# List of top-scoring protein chains for t2k-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.soe.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 3cbnA 151 7.82e-02 1cdy 178 2.20e-01 1cdy 2uxyA 341 3.81e-01 2aukA 190 5.22e-01 2dyuA 334 9.24e-01 1x3cA 73 1.76e+00 g.37.1.1 121660 1z4vA 532 1.93e+00 2gysA 419 2.30e+00 b.1.2.1,b.1.2.1,b.1.2.1,b.1.2.1 135865,135866,135867,135868 2ny1B 184 2.61e+00 b.1.1.1,b.1.1.3 138764,138765 2r0hA 164 2.66e+00 1wj2A 78 2.69e+00 g.79.1.1 114689 1w6tA 444 3.03e+00 c.1.11.1,d.54.1.1 120670,120671 2axwA 134 3.23e+00 1xf1A 926 3.25e+00 2pa6A 427 3.31e+00 2co7B 221 3.73e+00 2d7nA 93 3.88e+00 b.1.18.10 131322 2b79A 144 5.15e+00 1ok7A 366 6.20e+00 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1jj2A 239 6.25e+00 1rl2A b.34.5.3,b.40.4.5 63084,63085 1edqA 540 6.51e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1ctn 540 7.04e+00 1ctn 2dg1A 333 7.62e+00 b.68.6.1 131493 1iz6A 138 7.64e+00 b.34.5.2,b.40.4.5 76976,76977 1k9tA 540 8.23e+00 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 1h03P 125 8.32e+00 g.18.1.1,g.18.1.1 83411,83412 2gibA 103 8.58e+00 d.254.1.2 135225 1o12A 376 8.76e+00 b.92.1.5,c.1.9.10 80758,80759 2q4nA 166 9.02e+00 b.60.1.8 139871 1o20A 427 1.03e+01 c.82.1.1 86556 1cqyA 99 1.07e+01 1b9zA b.3.1.1 22527 2aydA 76 1.10e+01 1ij8A 128 1.13e+01 b.61.1.1 62480 1f2fA 104 1.14e+01 1fmk d.93.1.1 40455 1nqnA 122 1.20e+01 b.61.1.1 86042 1vemA 516 1.23e+01 b.3.1.1,c.1.8.1 120021,120022 2ehzA 302 1.24e+01 1voqa 90 1.25e+01 1evhA 112 1.28e+01 1evhA b.55.1.4 26997 1j6uA 469 1.29e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1l4sA 112 1.29e+01 d.204.1.1 77693 1itcA 516 1.31e+01 b.3.1.1,c.1.8.1 83705,83706 1qhlA 227 1.31e+01 1qhlA c.37.1.12 32382 2a13A 166 1.35e+01 b.60.1.8 125971 1qu1A 155 1.35e+01 1qu1A h.3.1.1 45670 2e27H 126 1.39e+01 2ftwA 521 1.40e+01 b.92.1.3,c.1.9.6 134083,134084 2pmqA 377 1.40e+01 1dmhA 311 1.46e+01 1dmhA b.3.6.1 22633 2d1kC 32 1.48e+01 3cniA 156 1.52e+01 1hgeB 175 1.53e+01 1hgeB h.3.1.1 45680 2viuB 175 1.54e+01 1hgeB h.3.1.1 45676 1tf6A 190 1.56e+01 1tf6A g.37.1.1,g.37.1.1,g.37.1.1,g.37.1.1,g.37.1.1,g.37.1.1 45060,45061,45062,45063,45064,45065 1pzsA 208 1.57e+01 b.1.8.1 104397 1utcA 363 1.57e+01 a.118.1.4,b.69.6.1 99914,99915 1nrvA 105 1.61e+01 d.93.1.1 86126 2vqiA 515 1.64e+01 1led 243 1.67e+01 1led 1n9lA 109 1.67e+01 d.110.3.6 85468 1ledA 243 1.67e+01 b.29.1.1 24039 1vyoA 128 1.67e+01 