# List of top-scoring protein chains for t04-100-30-bys-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 7.29e-03 1t6kA 278 1.74e-02 1xubA 298 2.01e-02 1tm0A 350 7.74e-02 d.21.1.3 107147 2gkeA 274 1.53e-01 1o0pA 104 1.73e-01 d.58.7.1 86535 1gqzA 274 1.75e-01 d.21.1.1,d.21.1.1 83311,83312 1w61A 414 2.36e-01 1xttA 216 2.46e-01 1dp4A 435 2.70e-01 1dp4A c.93.1.1 35710 1sr8A 298 3.06e-01 e.54.1.1 105959 1pj5A 830 7.68e-01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1p3dA 475 7.89e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2b3nA 159 8.59e-01 1bwzA 274 9.44e-01 1bwzA d.21.1.1,d.21.1.1 38337,38338 2gjgA 248 1.10e+00 1josA 128 1.38e+00 d.52.7.1 84191 1nnxA 109 1.54e+00 b.40.10.1 92013 1j5pA 253 1.65e+00 d.81.1.3,c.2.1.3 71577,83092 2aioA 269 1.74e+00 1f2rI 100 1.79e+00 1c9fA d.15.2.1 37641 1qx4A 274 1.83e+00 b.43.4.2,c.25.1.1 104624,104625 1d0iA 156 2.01e+00 2dhqA c.23.13.1 31383 1ogsA 497 2.19e+00 b.71.1.2,c.1.8.3 86997,86998 2azpA 318 2.33e+00 1mkiA 330 2.39e+00 e.3.1.2 84994 1oe4A 247 2.66e+00 c.18.1.3 86895 1gtzA 156 2.85e+00 c.23.13.1 70539 1f3uA 118 2.92e+00 1f3uA b.65.1.1 27521 2cw8A 537 3.18e+00 1ynfA 458 3.19e+00 1bupA 386 3.40e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1o8bA 219 3.41e+00 c.124.1.4,d.58.40.1 81180,81181 1a8rA 221 3.41e+00 1a8rA d.96.1.1 40587 1kay 381 3.66e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1vdkA 466 4.03e+00 a.127.1.1 100561 2fr2A 172 4.53e+00 1q15A 503 4.95e+00 c.26.2.1,d.153.1.1 95538,95539 1ygs 234 5.16e+00 1ygs b.26.1.1 23907 1smlA 269 5.24e+00 1smlA d.157.1.1 42053 1vljA 407 5.32e+00 e.22.1.2 108832 1ym5A 300 5.34e+00 1wznA 252 5.51e+00 1vl2A 421 5.53e+00 c.26.2.1,d.210.1.1 108708,108709 1rsy 152 5.59e+00 1rsy b.7.1.2 23192 1gv3A 248 5.63e+00 a.2.11.1,d.44.1.1 70585,70586 1jc9A 269 5.73e+00 d.171.1.1 66490 3tdt 274 5.73e+00 3tdt b.81.1.2 28053 1umkA 275 5.88e+00 1ycoA 279 5.97e+00 1o17A 345 6.17e+00 a.46.2.1,c.27.1.1 80765,80766 1rzhL 281 6.31e+00 f.26.1.1 98164 1sziA 247 6.43e+00 a.24.23.1 106159 1kkcA 221 6.92e+00 a.2.11.1,d.44.1.1 68660,68661 1s1qA 145 7.06e+00 d.20.1.2 98351 1wcqA 601 7.38e+00 1w8oA 601 7.73e+00 1qjtA 99 7.75e+00 1eh2 a.39.1.6 17335 1jogA 146 9.47e+00 a.24.16.2 77142 1dazC 99 9.55e+00 1hvc b.50.1.1 26501 2f4nA 273 9.82e+00 1y791 680 1.03e+01 1r5eA 115 1.04e+01 1wekA 217 1.05e+01 1alu 186 1.09e+01 1alu a.26.1.1 16826 1oo0A 147 1.11e+01 d.232.1.1 87182 1nksA 194 1.13e+01 1nksA c.37.1.1 31886 1h0bA 256 1.13e+01 b.29.1.11 83422 1tafB 70 1.18e+01 1tafB a.22.1.3 16482 1vh5A 148 1.19e+01 d.38.1.5 100642 1g5cA 170 1.24e+01 1g5cA c.53.2.1 60264 1go4A 205 1.25e+01 d.135.1.1 70292 1ru0A 105 1.28e+01 1dkqA 410 1.28e+01 1dklA c.60.1.2 33998 1vhzA 198 1.29e+01 d.113.1.1 100718 1q3iA 214 1.30e+01 d.220.1.1 104524 2aneA 125 1.31e+01 1mxmA 254 1.40e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 2cxcA 144 1.41e+01 