 1hp1A 516 7.81e+00 d.114.1.1,d.159.1.2 70976,70977 1rzuA 485 7.96e+00 c.87.1.8 105140 2af4C 333 8.13e+00 1ush 550 8.37e+00 1ush d.114.1.1,d.159.1.2 40923,42079 1uag 437 8.46e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 4uagA 437 8.68e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1pj5A 830 8.83e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1vljA 407 8.85e+00 e.22.1.2 108832 1dkqA 410 8.89e+00 1dklA c.60.1.2 33998 1vpjA 192 9.67e+00 1q5dA 419 9.83e+00 a.104.1.1 95891 1cmxA 236 1.00e+01 1uch d.3.1.6 37130 1wudA 89 1.01e+01 2fr2A 172 1.02e+01 1a8z 153 1.03e+01 1rcy b.6.1.1 23020 1jf9A 408 1.05e+01 1c0nA c.67.1.3 62931 2aliA 158 1.05e+01 1dkmA 410 1.06e+01 1dklA c.60.1.2 34000 1e1oA 504 1.06e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 2calA 154 1.07e+01 1n0wA 243 1.09e+01 c.37.1.11 79772 1e30A 155 1.11e+01 1rcy b.6.1.1 23016 1wosA 364 1.13e+01 b.44.2.1,d.250.1.1 109468,109469 1sdjA 310 1.14e+01 d.21.1.2,d.21.1.2 98807,98808 1ih7A 903 1.15e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1lo7A 141 1.16e+01 d.38.1.1 74144 1gv3A 248 1.19e+01 a.2.11.1,d.44.1.1 70585,70586 1q1rA 431 1.22e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1fjgK 129 1.25e+01 1fjfK c.55.4.1 33733 1clqA 903 1.26e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1oohA 126 1.27e+01 a.39.2.1 93383 2fs2A 151 1.35e+01 1bvqA 141 1.39e+01 1bvqA d.38.1.1 38542 1i7pA 274 1.41e+01 b.43.4.2,c.25.1.1 66048,66049 1z94A 147 1.41e+01 1lylA 504 1.41e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1w30A 201 1.42e+01 1ztdA 133 1.44e+01 1a3z 155 1.45e+01 1rcy b.6.1.1 23019 1rcy 151 1.46e+01 1rcy b.6.1.1 23018 1efuA 385 1.49e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1y9wA 140 1.56e+01 1wtaA 275 1.62e+01 1f3uA 118 1.67e+01 1f3uA b.65.1.1 27521 1b26A 416 1.71e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1z54A 132 1.74e+01 1ksr 100 1.74e+01 1qfhA b.1.18.10 21897 1c0nA 406 1.76e+01 1c0nA c.67.1.3 34433 1dklA 410 1.77e+01 1dklA c.60.1.2 33996 2bw8A 227 1.78e+01 1f08A 148 1.80e+01 1f08A d.89.1.2 59564 1j6uA 469 1.83e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 2a35A 215 1.87e+01 1yozA 116 1.87e+01 1p5zB 263 1.89e+01 c.37.1.1 87815 1ogdA 131 1.91e+01 c.133.1.1 92893 1k8kE 178 1.93e+01 a.148.1.1 68311 1g7tA 594 1.99e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1prxB 224 1.99e+01 1prxA c.47.1.10 33077 2eiaB 206 2.01e+01 1eia a.28.3.1,a.73.1.1 16950,18330 1u9yA 284 2.04e+01 1v7oA 165 2.04e+01 d.67.1.2 100480 1fi8A 228 2.05e+01 5ptp b.47.1.2 26374 1qfhA 212 2.11e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1nrjB 218 2.12e+01 c.37.1.8 86125 1ksyA 154 2.12e+01 d.89.1.2 72948 1rsy 152 2.14e+01 1rsy b.7.1.2 23192 1te6A 439 2.20e+01 