2polA 366 1.70e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 2p3nA 256 1.72e+01 1bpoA 494 1.74e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 2p19A 149 1.76e+01 2oojA 141 1.77e+01 1ft9A 222 1.80e+01 1ft9A a.4.5.4,b.82.3.1 16107,28131 1y8xA 160 1.81e+01 d.20.1.1 122769 2pulA 397 1.86e+01 2iw0A 254 1.90e+01 c.6.2.3 137737 1ikpA 613 1.91e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1fltX 95 1.92e+01 1fltX b.1.1.4 21765 2pkhA 148 1.94e+01 3b47A 134 1.94e+01 1qtyT 101 1.94e+01 1fltX b.1.1.4 21769 2i4iA 417 1.95e+01 1shaA 104 1.98e+01 1fmk d.93.1.1 40424 2j0nA 200 1.98e+01 a.250.1.1 137899 2pijA 67 1.99e+01 1dpeA 507 2.00e+01 c.94.1.1 35799 1yz7A 188 2.02e+01 1dppA 507 2.02e+01 1dpe c.94.1.1 35800 4enl 436 2.07e+01 4enl 2d7eA 105 2.09e+01 1ex2A 189 2.18e+01 1ex2A c.51.4.2 33225 2fymA 431 2.19e+01 c.1.11.1,d.54.1.1 134379,134380 1oohA 126 2.20e+01 a.39.2.1 93383 1avbA 226 2.26e+01 1led b.29.1.1 24158 1ifrA 121 2.27e+01 b.1.16.1 71203 1to2I 64 2.40e+01 d.40.1.1 112596 1hyvA 166 2.45e+01 1b9dA c.55.3.2 61424 2boyA 254 2.46e+01 2bycA 137 2.50e+01 d.58.10.2 129476 1c5cH 215 2.56e+01 1igtB b.1.1.1,b.1.1.2 20475,21439 1scjB 71 2.57e+01 1scjB d.58.3.2 39069 1jjfA 268 2.59e+01 c.69.1.2 66765 1tf3A 92 2.60e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45057,45058,45059 1qreA 247 2.61e+01 1qreA b.81.1.5 28066 2cfxA 144 2.63e+01 a.4.5.32,d.58.4.2 130395,130396 1exqA 154 2.68e+01 1b9dA c.55.3.2 33646 1b9dA 163 2.70e+01 1b9dA c.55.3.2 33649 2vl7A 540 2.74e+01 1b9zA 516 2.76e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1fx5A 242 2.77e+01 1led b.29.1.1 24135 1lkkA 105 2.77e+01 1lckA d.93.1.1 40412 1kopA 223 2.78e+01 2cba b.74.1.1 27966 1iwmA 186 2.79e+01 b.125.1.2 83758 1jsdB 176 2.84e+01 h.3.1.1 63259 1d0dA 60 2.85e+01 1kigI g.8.1.2 44566 1itg 166 2.87e+01 1b9dA 1aym1 285 2.88e+01 1aym1 2nwbA 400 2.90e+01 2dvkA 188 2.93e+01 1thjA 214 2.95e+01 1qreA b.81.1.5 28072 1gmuA 143 3.02e+01 b.107.1.1,d.58.38.1 65335,65336 2ol1A 147 3.03e+01 1d2eA 397 3.08e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1q5hA 147 3.11e+01 b.85.4.1 95893 1m7sA 484 3.11e+01 e.5.1.1 74574 1tmxA 293 3.13e+01 3b42A 135 3.14e+01 1lf2A 331 3.20e+01 b.50.1.2 77914 2i75A 320 3.24e+01 1o4rA 108 3.37e+01 d.93.1.1 92469 2c1sA 126 3.41e+01 1bpwA 503 3.43e+01 1bpwA c.82.1.1 35365 1zd0A 150 3.57e+01 d.329.1.1 124927 1ypcI 64 3.57e+01 2sniI d.40.1.1 38570 1iyxA 432 3.60e+01 c.1.11.1,d.54.1.1 