1q87A 221 1.43e+01 e.47.1.1 96192 1a8i 842 1.47e+01 1a8i c.87.1.4 35490 2aliA 158 1.48e+01 2eutA 294 1.50e+01 1z53A 294 1.50e+01 1dkmA 410 1.53e+01 1dklA c.60.1.2 34000 1dwkA 156 1.56e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1eueA 86 1.62e+01 1cyo d.120.1.1 59504 1nnsA 326 1.62e+01 c.88.1.1 85910 1p1mA 406 1.64e+01 b.92.1.4,c.1.9.9 87696,87697 1k66A 149 1.66e+01 c.23.1.1 90941 1r44A 202 1.68e+01 d.65.1.4 104787 1twuA 139 1.68e+01 d.32.1.8 107413 1evhA 112 1.71e+01 1evhA b.55.1.4 26997 1wudA 89 1.72e+01 1tdtA 259 1.73e+01 3tdt b.81.1.2 28055 2a8yA 270 1.81e+01 1iznB 277 1.82e+01 e.43.1.2 83848 2bw8A 227 1.85e+01 1hekA 131 1.89e+01 a.61.1.5 65818 1m5yA 408 1.91e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1awd 94 1.91e+01 1awd d.15.4.1 37673 1i7pA 274 2.05e+01 b.43.4.2,c.25.1.1 66048,66049 1h5uA 842 2.06e+01 1a8i c.87.1.4 60655 4uagA 437 2.09e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1j6pA 418 2.18e+01 b.92.1.4,c.1.9.9 77089,77090 1gmuA 143 2.28e+01 b.107.1.1,d.58.38.1 65335,65336 1jdrA 294 2.34e+01 1ryc a.93.1.1 62908 1zbyA 294 2.36e+01 2d0oA 610 2.37e+01 1rzhM 307 2.42e+01 f.26.1.1 98165 2a13A 166 2.50e+01 1y9wA 140 2.53e+01 1avbA 226 2.55e+01 1led b.29.1.1 24158 1v7oA 165 2.56e+01 d.67.1.2 100480 1jhjA 171 2.61e+01 b.18.1.9 66714 1ztdA 133 2.62e+01 1mo9A 523 2.62e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1t6cA 315 2.62e+01 c.55.1.8,c.55.1.8 106558,106559 2fkbA 180 2.69e+01 2g1lA 104 2.69e+01 1ewqA 765 2.72e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1euhA 475 2.77e+01 1euhA c.82.1.1 35369 2acfA 182 2.86e+01 2biqA 219 2.87e+01 1xtqA 177 2.88e+01 2gsq 202 2.88e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1ygaA 342 2.89e+01 1eexA 554 3.01e+01 1dioA c.1.19.3 29650 1mqoA 227 3.13e+01 d.157.1.1 103846 1ixlA 131 3.15e+01 d.38.1.5 90717 1z94A 147 3.25e+01 1lk5A 229 3.28e+01 c.124.1.4,d.58.40.1 73960,73961 1zhhB 242 3.31e+01 1pzsA 208 3.35e+01 b.1.8.1 104397 1zwxA 301 3.44e+01 1ftrA 296 3.46e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1e1oA 504 3.55e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 2sli 679 3.55e+01 2sli b.29.1.9,b.68.1.1 24274,27611 2a35A 215 3.59e+01 1q1rA 431 3.60e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1sdjA 310 3.61e+01 d.21.1.2,d.21.1.2 98807,98808 1pg4A 652 3.63e+01 e.23.1.1 88067 1kskA 234 3.66e+01 d.66.1.5,d.265.1.3 72920,90389 1evsA 187 3.67e+01 1evsA a.26.1.1 16845 1ualA 274 3.71e+01 c.116.1.4 88383 1wosA 364 3.73e+01 b.44.2.1,d.250.1.1 109468,109469 1wab 232 3.73e+01 1wab c.23.10.3 31341 1rm6A 769 3.75e+01 1ui7A 638 3.79e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1siiA 646 3.83e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1mkrA 294 3.87e+01 a.93.1.1 84997 2b6eA 146 3.88e+01 1gtkA 313 3.90e+01 c.94.1.1,d.50.2.1 76346,76347 1dszB 85 3.95e+01 2nllB g.39.1.2 45108 1w6gA 646 3.96e+01 