# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1regX 122 3.69e-01 1regX d.58.27.1 39406 1wmaA 276 5.45e-01 2ew8A 249 8.36e-01 2bgkA 278 1.49e+00 2f9dA 125 1.53e+00 1t3gA 159 1.63e+00 1n5dA 288 1.72e+00 c.2.1.2 80030 1hu4A 288 1.72e+00 1hu4A 1r1dA 247 2.18e+00 c.69.1.29 96813 1vig 71 2.39e+00 1vih d.51.1.1 38806 2bwnA 401 2.52e+00 1m3sA 186 2.73e+00 c.80.1.3 78573 1tqhA 247 2.79e+00 c.69.1.29 107225 1mpyA 307 2.97e+00 1mpyA d.32.1.3,d.32.1.3 38508,38509 1f0cA 305 3.52e+00 1c8oA e.1.1.1 42676 1ht6A 405 3.92e+00 b.71.1.1,c.1.8.1 83629,83630 1g59A 468 4.23e+00 a.97.1.1,c.26.1.1 60257,60258 1b2jA 54 5.25e+00 1rb9 g.41.5.1 45231 4rxn 54 5.33e+00 1rb9 g.41.5.1 45226 5rxn 54 5.33e+00 1rb9 g.41.5.1 45225 1b13A 54 5.37e+00 1rb9 g.41.5.1 45227 1m93B 245 5.38e+00 2bd0A 244 5.38e+00 1iro 54 5.60e+00 1rb9 g.41.5.1 45223 2ci1A 275 5.71e+00 2d4pA 141 5.78e+00 1ek8A 185 5.94e+00 1ek8A d.67.3.1 59444 1g61A 228 6.29e+00 1g61A d.126.1.1 41126 1tzbA 302 6.29e+00 c.80.1.1 107470 1x9iA 302 6.30e+00 1c8oA 300 6.33e+00 1c8oA e.1.1.1 42677 9apiA 347 6.35e+00 1ovaA e.1.1.1 42630 12asA 330 6.42e+00 12asA d.104.1.1 40783 1o7kA 131 6.54e+00 d.189.1.1 81144 1b2oA 54 6.56e+00 1rb9 g.41.5.1 45233 1jmaA 290 6.67e+00 b.1.1.1 63177 2ghrA 302 6.78e+00 1wiwA 290 7.30e+00 2b9dA 52 7.38e+00 1bfd 528 7.43e+00 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1q6zA 528 7.52e+00 1u5mA 73 8.05e+00 2tmnE 316 8.31e+00 1hyt d.92.1.2 59055 1keiA 316 8.32e+00 d.92.1.2 77349 6tmnE 316 8.56e+00 1hyt d.92.1.2 59071 1hyt 316 8.80e+00 1hyt d.92.1.2 59005 8tlnE 316 8.80e+00 1hyt d.92.1.2 59075 1zw8A 64 9.38e+00 2c36A 285 9.68e+00 1sty 150 9.81e+00 1snc b.40.1.1 24812 1zo0A 126 1.00e+01 1vcvA 226 1.01e+01 1ugpA 203 1.01e+01 d.149.1.1 107831 2fiuA 99 1.02e+01 1ireA 204 1.03e+01 d.149.1.1 76769 1wdtA 665 1.04e+01 1wdyA 285 1.07e+01 1e15A 499 1.08e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 27810,29006,38440 1us8A 147 1.10e+01 c.37.1.12 99859 1zymA 258 1.11e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1xqaA 113 1.12e+01 1l4aE 79 1.13e+01 h.1.15.1 73563 1ey4A 149 1.14e+01 1snc b.40.1.1 24815 1mkeA 152 1.15e+01 b.55.1.4 79231 1eza 259 1.25e+01 1zymA a.60.10.1,c.8.1.2 18113,30708 1z2wA 192 1.25e+01 1gd5A 130 1.28e+01 1gd5A d.189.1.1 60439 2d83A 363 1.30e+01 1e6pA 499 1.32e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1vih 71 1.33e+01 1vih d.51.1.1 38807 1jg7A 351 1.34e+01 1c3jA c.87.1.1 62945 1vid 221 1.36e+01 1vid c.66.1.1 34178 1wimA 94 1.38e+01 1jixA 351 1.46e+01 1c3jA c.87.1.1 63081 1h1dA 221 1.48e+01 c.66.1.1 83452 1ocsA 162 1.51e+01 d.189.1.1 92776 4uagA 437 1.52e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1uag 437 