# 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 1.13e-02 1t6kA 278 2.84e-02 1xubA 298 3.12e-02 1tm0A 350 6.99e-02 d.21.1.3 107147 2gkeA 274 1.15e-01 1gqzA 274 1.39e-01 d.21.1.1,d.21.1.1 83311,83312 1dp4A 435 1.97e-01 1dp4A c.93.1.1 35710 1w61A 414 2.48e-01 1o0pA 104 2.77e-01 d.58.7.1 86535 1sr8A 298 2.99e-01 e.54.1.1 105959 1o17A 345 3.35e-01 a.46.2.1,c.27.1.1 80765,80766 1xttA 216 3.66e-01 1bwzA 274 7.68e-01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1pj5A 830 8.06e-01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1p3dA 475 8.48e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2gjgA 248 1.04e+00 2b3nA 159 1.05e+00 1josA 128 1.09e+00 d.52.7.1 84191 2aioA 269 1.30e+00 1nnxA 109 2.01e+00 b.40.10.1 92013 1f2rI 100 2.05e+00 1c9fA d.15.2.1 37641 1mkiA 330 2.15e+00 e.3.1.2 84994 1h0bA 256 2.31e+00 b.29.1.11 83422 1oe4A 247 2.34e+00 c.18.1.3 86895 1j5pA 253 2.44e+00 d.81.1.3,c.2.1.3 71577,83092 1d0iA 156 2.69e+00 2dhqA c.23.13.1 31383 1ogsA 497 3.14e+00 b.71.1.2,c.1.8.3 86997,86998 2bw8A 227 3.31e+00 1qx4A 274 3.44e+00 b.43.4.2,c.25.1.1 104624,104625 1bupA 386 3.66e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1qwnA 1045 3.79e+00 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1gtzA 156 3.84e+00 c.23.13.1 70539 1kay 381 3.90e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1a8rA 221 3.98e+00 1a8rA d.96.1.1 40587 1smlA 269 4.15e+00 1smlA d.157.1.1 42053 1f3uA 118 4.20e+00 1f3uA b.65.1.1 27521 1ym5A 300 4.48e+00 1ynfA 458 4.63e+00 2azpA 318 4.77e+00 1vdkA 466 4.88e+00 a.127.1.1 100561 2cw8A 537 5.00e+00 1q15A 503 5.65e+00 c.26.2.1,d.153.1.1 95538,95539 1o8bA 219 5.86e+00 c.124.1.4,d.58.40.1 81180,81181 1gv3A 248 5.95e+00 a.2.11.1,d.44.1.1 70585,70586 2fr2A 172 6.27e+00 1vl2A 421 6.30e+00 c.26.2.1,d.210.1.1 108708,108709 1wznA 252 6.37e+00 1nscA 390 6.46e+00 2qwc b.68.1.1 27591 1sziA 247 6.82e+00 a.24.23.1 106159 1jc9A 269 6.85e+00 d.171.1.1 66490 1ycoA 279 7.10e+00 1vljA 407 7.39e+00 e.22.1.2 108832 1r44A 202 7.73e+00 d.65.1.4 104787 1ygs 234 7.80e+00 1ygs b.26.1.1 23907 3tdt 274 7.85e+00 3tdt b.81.1.2 28053 1rsy 152 8.10e+00 1rsy b.7.1.2 23192 1rzhL 281 8.33e+00 f.26.1.1 98164 1htyA 1015 8.45e+00 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1qjtA 99 8.50e+00 1eh2 a.39.1.6 17335 1dazC 99 8.72e+00 1hvc b.50.1.1 26501 1umkA 275 8.80e+00 1kkcA 221 9.86e+00 a.2.11.1,d.44.1.1 68660,68661 1s1qA 145 1.01e+01 d.20.1.2 98351 1zm0A 114 1.08e+01 2f4nA 273 1.09e+01 1y791 680 1.09e+01 1r5eA 115 1.17e+01 1nksA 194 1.20e+01 1nksA c.37.1.1 31886 1br9 194 1.23e+01 1br9 b.40.3.1 25235 1xtqA 177 1.23e+01 1dkqA 410 1.27e+01 1dklA c.60.1.2 33998 1jogA 146 1.30e+01 a.24.16.2 77142 1wekA 217 1.30e+01 1m0dA 138 1.35e+01 c.52.1.17 74354 1alu 186 1.36e+01 1alu a.26.1.1 16826 1qipA 183 1.39e+01 1qipA d.32.1.1 38470 1tafB 70 1.41e+01 1tafB a.22.1.3 16482 1oo0A 147 1.43e+01 d.232.1.1 87182 1ru0A 