# List of top-scoring protein chains for t06-100-30-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 1xubA 298 8.86e-03 2gkeA 274 6.84e-02 1gqzA 274 8.28e-02 d.21.1.1,d.21.1.1 83311,83312 1xttA 216 2.49e-01 1qx4A 274 3.08e-01 b.43.4.2,c.25.1.1 104624,104625 1p3dA 475 3.30e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1dp4A 435 3.45e-01 1dp4A c.93.1.1 35710 1sr8A 298 3.96e-01 e.54.1.1 105959 1josA 128 5.99e-01 d.52.7.1 84191 1pj5A 830 6.29e-01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1nnxA 109 9.34e-01 b.40.10.1 92013 1umkA 275 1.07e+00 1o17A 345 1.58e+00 a.46.2.1,c.27.1.1 80765,80766 1mkiA 330 1.82e+00 e.3.1.2 84994 1ogsA 497 1.88e+00 b.71.1.2,c.1.8.3 86997,86998 1vdkA 466 1.93e+00 a.127.1.1 100561 1oe4A 247 1.97e+00 c.18.1.3 86895 1bupA 386 2.05e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1o8bA 219 2.45e+00 c.124.1.4,d.58.40.1 81180,81181 1gtzA 156 2.48e+00 c.23.13.1 70539 1vl2A 421 2.74e+00 c.26.2.1,d.210.1.1 108708,108709 1a8rA 221 2.83e+00 1a8rA d.96.1.1 40587 1sziA 247 3.14e+00 a.24.23.1 106159 1q15A 503 3.18e+00 c.26.2.1,d.153.1.1 95538,95539 1jc9A 269 3.29e+00 d.171.1.1 66490 1rsy 152 3.34e+00 1rsy b.7.1.2 23192 1f3uA 118 3.34e+00 1f3uA b.65.1.1 27521 1j5pA 253 4.29e+00 d.81.1.3,c.2.1.3 71577,83092 1vljA 407 4.42e+00 e.22.1.2 108832 1rzhL 281 4.42e+00 f.26.1.1 98164 1qjtA 99 4.56e+00 1eh2 a.39.1.6 17335 1g5cA 170 5.00e+00 1g5cA c.53.2.1 60264 1s1qA 145 5.52e+00 d.20.1.2 98351 1r5eA 115 5.78e+00 1nnsA 326 6.50e+00 c.88.1.1 85910 1iznB 277 6.63e+00 e.43.1.2 83848 1oo0A 147 6.72e+00 d.232.1.1 87182 1alu 186 6.76e+00 1alu a.26.1.1 16826 1dkqA 410 6.79e+00 1dklA c.60.1.2 33998 1dwkA 156 6.93e+00 1dw9A a.35.1.4,d.72.1.1 17075,39606 1jogA 146 7.24e+00 a.24.16.2 77142 1mxmA 254 7.33e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1q87A 221 7.44e+00 e.47.1.1 96192 1dkmA 410 7.89e+00 1dklA c.60.1.2 34000 1evhA 112 8.11e+00 1evhA b.55.1.4 26997 1gmuA 143 8.36e+00 b.107.1.1,d.58.38.1 65335,65336 1pg4A 652 8.74e+00 e.23.1.1 88067 1ru0A 105 8.78e+00 1vh5A 148 9.46e+00 d.38.1.5 100642 1tafB 70 9.72e+00 1tafB a.22.1.3 16482 1awd 94 1.02e+01 1awd d.15.4.1 37673 1rzhM 307 1.09e+01 f.26.1.1 98165 1jhjA 171 1.12e+01 b.18.1.9 66714 1q3iA 214 1.16e+01 d.220.1.1 104524 1rm6A 769 1.17e+01 1eueA 86 1.17e+01 1cyo d.120.1.1 59504 1k66A 149 1.23e+01 c.23.1.1 90941 1hekA 131 1.28e+01 a.61.1.5 65818 1euhA 475 1.31e+01 1euhA c.82.1.1 35369 1nscA 390 1.32e+01 2qwc b.68.1.1 27591 1ixlA 131 1.34e+01 d.38.1.5 90717 1r44A 202 1.37e+01 d.65.1.4 104787 1avbA 226 1.38e+01 1led b.29.1.1 24158 1evsA 187 1.46e+01 1evsA a.26.1.1 16845 1t6cA 315 1.49e+01 c.55.1.8,c.55.1.8 106558,106559 1kveA 63 1.50e+01 1kveA d.70.1.2 