1f08A 148 4.03e+01 1f08A d.89.1.2 59564 1lp8A 254 4.07e+01 d.165.1.1 91082 1rl0A 255 4.07e+01 1wvqA 167 4.08e+01 1yqfA 203 4.10e+01 1mngA 203 4.13e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 2blcA 238 4.14e+01 2lhb 149 4.15e+01 2fal a.1.1.2 15597 2fn0A 437 4.15e+01 1rjoA 646 4.22e+01 1v9yA 167 4.23e+01 d.110.3.2 108454 1b56 135 4.24e+01 1hmt b.60.1.2 27183 1fuxA 166 4.26e+01 1fjjA b.17.1.2 60034 1u3wA 374 4.27e+01 1nzaA 103 4.29e+01 d.58.5.2 86444 1wtaA 275 4.37e+01 1p5dX 463 4.38e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1vf8A 377 4.39e+01 1dseA 292 4.43e+01 1ryc a.93.1.1 59130 2yhx 457 4.45e+01 2yhx i.12.1.1 46024 1kpf 126 4.45e+01 1kpf d.13.1.1 37507 2d4qA 257 4.47e+01 2cpgA 45 4.55e+01 2cpgA a.43.1.3 17455 1g5aA 628 4.56e+01 b.71.1.1,c.1.8.1 65152,65153 2aaa 484 4.62e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1uolA 219 4.62e+01 b.2.5.2 99695 1i1iP 681 4.67e+01 1i1iP d.92.1.5 40297 1sltA 134 4.69e+01 1c1lA b.29.1.3 24186 1odkA 235 4.78e+01 c.56.2.1 86863 1lyqA 104 4.83e+01 b.1.18.17 78302 2madH 373 4.85e+01 2bbkH b.69.2.1 27639 1nbwA 607 4.90e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1tkeA 224 4.95e+01 1ijyA 130 4.96e+01 1ijxA a.141.1.1 62517 1bdo 80 4.98e+01 1bdo b.84.1.1 28214 1vhyA 257 4.98e+01 b.122.1.2,c.116.1.5 100714,100715 1lox 662 5.01e+01 1lox a.119.1.2,b.12.1.1 19238,23638 3sil 379 5.06e+01 3sil b.68.1.1 27542 1jf9A 408 5.10e+01 1c0nA c.67.1.3 62931 1lylA 504 5.14e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1oj6A 151 5.17e+01 a.1.1.2 93088 1e9lA 377 5.33e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1hf8A 289 5.34e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1wriA 93 5.39e+01 1wc9A 169 5.40e+01 1b4vA 504 5.42e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1zoyC 140 5.44e+01 2gfgA 193 5.44e+01 1kveA 63 5.50e+01 1kveA d.70.1.2 39590 1iwmA 186 5.50e+01 b.125.1.2 83758 1voqa 90 5.53e+01 1eulA 994 5.56e+01 1eulA 1pyoA 167 5.57e+01 c.17.1.1 95370 1v9fA 325 5.58e+01 d.265.1.3 108448 1q5zA 177 5.63e+01 a.196.1.1 95954 1otfA 62 5.66e+01 1otfA d.80.1.1 39820 1qwkA 317 5.75e+01 c.1.7.1 96482 1jl0A 334 5.75e+01 1jenA d.156.1.1 63155 1nh0A 99 5.81e+01 b.50.1.1 91869 1vjfA 180 5.83e+01 d.116.1.1 100809 1l0wA 580 5.83e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1nrkA 328 5.83e+01 b.44.2.1,d.250.1.1 92089,92090 1wuiL 534 5.84e+01 1mqvA 125 5.85e+01 a.24.3.2 79415 1mxtA 504 5.86e+01 c.3.1.2,d.16.1.1 79671,79672 1o0iA 138 5.87e+01 d.38.1.5 86532 1yuwA 554 5.89e+01 1zkiA 133 5.91e+01 1rqpA 299 5.92e+01 b.141.1.1,c.132.1.1 97754,97755 2b8nA 429 5.94e+01 1avk 638 5.94e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1jenA 267 5.96e+01 1jenA 1m2xA 223 5.97e+01 d.157.1.1 84764 1xm0A 147 6.04e+01 1k3sA 113 6.06e+01 d.198.1.1 68120 1n4wA 504 6.08e+01 c.3.1.2,d.16.1.1 91676,91677 1ubkL 534 6.27e+01 e.18.1.1 88422 1jnyA 435 