c.1.11.1,d.54.1.1 106797,106798 1xjvA 294 2.22e+01 1psuA 140 2.22e+01 d.38.1.5 88285 1nnxA 109 2.31e+01 b.40.10.1 92013 1bdo 80 2.32e+01 1bdo b.84.1.1 28214 1vllA 334 2.35e+01 c.2.1.13 108834 1q15A 503 2.35e+01 c.26.2.1,d.153.1.1 95538,95539 1r5eA 115 2.38e+01 1h0bA 256 2.40e+01 b.29.1.11 83422 1mngA 203 2.40e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1h2bA 359 2.40e+01 b.35.1.2,c.2.1.1 90543,90544 1hf8A 289 2.48e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1ygaA 342 2.48e+01 1pyoA 167 2.51e+01 c.17.1.1 95370 1db2A 377 2.52e+01 1sek e.1.1.1 42672 1iugA 352 2.53e+01 c.67.1.3 90699 1xtqA 177 2.54e+01 1kk1A 410 2.54e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1ygs 234 2.60e+01 1ygs b.26.1.1 23907 1hg2A 289 2.61e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1j5eK 129 2.70e+01 c.55.4.1 71554 1x8vA 455 2.70e+01 1alu 186 2.80e+01 1alu a.26.1.1 16826 1a8l 226 2.83e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1ba1 386 2.85e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 2fkbA 180 2.86e+01 1nksA 194 2.87e+01 1nksA c.37.1.1 31886 1q2yA 140 2.88e+01 d.108.1.1 95655 1c9kB 180 2.89e+01 1c9kB c.37.1.11 32364 1ats 386 2.90e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1s0uA 408 2.95e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1wlpB 138 2.97e+01 1aipA 405 2.97e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 2d4qA 257 3.02e+01 4sli 679 3.03e+01 2sli b.29.1.9,b.68.1.1 24275,27612 1hg5A 289 3.05e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 1gskA 513 3.07e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1lox 662 3.11e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1g9oA 91 3.18e+01 1pdr b.36.1.1 60400 1lr0A 129 3.18e+01 d.212.1.1 74213 1b0zA 445 3.19e+01 2pgi c.80.1.2 35309 2pgi 445 3.19e+01 2pgi c.80.1.2 35308 1c7qA 445 3.21e+01 2pgi c.80.1.2 35307 1wxxA 382 3.26e+01 1srqA 341 3.27e+01 e.55.1.1 105967 1k24A 253 3.29e+01 f.4.4.2 72002 1n13B 113 3.30e+01 1i1iP 681 3.32e+01 1i1iP d.92.1.5 40297 1rzhL 281 3.32e+01 f.26.1.1 98164 1t0qC 86 3.32e+01 d.15.12.1 106222 1r5jA 337 3.46e+01 c.77.1.5 97097 1u3wA 374 3.56e+01 2b5lC 222 3.57e+01 1b8fA 509 3.58e+01 1b8fA a.127.1.2 19434 1y791 680 3.59e+01 1wnfA 328 3.64e+01 1t6aA 126 3.64e+01 d.129.8.1 106555 1h2aL 567 3.73e+01 1h2rL e.18.1.1 43299 1q0pA 223 3.75e+01 c.62.1.1 95507 1kpf 126 3.76e+01 1kpf d.13.1.1 37507 1agnA 373 3.78e+01 2ohxA b.35.1.2,c.2.1.1 24737,29753 1tkeA 224 3.81e+01 1u55A 188 3.85e+01 d.278.1.1 107677 1h2rL 534 3.87e+01 1h2rL e.18.1.1 43298 1q5zA 177 3.94e+01 a.196.1.1 95954 1tfe 145 3.95e+01 1tfe d.43.1.1 38680 1w9sA 142 3.95e+01 1i92A 91 4.05e+01 1pdr b.36.1.1 61990 1ftrA 296 4.08e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 