39590 1bdo 80 1.52e+01 1bdo b.84.1.1 28214 1fuxA 166 1.53e+01 1fjjA b.17.1.2 60034 1h5uA 842 1.58e+01 1a8i c.87.1.4 60655 1p1mA 406 1.59e+01 b.92.1.4,c.1.9.9 87696,87697 1go4A 205 1.60e+01 d.135.1.1 70292 1ubkL 534 1.61e+01 e.18.1.1 88422 4uagA 437 1.67e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 2sli 679 1.68e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1v9yA 167 1.75e+01 d.110.3.2 108454 1mo9A 523 1.80e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1eexA 554 1.80e+01 1dioA c.1.19.3 29650 1odkA 235 1.84e+01 c.56.2.1 86863 1rjoA 646 1.85e+01 1e1oA 504 1.88e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1prxA 224 2.00e+01 1prxA c.47.1.10 33076 1hg8A 349 2.03e+01 b.80.1.3 65830 1ftrA 296 2.06e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1lk5A 229 2.07e+01 c.124.1.4,d.58.40.1 73960,73961 1jf9A 408 2.08e+01 1c0nA c.67.1.3 62931 1pzsA 208 2.26e+01 b.1.8.1 104397 1os8A 223 2.29e+01 b.47.1.1 93481 1f08A 148 2.29e+01 1f08A d.89.1.2 59564 1pyoA 167 2.33e+01 c.17.1.1 95370 1q1rA 431 2.42e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1mngA 203 2.45e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1qipA 183 2.49e+01 1qipA d.32.1.1 38470 1rzuA 485 2.51e+01 c.87.1.8 105140 1dszB 85 2.57e+01 2nllB g.39.1.2 45108 1lyqA 104 2.58e+01 b.1.18.17 78302 1tkeA 224 2.64e+01 1mqvA 125 2.65e+01 a.24.3.2 79415 1sdjA 310 2.66e+01 d.21.1.2,d.21.1.2 98807,98808 1mqoA 227 2.67e+01 d.157.1.1 103846 1iwmA 186 2.69e+01 b.125.1.2 83758 1b56 135 2.70e+01 1hmt b.60.1.2 27183 1ijyA 130 2.79e+01 1ijxA a.141.1.1 62517 1xe7A 203 2.81e+01 1rybA 212 2.87e+01 c.56.3.1 98098 2biqA 219 2.87e+01 1nbwA 607 2.92e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1rl0A 255 2.97e+01 1g5aA 628 2.97e+01 b.71.1.1,c.1.8.1 65152,65153 1whzA 70 2.99e+01 1m2xA 223 3.01e+01 d.157.1.1 84764 2gfgA 193 3.06e+01 1rqpA 299 3.14e+01 b.141.1.1,c.132.1.1 97754,97755 1qwkA 317 3.19e+01 c.1.7.1 96482 1q5zA 177 3.20e+01 a.196.1.1 95954 1jl0A 334 3.20e+01 1jenA d.156.1.1 63155 1p5dX 463 3.24e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1jb9A 316 3.26e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1jnyA 435 3.29e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1uwkA 557 3.34e+01 e.51.1.1 108065 1hf8A 289 3.38e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1ecfA 504 3.40e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1gtkA 313 3.41e+01 c.94.1.1,d.50.2.1 76346,76347 1n13B 113 3.43e+01 1gz2A 142 3.45e+01 d.169.1.1 83392 1usmA 80 3.45e+01 d.74.1.1 99876 1bu6O 501 3.55e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1kpf 126 3.70e+01 1kpf d.13.1.1 37507 1tw9A 206 3.80e+01 a.45.1.1,c.47.1.5 107381,107382 