105 1.45e+01 2eutA 294 1.46e+01 1vh5A 148 1.47e+01 d.38.1.5 100642 1dkmA 410 1.51e+01 1dklA c.60.1.2 34000 2h0bA 184 1.52e+01 2cxcA 144 1.52e+01 1z53A 294 1.54e+01 1h9dB 134 1.55e+01 2jhbA b.54.1.1 60822 1zwxA 301 1.55e+01 1gmuA 143 1.58e+01 b.107.1.1,d.58.38.1 65335,65336 2aliA 158 1.68e+01 1vhzA 198 1.68e+01 d.113.1.1 100718 1a8i 842 1.70e+01 1a8i c.87.1.4 35490 2d93A 134 1.71e+01 1eueA 86 1.75e+01 1cyo d.120.1.1 59504 1k66A 149 1.77e+01 c.23.1.1 90941 1mxmA 254 1.78e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1pg4A 652 1.83e+01 e.23.1.1 88067 2gsq 202 1.87e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1wudA 89 1.87e+01 1p1mA 406 1.88e+01 b.92.1.4,c.1.9.9 87696,87697 1m5yA 408 1.89e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1q87A 221 1.92e+01 e.47.1.1 96192 1twuA 139 1.92e+01 d.32.1.8 107413 1ygaA 342 1.93e+01 2aneA 125 1.97e+01 1g5cA 170 2.02e+01 1g5cA c.53.2.1 60264 1go4A 205 2.03e+01 d.135.1.1 70292 1gmiA 136 2.04e+01 b.7.1.1 65309 1z54A 132 2.05e+01 1evhA 112 2.12e+01 1evhA b.55.1.4 26997 1dwkA 156 2.16e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1rzhM 307 2.18e+01 f.26.1.1 98165 2d0oA 610 2.21e+01 1z94A 147 2.22e+01 2a8yA 270 2.26e+01 1hekA 131 2.27e+01 a.61.1.5 65818 1awd 94 2.28e+01 1awd d.15.4.1 37673 1jdrA 294 2.30e+01 1ryc a.93.1.1 62908 1tdtA 259 2.32e+01 3tdt b.81.1.2 28055 1dmhA 311 2.34e+01 1dmhA b.3.6.1 22633 1zbyA 294 2.39e+01 1nnsA 326 2.43e+01 c.88.1.1 85910 1j6pA 418 2.45e+01 b.92.1.4,c.1.9.9 77089,77090 4uagA 437 2.47e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1h5uA 842 2.47e+01 1a8i c.87.1.4 60655 1wosA 364 2.51e+01 b.44.2.1,d.250.1.1 109468,109469 1qfgA 725 2.56e+01 1by5A f.4.3.3 43803 1rm6A 769 2.56e+01 1ztdA 133 2.67e+01 1zzcA 198 2.67e+01 1dgfA 497 2.70e+01 1cf9A e.5.1.1 42782 1iznB 277 2.77e+01 e.43.1.2 83848 1avbA 226 2.82e+01 1led b.29.1.1 24158 1y9wA 140 2.89e+01 1vhyA 257 2.95e+01 b.122.1.2,c.116.1.5 100714,100715 2a13A 166 2.98e+01 1euhA 475 3.14e+01 1euhA c.82.1.1 35369 1ewqA 765 3.18e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1i7pA 274 3.27e+01 b.43.4.2,c.25.1.1 66048,66049 1zhhB 242 3.27e+01 1jhjA 171 3.30e+01 b.18.1.9 66714 1eexA 554 3.34e+01 1dioA c.1.19.3 29650 1evsA 187 3.42e+01 1evsA a.26.1.1 16845 1v7oA 165 3.42e+01 d.67.1.2 100480 2a35A 215 3.43e+01 1wab 232 3.47e+01 1wab c.23.10.3 31341 2d4qA 257 3.48e+01 1mo9A 523 3.49e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1w0hA 204 3.55e+01 1mngA 203 3.59e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1rybA 212 3.63e+01 c.56.3.1 98098 2bh9A 489 3.67e+01 1mkrA 294 3.67e+01 a.93.1.1 84997 1fzrA 138 3.68e+01 1fzrA c.52.1.17 33336 1v9yA 167 3.68e+01 d.110.3.2 108454 1ixlA 131 3.71e+01 d.38.1.5 90717 2fkbA 180 3.71e+01 1b56 135 3.76e+01 1hmt b.60.1.2 27183 1bdo 80 3.78e+01 1bdo b.84.1.1 28214 1q3iA 214 3.90e+01 d.220.1.1 104524 2acfA 182 3.96e+01 1ualA 274 4.00e+01 