83815,83816 3czbA 351 3.63e+01 1lw6I 64 3.65e+01 d.40.1.1 74294 1e2wA 251 3.67e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1m85A 484 3.73e+01 e.5.1.1 74578 1vluA 468 3.73e+01 c.82.1.1 108864 2furA 209 3.77e+01 b.45.1.1 134185 1yg9A 330 3.78e+01 2bf6A 449 3.79e+01 2iiaA 131 3.80e+01 2hf2A 283 3.83e+01 2vosA 487 3.87e+01 1rfeA 162 3.91e+01 b.45.1.1 111796 1vqoA 240 3.95e+01 b.34.5.3,b.40.4.5 120361,120362 2dknA 255 3.96e+01 2fcfA 103 3.98e+01 b.36.1.1 133267 1bl3A 160 4.03e+01 1b9dA c.55.3.2 33655 2cwsA 237 4.03e+01 2a7bA 120 4.04e+01 b.1.10.2 126333 1zeeA 403 4.04e+01 a.266.1.2 124981 1xneA 113 4.07e+01 b.122.1.6 115579 1um5H 217 4.09e+01 b.1.1.1,b.1.1.2 113302,113303 1x6oA 174 4.11e+01 b.34.5.2,b.40.4.5 109493,109494 3c26A 266 4.12e+01 2r8rA 228 4.15e+01 3cnqP 80 4.21e+01 1t4wA 196 4.34e+01 b.2.5.2 106427 1ru0A 105 4.36e+01 d.74.1.1 111937 1gzcA 239 4.37e+01 b.29.1.1 70803 1xtmA 175 4.41e+01 1jmxB 349 4.43e+01 b.69.2.2 66906 1s4iA 175 4.45e+01 1ze3C 205 4.49e+01 b.1.11.1,b.7.2.1 124974,124975 1lj5A 379 4.54e+01 e.1.1.1 73928 1ztxL 212 4.56e+01 1spbP 78 4.60e+01 1scjB d.58.3.2 39068 1seiA 130 4.60e+01 1seiA d.140.1.1 41463 1dqpA 230 4.63e+01 1dqnA c.61.1.1 34069 2hnuA 81 4.64e+01 2v2gA 233 4.66e+01 1wosA 364 4.68e+01 b.44.2.1,d.250.1.1 109468,109469 1nepA 130 4.69e+01 b.1.18.7 80440 1xtlA 175 4.69e+01 1jetA 517 4.75e+01 1jevA c.94.1.1 35718 2ef7A 133 4.84e+01 1o7dC 159 4.93e+01 b.30.5.6 86640 1qpxA 218 4.93e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1mvfD 82 4.94e+01 b.129.1.1 85143 1dqnA 230 4.94e+01 1dqnA c.61.1.1 34067 3d26A 301 4.94e+01 2v6oA 596 4.95e+01 1i0rA 169 4.97e+01 1i0rA b.45.1.2 61489 2z0tA 109 5.00e+01 3by3A 301 5.05e+01 2j2zA 218 5.08e+01 b.1.11.1,b.7.2.1 137974,137975 1bhe 376 5.09e+01 1bhe 1bheA 376 5.09e+01 b.80.1.3 28030 2oynA 146 5.13e+01 1rd5A 262 5.25e+01 c.1.2.4 111772 1coaI 64 5.30e+01 2sniI d.40.1.1 38574 1vlgA 176 5.33e+01 a.25.1.1 108816 1nmtA 392 5.34e+01 1nmtA d.108.1.2,d.108.1.2 40823,40824 1lm8V 160 5.37e+01 b.3.3.1 74035 1lqbC 162 5.52e+01 b.3.3.1 74186 1ravA 127 5.53e+01 1swuA b.61.1.1 27409 2iumA 248 5.53e+01 3c0fB 91 5.54e+01 1y55X 126 5.56e+01 2r78A 117 5.59e+01 1n1tA 641 5.64e+01 b.29.1.15,b.68.1.1 79821,79822 3b34A 891 5.66e+01 1prn 289 5.67e+01 3prn 1plc 99 5.71e+01 1plc 1plcA 99 5.71e+01 b.6.1.1 22846 2ejwA 332 5.71e+01 2e12A 101 5.74e+01 1v05A 96 5.74e+01 b.1.18.10 113465 1pgl1 185 5.81e+01 1ybdA 