2a74A 643 4.11e+01 1i5sA 367 4.14e+01 1bg2 c.37.1.9 61822 1on3A 523 4.14e+01 c.14.1.4,c.14.1.4 87107,87108 1kay 381 4.14e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 2cw8A 537 4.15e+01 1zq1C 633 4.23e+01 1vl2A 421 4.24e+01 c.26.2.1,d.210.1.1 108708,108709 1ru0A 105 4.28e+01 1dykA 394 4.42e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1wuiL 534 4.48e+01 2sli 679 4.57e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1o0iA 138 4.58e+01 d.38.1.5 86532 1g7sA 594 4.60e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1h5zA 455 4.60e+01 a.104.1.1 90622 1bebA 162 4.63e+01 1bebA b.60.1.1 27115 1g8pA 350 4.63e+01 1g8pA c.37.1.20 60376 1ivnA 190 4.64e+01 c.23.10.5 83719 1wznA 252 4.67e+01 1hzxA 349 4.67e+01 1f88A f.13.1.2 61466 2fbqA 235 4.69e+01 1aijL 281 4.69e+01 6prcL f.26.1.1 43461 1spf 35 4.70e+01 1spf j.35.1.1 46254 1s4bP 674 4.72e+01 d.92.1.5 105252 1ixlA 131 4.82e+01 d.38.1.5 90717 2c4xA 260 4.88e+01 3mefA 69 4.90e+01 1mjc b.40.4.5 25320 1vm7A 311 4.92e+01 c.72.1.1 108884 1ecfB 504 4.92e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1ui8A 638 4.97e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1abbA 828 4.99e+01 1a8i c.87.1.4 35536 1hpm 386 4.99e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1a8i 842 5.07e+01 1a8i c.87.1.4 35490 1lj5A 379 5.07e+01 e.1.1.1 73928 1prxA 224 5.09e+01 1prxA c.47.1.10 33076 1z7bA 358 5.09e+01 1w77A 228 5.10e+01 2a1kA 233 5.14e+01 1izmA 184 5.16e+01 a.199.1.1 90725 1o17A 345 5.20e+01 a.46.2.1,c.27.1.1 80765,80766 1ukkA 142 5.20e+01 d.227.1.1 99491 2akzA 439 5.21e+01 1snzA 344 5.23e+01 b.30.5.4 98930 1bupA 386 5.25e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 2fymA 431 5.25e+01 1ng2A 193 5.28e+01 b.34.2.1,b.34.2.1 85660,85661 1siiA 646 5.36e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1x9dA 538 5.39e+01 1jp4A 308 5.40e+01 1jp4A e.7.1.1 63223 1kpeA 126 5.46e+01 1kpf d.13.1.1 37508 1cbuA 180 5.47e+01 1c9kB c.37.1.11 32360 1h4xA 117 5.53e+01 1auz c.13.2.1 60626 2f1kA 279 5.54e+01 1awd 94 5.55e+01 1awd d.15.4.1 37673 1mzgA 146 5.55e+01 d.224.1.1 79696 2b6eA 146 5.64e+01 1b76A 442 5.68e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 2aneA 125 5.69e+01 2fvhA 120 5.69e+01 1ubkL 534 5.74e+01 e.18.1.1 88422 1josA 128 5.80e+01 d.52.7.1 84191 1fjgR 88 5.84e+01 1fjfR a.4.8.1 16252 1qyaA 307 5.84e+01 d.21.1.2,d.21.1.2 104653,104654 1xm8A 254 5.84e+01 1rjoA 646 5.85e+01 1iqyA 638 5.95e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1wxiA 275 5.96e+01 1lghB 45 6.02e+01 1lghB f.3.1.1 43734 1m5yA 408 6.06e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1r44A 202 6.10e+01 d.65.1.4 104787 1l9hA 349 6.16e+01 f.13.1.2 73720 1c3gA 170 6.18e+01 1c3gA b.4.1.1,b.4.1.1 22831,22832 