1izmA 184 3.82e+01 a.199.1.1 90725 1x99A 145 3.86e+01 1o20A 427 4.00e+01 c.82.1.1 86556 1i1nA 226 4.01e+01 c.66.1.7 71102 1gmiA 136 4.16e+01 b.7.1.1 65309 1sz7A 200 4.27e+01 1bhdA 118 4.29e+01 1bkrA a.40.1.1 17398 1jb7A 495 4.29e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1rreA 200 4.32e+01 d.14.1.10 97791 1w0nA 131 4.33e+01 1te0A 318 4.33e+01 1es9A 232 4.37e+01 1wab c.23.10.3 31340 1ash 150 4.38e+01 1ash a.1.1.2 15622 1ogdA 131 4.43e+01 c.133.1.1 92893 1n4wA 504 4.49e+01 c.3.1.2,d.16.1.1 91676,91677 1v8yA 170 4.50e+01 1snzA 344 4.57e+01 b.30.5.4 98930 1eumA 165 4.66e+01 1eumA a.25.1.1 59507 1o0iA 138 4.71e+01 d.38.1.5 86532 1dpgA 485 4.77e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1d3yA 301 4.79e+01 1d3yA e.12.1.1 43252 3sil 379 4.80e+01 3sil b.68.1.1 27542 3proC 166 4.81e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1sc3A 178 4.89e+01 c.17.1.1 105416 1r69 69 4.90e+01 1r69 a.35.1.2 17028 1mkmA 249 4.92e+01 a.4.5.33,d.110.2.2 79242,79243 1cjaA 342 4.97e+01 1cjaA d.144.1.3 41708 1nh0A 99 4.98e+01 b.50.1.1 91869 1fp2A 352 5.00e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1rmg 422 5.01e+01 1rmg b.80.1.3 28029 1kbvA 327 5.02e+01 b.6.1.3,b.6.1.3 68395,68396 1avyA 74 5.03e+01 1avyB h.1.17.1 45656 1rttA 193 5.06e+01 c.23.5.4 105098 1pa7A 130 5.07e+01 a.40.1.1 94410 1pea 385 5.12e+01 1pea c.93.1.1 35662 1a91 79 5.14e+01 1a91 f.17.1.1 43635 1w0hA 204 5.14e+01 1n0wA 243 5.21e+01 c.37.1.11 79772 1brwA 433 5.22e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1c7qA 445 5.23e+01 2pgi c.80.1.2 35307 1jihA 531 5.24e+01 d.240.1.1,e.8.1.7 90374,90375 1f74A 293 5.34e+01 1nal3 c.1.10.1 29079 1mvfD 82 5.36e+01 b.129.1.1 85143 1nzaA 103 5.38e+01 d.58.5.2 86444 1guzA 310 5.49e+01 c.2.1.5,d.162.1.1 65586,65587 1s4bP 674 5.49e+01 d.92.1.5 105252 1ckmA 330 5.49e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1r2mA 71 5.58e+01 b.138.1.1 96871 1jae 471 5.60e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1nqkA 381 5.62e+01 c.1.16.4 92050 1bgvA 449 5.64e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1v9fA 325 5.66e+01 d.265.1.3 108448 1df7A 159 5.68e+01 3dfr c.71.1.1 34885 1k8kE 178 5.72e+01 a.148.1.1 68311 1p5zB 263 5.80e+01 c.37.1.1 87815 1lj5A 379 5.85e+01 e.1.1.1 73928 1ejdA 419 5.99e+01 1uae d.68.2.2 39576 1otfA 62 5.99e+01 1otfA d.80.1.1 39820 1rkqA 282 6.02e+01 c.108.1.10 97621 1n1tA 641 6.06e+01 b.29.1.15,b.68.1.1 79821,79822 1tueB 218 6.08e+01 b.91.1.1 107324 1dcoA 104 6.12e+01 1dcpA d.74.1.1 39680 1j3aA 142 6.12e+01 c.21.1.1 77070 1e58A 249 6.13e+01 1qhfA c.60.1.1 59262 1pfsA 78 6.22e+01 1pfsA b.40.4.7 25391 1jssA 224 6.25e+01 d.129.3.2 71844 1f3uB 171 6.28e+01 1f3uB b.65.1.1 27525 