239 5.86e+01 c.73.1.3 122884 2h5oA 234 5.93e+01 1l4iA 206 5.99e+01 b.1.11.1,b.7.2.1 73564,73565 1n0lA 224 6.00e+01 b.1.11.1,b.7.2.1 79744,79745 1s1qA 145 6.03e+01 d.20.1.2 98351 1kveB 77 6.04e+01 1kveB 2b3yA 888 6.08e+01 c.8.2.1,c.83.1.1 127803,127804 2v6vA 156 6.10e+01 1b3cA 64 6.11e+01 1aho g.3.7.1 44121 1ituA 369 6.17e+01 c.1.9.7 71423 1tk1A 260 6.18e+01 d.248.1.1 107066 1g2rA 100 6.19e+01 1g2rA d.192.1.1 60231 1a7cA 379 6.25e+01 1sek e.1.1.1 42660 1nif 340 6.25e+01 1nif 2h1tA 188 6.26e+01 2z4tA 514 6.27e+01 1pa2A 306 6.31e+01 1bgp a.93.1.1 18693 1fce 629 6.37e+01 1fce 1iicA 422 6.42e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 2gr8A 99 6.43e+01 d.24.1.4 135522 2f4wA 187 6.44e+01 d.20.1.1 132958 1jxgA 100 6.47e+01 b.6.1.1 67413 1faeA 629 6.51e+01 1fce a.102.1.2 18837 1g9gA 629 6.57e+01 a.102.1.2 83279 1pfzA 380 6.57e+01 1smrA b.50.1.2 26881 1g3p 217 6.57e+01 1g3p 1g3pA 217 6.57e+01 b.37.1.1,b.37.1.1 24788,24789 1qtfA 246 6.59e+01 1agjA b.47.1.1 25830 2v3mA 131 6.65e+01 2hm7A 310 6.65e+01 1e4fT 419 6.67e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1s21A 206 6.71e+01 d.166.1.4 105222 1flrL 219 6.80e+01 8fabA b.1.1.1,b.1.1.2 19904,20998 3bwxA 285 6.86e+01 2ywqA 105 6.88e+01 2ntiA 249 6.91e+01 1huuA 90 6.91e+01 1huuA a.55.1.1 17897 2p4bA 295 6.94e+01 1vkyA 347 6.95e+01 e.53.1.1 108696 1dymA 402 7.03e+01 1celA b.29.1.10 24304 1wqbA 32 7.05e+01 1ko3A 230 7.06e+01 d.157.1.1 90974 1ms9A 648 7.12e+01 b.29.1.15,b.68.1.1 85088,85089 1pcfA 66 7.16e+01 1pcfA d.18.1.1 38142 1jqsB 32 7.18e+01 i.1.1.1 63238 1prxA 224 7.24e+01 1prxA c.47.1.10 33076 2px7A 236 7.24e+01 2uywA 130 7.26e+01 1azdA 237 7.28e+01 1nls b.29.1.1 24020 2aqmA 154 7.30e+01 2fr2A 172 7.31e+01 b.60.1.8 133963 1yaiA 151 7.38e+01 1yaiA b.1.8.1 22289 2p6yA 142 7.43e+01 2bngA 149 7.45e+01 1g61A 228 7.46e+01 1g61A d.126.1.1 41126 2atjA 308 7.48e+01 1bgp a.93.1.1 18675 1a4sA 503 7.49e+01 1bpwA c.82.1.1 35361 2vbuA 136 7.54e+01 1mkeA 152 7.54e+01 b.55.1.4 79231 1y0yA 353 7.56e+01 b.49.3.1,c.56.5.4 122514,122515 1rlmA 271 7.58e+01 c.108.1.10 111860 2vadA 223 7.58e+01 1gwuA 309 7.60e+01 a.93.1.1 83351 1lenA 181 7.62e+01 1led b.29.1.1 24032 1mmsA 140 7.72e+01 1mmsA a.4.7.1,d.47.1.1 16247,38766 1kd6A 179 7.75e+01 b.97.1.1 68459 7atjA 308 7.78e+01 1bgp a.93.1.1 18673 1q2lA 939 7.81e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 1j1nA 492 7.89e+01 c.94.1.1 83978 1e1aA 314 7.94e+01 1e1aA b.68.6.1 59155