c.116.1.4 88383 1dszB 85 4.02e+01 2nllB g.39.1.2 45108 1f08A 148 4.07e+01 1f08A d.89.1.2 59564 1e1oA 504 4.08e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1yqfA 203 4.09e+01 2fn0A 437 4.15e+01 1rzuA 485 4.17e+01 c.87.1.8 105140 1wmhB 86 4.18e+01 1ui7A 638 4.45e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1siiA 646 4.46e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 2b6eA 146 4.46e+01 1jf9A 408 4.47e+01 1c0nA c.67.1.3 62931 1os8A 223 4.49e+01 b.47.1.1 93481 2lhb 149 4.51e+01 2fal a.1.1.2 15597 1td2A 287 4.57e+01 c.72.1.5 106765 1nxzA 246 4.61e+01 b.122.1.2,c.116.1.5 86391,86392 1hg8A 349 4.66e+01 b.80.1.3 65830 1fuxA 166 4.67e+01 1fjjA b.17.1.2 60034 1nh0A 99 4.68e+01 b.50.1.1 91869 1w6gA 646 4.75e+01 1mqoA 227 4.76e+01 d.157.1.1 103846 1q1rA 431 4.78e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1sdjA 310 4.81e+01 d.21.1.2,d.21.1.2 98807,98808 2sli 679 4.84e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1rjoA 646 4.86e+01 1sgt 223 4.87e+01 5ptp b.47.1.1 25814 1dseA 292 4.87e+01 1ryc a.93.1.1 59130 2g1lA 104 4.87e+01 1oj6A 151 4.88e+01 a.1.1.2 93088 1u3wA 374 4.91e+01 1nbwA 607 4.96e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 2dbbA 151 4.99e+01 2cpgA 45 5.12e+01 2cpgA a.43.1.3 17455 1nzaA 103 5.14e+01 d.58.5.2 86444 1qwkA 317 5.15e+01 c.1.7.1 96482 1n13B 113 5.18e+01 1xe7A 203 5.24e+01 1eulA 994 5.24e+01 1eulA 2blcA 238 5.25e+01 1w8oA 601 5.27e+01 1i1iP 681 5.31e+01 1i1iP d.92.1.5 40297 1lp8A 254 5.35e+01 d.165.1.1 91082 1rl0A 255 5.35e+01 1gtkA 313 5.36e+01 c.94.1.1,d.50.2.1 76346,76347 1m2xA 223 5.38e+01 d.157.1.1 84764 1g5aA 628 5.43e+01 b.71.1.1,c.1.8.1 65152,65153 1t6cA 315 5.45e+01 c.55.1.8,c.55.1.8 106558,106559 1wvqA 167 5.45e+01 1d8cA 723 5.52e+01 1d8cA c.1.13.1 29325 1lk5A 229 5.57e+01 c.124.1.4,d.58.40.1 73960,73961 1tkeA 224 5.70e+01 1sltA 134 5.72e+01 1c1lA b.29.1.3 24186 1odkA 235 5.79e+01 c.56.2.1 86863 1ijyA 130 5.84e+01 1ijxA a.141.1.1 62517 1voqa 90 5.85e+01 1ftrA 296 5.90e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1eumA 165 5.93e+01 1eumA a.25.1.1 59507 1hf8A 289 6.01e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1mqvA 125 6.02e+01 a.24.3.2 79415 1zoyC 140 6.03e+01 1xm0A 147 6.03e+01 1lylA 504 6.07e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1kzkA 99 6.08e+01 b.50.1.1 73371 1vf8A 377 6.10e+01 1wriA 93 6.13e+01 1ntn 72 6.15e+01 3ebx g.7.1.1 44414 1lox 662 6.15e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1pyoA 167 6.21e+01 c.17.1.1 95370 1wtaA 275 6.24e+01 1kpf 126 6.25e+01 1kpf d.13.1.1 37507 1es9A 232 6.30e+01 1wab c.23.10.3 31340 1or7C 90 6.32e+01 a.180.1.1 87336 1o0iA 138 6.36e+01 d.38.1.5 86532 1vjfA 180 6.37e+01 d.116.1.1 100809 2yhx 457 6.37e+01 2yhx i.12.1.1 46024 1q5zA 177 6.39e+01 a.196.1.1 95954 1rqpA 299 6.41e+01 b.141.1.1,c.132.1.1 97754,97755 1io1A 398 6.45e+01 1io1A e.32.1.1 62611 1p5dX 463 