1oa8A 133 6.28e+01 b.145.1.1 92698 1nmoA 247 6.32e+01 c.135.1.1 91980 1c96A 753 6.41e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1k3sA 113 6.41e+01 d.198.1.1 68120 1o75A 415 6.43e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 1w9aA 147 6.47e+01 1m0uA 249 6.54e+01 a.45.1.1,c.47.1.5 78359,78360 1d9cA 121 6.54e+01 1d9cA a.26.1.3 16901 1i2aA 219 6.57e+01 e.24.1.1 90660 1ppjF 110 6.61e+01 f.27.1.1 104262 1pjr 724 6.62e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 1xy7A 166 6.68e+01 1oa2A 218 6.70e+01 b.29.1.11 86721 1lo7A 141 6.72e+01 d.38.1.1 74144 1jp4A 308 6.84e+01 1jp4A e.7.1.1 63223 1bkjA 240 6.87e+01 1bkjA d.90.1.1 40243 1tfe 145 6.89e+01 1tfe d.43.1.1 38680 1qg7A 67 6.90e+01 1a15A d.9.1.1 37449 1q4gA 553 6.91e+01 a.93.1.2,g.3.11.1 95789,95790 1tjyA 316 6.94e+01 c.93.1.1 107062 1wubA 178 6.98e+01 1qwtA 255 7.05e+01 b.26.1.3 96501 1ryiA 382 7.07e+01 1g8iA 190 7.11e+01 1rec a.39.1.5 60363 1w96A 554 7.13e+01 1f60A 458 7.28e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1tl2A 236 7.29e+01 1tl2A b.67.1.1 27541 1fjgI 128 7.29e+01 1fjfI d.14.1.1 37559 1k6dA 220 7.36e+01 c.124.1.2 72082 1lfpA 249 7.37e+01 e.39.1.1 73885 1nowA 507 7.42e+01 c.1.8.6,d.92.2.1 85936,85937 1hbnC 248 7.45e+01 1mroC d.58.31.1 60902 1wouA 123 7.47e+01 c.47.1.16 109471 1swvA 267 7.51e+01 1fi2A 201 7.57e+01 1fi2A b.82.1.2 59845 1iicA 422 7.57e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 2ga9D 469 7.62e+01 1tu5A 746 7.64e+01 1a6jA 163 7.78e+01 1a6jA d.112.1.1 40915 1hrnA 337 7.82e+01 1smrA b.50.1.2 26869 1t9bA 677 7.89e+01 1r7lA 110 7.92e+01 d.277.1.1 104837 1vkkA 154 7.96e+01 d.109.1.2 108669 1xm3A 264 7.96e+01 1bebA 162 8.07e+01 1bebA b.60.1.1 27115 1f5vA 240 8.08e+01 1bkjA d.90.1.1 40255 1vhh 162 8.12e+01 1vhh d.65.1.2 39550 1wqjB 80 8.14e+01 1to6A 371 8.17e+01 c.141.1.1 107170 1y93A 159 8.18e+01 1jniA 123 8.18e+01 a.138.1.3 71761 1cghA 224 8.21e+01 1a7s b.47.1.2 26290 1iscA 192 8.31e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1j1nA 492 8.37e+01 c.94.1.1 83978 1i24A 404 8.43e+01 c.2.1.2 83663 1g8kB 133 8.44e+01 1g8jB b.33.1.1 24435 1gtmA 419 8.45e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1qfhA 212 8.46e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1aozA 552 8.61e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1ie9A 259 8.61e+01 1db1A a.123.1.1 62318 1lwdA 413 8.62e+01 c.77.1.1 78265 1ku0A 388 8.62e+01 c.69.1.18 72994 1mucA 373 8.65e+01 1mucA c.1.11.2,d.54.1.1 29236,38880 1ebfA 358 8.67e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1x8vA 455 8.70e+01 1rypD 241 8.77e+01 1rypD d.153.1.4 41935 1fs5A 266 8.86e+01 c.124.1.1 65044 1h99A 224 8.88e+01 a.142.1.1,a.142.1.1 60814,60815