2lhb 149 6.30e+01 2fal a.1.1.2 15597 1w9yA 319 6.32e+01 1c96A 753 6.36e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1wlsA 328 6.38e+01 2a8yA 270 6.39e+01 1h8cA 82 6.40e+01 1h8cA d.15.1.2 37608 1w6gA 646 6.40e+01 1pdz 434 6.45e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1cqeA 580 6.50e+01 1cqeA a.93.1.2,g.3.11.1 18703,44246 1o70A 324 6.51e+01 b.118.1.1,b.118.1.1 81115,81116 1ceeB 59 6.53e+01 1ceeB 1tx4B 178 6.55e+01 1ctqA c.37.1.8 32045 1e9xA 455 6.57e+01 1ea1A a.104.1.1 18969 1ffkN 95 6.57e+01 1ffkN b.34.5.1 24606 1kkcA 221 6.57e+01 a.2.11.1,d.44.1.1 68660,68661 1ykdA 398 6.62e+01 1q1fA 151 6.69e+01 a.1.1.2 104476 1fuxA 166 6.80e+01 1fjjA b.17.1.2 60034 1fmaE 150 6.81e+01 1fmaE d.41.5.1 38630 1f88A 348 6.82e+01 1f88A f.13.1.2 43429 1ynbA 173 6.83e+01 1el6A 219 6.84e+01 1el6B d.182.1.1 42606 1jcfA 344 6.87e+01 c.55.1.1,c.55.1.1 62878,62879 1amj 754 6.88e+01 1amj c.8.2.1,c.83.1.1 30725,35401 1nqkA 381 6.92e+01 c.1.16.4 92050 1txvA 452 6.97e+01 1eza 259 7.05e+01 1zymA a.60.10.1,c.8.1.2 18113,30708 1f93A 104 7.07e+01 1dcpA d.74.1.1 39688 4rhn 115 7.08e+01 1kpf d.13.1.1 37495 1m0uA 249 7.11e+01 a.45.1.1,c.47.1.5 78359,78360 1g41A 444 7.11e+01 1do0A c.37.1.20 32450 1u13A 455 7.14e+01 a.104.1.1 107578 1b8eA 162 7.18e+01 1bebA b.60.1.1 59077 1bag 425 7.19e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1dtoA 221 7.27e+01 1dtoA b.91.1.1 28405 1io7A 368 7.27e+01 1f4tA a.104.1.1 18971 1gpb 842 7.28e+01 1a8i c.87.1.4 35478 1fxzA 476 7.31e+01 b.82.1.2,b.82.1.2 65059,65060 1jhjA 171 7.41e+01 b.18.1.9 66714 1o0vA 327 7.48e+01 b.1.1.2,b.1.1.2,b.1.1.2 80745,80746,80747 1ogsA 497 7.51e+01 b.71.1.2,c.1.8.3 86997,86998 2gfgA 193 7.53e+01 1ecfA 504 7.55e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ffkV 143 7.55e+01 1ffkV c.9.2.1 30849 1bhdA 118 7.59e+01 1bkrA a.40.1.1 17398 6acn 754 7.59e+01 1amj c.8.2.1,c.83.1.1 30721,35397 1lyqA 104 7.60e+01 b.1.18.17 78302 1lzjA 292 7.62e+01 c.68.1.9 74352 1dcpA 104 7.66e+01 1dcpA d.74.1.1 39672 1wq3A 322 7.67e+01 1atr 386 7.69e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 2d2yA 145 7.69e+01 2cr4A 126 7.73e+01 1ea1A 455 7.73e+01 1ea1A a.104.1.1 18970 1a7cA 379 7.76e+01 1sek e.1.1.1 42660 1ov3A 138 7.89e+01 b.34.2.1,b.34.2.1 87451,87452 2ajrA 331 7.91e+01 1gkmA 509 7.91e+01 a.127.1.2 70228 1q4gA 553 7.95e+01 a.93.1.2,g.3.11.1 95789,95790 2bsyA 278 7.96e+01 1i1nA 226 8.10e+01 c.66.1.7 71102 1ea0A 1479 8.11e+01 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 1mjc 69 8.15e+01 1mjc b.40.4.5 25319 1aipE 405 8.21e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1iae 200 8.23e+01 1iae d.92.1.8 40311 2dhqA 146 8.24e+01 2dhqA c.23.13.1 31382 1ast 200 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