6.47e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1yuwA 554 6.49e+01 2bm3A 166 6.50e+01 2bvbA 137 6.56e+01 1yspA 181 6.60e+01 1pzsA 208 6.64e+01 b.1.8.1 104397 1prxA 224 6.68e+01 1prxA c.47.1.10 33076 1iwmA 186 6.71e+01 b.125.1.2 83758 2gfgA 193 6.72e+01 1f06A 320 6.73e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1jnyA 435 6.73e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1h8gA 95 6.75e+01 b.109.1.1 65735 2a90A 240 6.75e+01 1k8tA 510 6.75e+01 e.41.1.1 68316 1qwtA 255 6.78e+01 b.26.1.3 96501 1xi3A 215 6.86e+01 c.1.3.1 109601 1lj5A 379 6.86e+01 e.1.1.1 73928 1jl0A 334 6.87e+01 1jenA d.156.1.1 63155 1cjcA 460 6.92e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 2dc3A 193 6.95e+01 1uisA 231 6.98e+01 d.22.1.1 99431 1fi2A 201 7.11e+01 1fi2A b.82.1.2 59845 1zkiA 133 7.12e+01 1gyfA 62 7.17e+01 1gyfA d.76.1.1 39749 1nrkA 328 7.17e+01 b.44.2.1,d.250.1.1 92089,92090 1izmA 184 7.21e+01 a.199.1.1 90725 1jenA 267 7.21e+01 1jenA 1l0wA 580 7.30e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1avk 638 7.32e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1c7qA 445 7.33e+01 2pgi c.80.1.2 35307 1whzA 70 7.54e+01 2erbA 125 7.55e+01 1ecfA 504 7.57e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1wcqA 601 7.58e+01 1yg9A 330 7.58e+01 1avyA 74 7.61e+01 1avyB h.1.17.1 45656 2et1A 201 7.63e+01 1usmA 80 7.65e+01 d.74.1.1 99876 1dtoA 221 7.68e+01 1dtoA b.91.1.1 28405 1a7cA 379 7.69e+01 1sek e.1.1.1 42660 1tw9A 206 7.69e+01 a.45.1.1,c.47.1.5 107381,107382 2airB 153 7.77e+01 1urvA 190 7.79e+01 1ut0A 190 7.79e+01 a.1.1.2 108012 1r69 69 7.81e+01 1r69 a.35.1.2 17028 1i2aA 219 7.91e+01 e.24.1.1 90660 1su4A 994 7.96e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1b4vA 504 8.01e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 2ghsA 326 8.02e+01 1e9lA 377 8.03e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1d3yA 301 8.04e+01 1d3yA e.12.1.1 43252 1zmaA 118 8.10e+01 2f1kA 279 8.16e+01 1uwkA 557 8.19e+01 e.51.1.1 108065 1wc9A 169 8.22e+01 1bu6O 501 8.26e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 2aaa 484 8.38e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1tzjA 338 8.45e+01 1h5zA 455 8.47e+01 a.104.1.1 90622 1otfA 62 8.52e+01 1otfA d.80.1.1 39820 1bhdA 118 8.53e+01 1bkrA a.40.1.1 17398 1xtzA 264 8.58e+01 2govA 195 8.70e+01 1x6vA 630 8.70e+01 1xnb 185 8.72e+01 1axkA b.29.1.11 24308 1e5eA 404 8.73e+01 1ibjA c.67.1.3 59265 3proC 166 8.73e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1rtm1 149 8.77e+01 1rtm1 1mhyB 395 8.78e+01 1mtyB a.25.1.2 16781 2fbqA 235 8.82e+01 1u3aA 189 8.83e+01 1i6iA 366 8.85e+01 1bg2 c.37.1.9 61844 1rcy 151 8.87e+01 1rcy b.6.1.1 23018 1e9xA 455 8.89e+01 1ea1A a.104.1.1 18969 1gz2A 142 8.89e+01 d.169.1.1 83392 3sil 379 8.94e+01 3sil b.68.1.1 27542 1h8vA 218 8.95e+01 2nlrA b.29.1.11 60795 1ycdA 243 8.95e+01 1mxtA 504 8.99e+01 c.3.1.2,d.16.1.1 79671,79672