6.30e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1xe7A 203 6.32e+01 2a90A 240 6.38e+01 1c7qA 445 6.41e+01 2pgi c.80.1.2 35307 1uisA 231 6.45e+01 d.22.1.1 99431 1ecfA 504 6.46e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1hg8A 349 6.48e+01 b.80.1.3 65830 1w0nA 131 6.49e+01 1xi3A 215 6.50e+01 c.1.3.1 109601 2c4xA 260 6.55e+01 1k2yX 463 6.63e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1pea 385 6.68e+01 1pea c.93.1.1 35662 1xtzA 264 6.68e+01 1or7C 90 6.72e+01 a.180.1.1 87336 1nscA 390 6.74e+01 2qwc b.68.1.1 27591 1h2rL 534 6.74e+01 1h2rL e.18.1.1 43298 1yspA 181 6.75e+01 1es9A 232 6.77e+01 1wab c.23.10.3 31340 1tw9A 206 6.84e+01 a.45.1.1,c.47.1.5 107381,107382 1sz7A 200 6.85e+01 1usmA 80 6.86e+01 d.74.1.1 99876 1ycdA 243 6.87e+01 1dtoA 221 6.94e+01 1dtoA b.91.1.1 28405 1whzA 70 6.97e+01 2ghsA 326 7.03e+01 1kzkA 99 7.05e+01 b.50.1.1 73371 2airB 153 7.07e+01 1rmg 422 7.09e+01 1rmg b.80.1.3 28029 1qipA 183 7.10e+01 1qipA d.32.1.1 38470 1h5zA 455 7.18e+01 a.104.1.1 90622 1izmA 184 7.20e+01 a.199.1.1 90725 1e9xA 455 7.29e+01 1ea1A a.104.1.1 18969 2bvbA 137 7.32e+01 1rzuA 485 7.34e+01 c.87.1.8 105140 2f1kA 279 7.34e+01 1qwtA 255 7.39e+01 b.26.1.3 96501 1mhyB 395 7.40e+01 1mtyB a.25.1.2 16781 2a6zA 222 7.42e+01 2bf6A 449 7.43e+01 1t8qA 336 7.50e+01 c.1.18.3 106669 1guzA 310 7.56e+01 c.2.1.5,d.162.1.1 65586,65587 1nxzA 246 7.63e+01 b.122.1.2,c.116.1.5 86391,86392 2g84A 197 7.64e+01 1yt5A 258 7.65e+01 1su4A 994 7.70e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1prxA 224 7.72e+01 1prxA c.47.1.10 33076 1k8tA 510 7.75e+01 e.41.1.1 68316 1lj5A 379 7.94e+01 e.1.1.1 73928 2govA 195 7.97e+01 2b71A 196 7.98e+01 1ui8A 638 8.04e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1urvA 190 8.12e+01 1ut0A 190 8.12e+01 a.1.1.2 108012 2erbA 125 8.20e+01 1yozA 116 8.21e+01 1fi8A 228 8.25e+01 5ptp b.47.1.2 26374 3proC 166 8.26e+01 3proC d.52.1.1,d.52.1.1 38812,38813 8acn 754 8.27e+01 1amj c.8.2.1,c.83.1.1 30724,35400 1mroC 247 8.27e+01 1mroC d.58.31.1 39437 1d8cA 723 8.28e+01 1d8cA c.1.13.1 29325 1louA 101 8.32e+01 1ris d.58.14.1 39323 1tzjA 338 8.33e+01 1zmaA 118 8.34e+01 4ubpC 570 8.36e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1vm7A 311 8.37e+01 c.72.1.1 108884 1fp2A 352 8.38e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 2gdzA 267 8.42e+01 1x6vA 630 8.44e+01 1u13A 455 8.45e+01 a.104.1.1 107578 2a5vA 213 8.48e+01 1wvcA 259 8.48e+01 1bhdA 118 8.55e+01 1bkrA a.40.1.1 17398 1i1nA 226 8.63e+01 c.66.1.7 71102 1lo7A 141 8.70e+01 d.38.1.1 74144 1o20A 427 8.72e+01 c.82.1.1 86556 1snzA 344 8.74e+01 b.30.5.4 98930 1gyfA 62 8.75e+01 1gyfA d.76.1.1 39749 1i6iA 366 8.92e+01 1bg2 c.37.1.9 61844 2fbmA 291 8.93e+01 1nmoA 247 8.93e+01 c.135.1.1 91980 1z54A 132 8.94e+01 1a91 79 8.96e+01 1a91 f.17.1.1 43635 1kbvA 327 8.98e+01 b.6.1.3,b.6.1.3 68395,68396 1rcy 151 8.98e+01 1rcy b.6.1.1 23018