1.53e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1yk4A 52 1.58e+01 1a8p 258 1.59e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 2fjbA 643 1.64e+01 1j77A 209 1.65e+01 1j77A a.132.1.2 62674 1gegA 256 1.69e+01 1ybvA c.2.1.2 29888 1qa6A 67 1.71e+01 1qa6A a.4.7.1 16240 1jnrA 643 1.72e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1w24A 182 1.74e+01 1goiA 499 1.74e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1s2oA 244 1.77e+01 1k3eA 156 1.84e+01 d.198.1.1 68103 1ve3A 227 1.86e+01 1ash 150 1.86e+01 1ash a.1.1.2 15622 1as4A 341 1.89e+01 1sek e.1.1.1 42623 1f2tA 149 1.92e+01 1f2tA c.37.1.12 32373 1bq9A 54 1.95e+01 1rb9 g.41.5.1 45238 2aaa 484 1.98e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1ka8A 100 2.03e+01 a.4.5.20 72241 1vkrA 125 2.05e+01 c.44.2.1 108689 2achA 360 2.08e+01 1c8oA e.1.1.1 42626 1vl8A 267 2.08e+01 c.2.1.2 108733 3csuA 310 2.16e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 1utaA 81 2.18e+01 d.58.52.1 108029 1pbyA 489 2.30e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1z5nA 242 2.36e+01 1v5aA 28 2.41e+01 1qlpA 394 2.42e+01 1ovaA e.1.1.1 42628 1yj7A 171 2.47e+01 1rdg 53 2.48e+01 1rb9 g.41.5.1 45221 2a0fA 310 2.52e+01 1snc 149 2.61e+01 1snc b.40.1.1 24813 1zosA 230 2.64e+01 7taa 478 2.65e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1ihoA 283 2.65e+01 1ihoA c.26.1.4 62390 2gzqA 200 2.66e+01 1gln 468 2.67e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1coaI 64 2.70e+01 2sniI d.40.1.1 38574 1ukuA 102 2.78e+01 d.58.5.2 99533 1zxcA 263 2.78e+01 1ksfX 758 2.81e+01 a.174.1.1,c.37.1.20,c.37.1.20 77522,77523,77524 1d1qA 161 2.86e+01 1dg9A c.44.1.1 32642 1xaoA 121 2.86e+01 1bkcE 256 2.98e+01 1bkcA d.92.1.10 40333 1ass 159 2.99e+01 1a6dA c.8.5.2 30818 1ovqA 138 3.06e+01 c.55.3.8 93607 1c3hA 137 3.07e+01 b.22.1.1 90405 1udxA 416 3.09e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1g26A 31 3.12e+01 1g26A g.3.16.1 44381 1iujA 106 3.17e+01 d.58.4.5 90701 1jae 471 3.20e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1sc3A 178 3.21e+01 c.17.1.1 105416 1y7bA 542 3.22e+01 830cA 168 3.22e+01 1ck7A d.92.1.11 40400 1jkiA 533 3.23e+01 c.2.1.3,d.81.1.3 71704,71705 1tkkA 366 3.26e+01 c.1.11.2,d.54.1.1 107089,107090 1gn0A 108 3.31e+01 c.46.1.3 65358 1is1A 185 3.41e+01 d.67.3.1 83704 1z6oM 191 3.42e+01 1p1jA 533 3.43e+01 c.2.1.3,d.81.1.3 87687,87688 1x1tA 260 3.45e+01 1l0wA 580 3.49e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1ejdA 419 3.52e+01 1uae d.68.2.2 39576 2sniI 83 3.54e+01 2sniI d.40.1.1 38573 1lw6I 64 3.55e+01 d.40.1.1 74294 1pieA 419 3.57e+01 d.14.1.5,d.58.26.7 94706,94707 2axyA 73 3.60e+01 1xg5A 279 3.60e+01 1s7kA 182 3.64e+01 1ypcI 64 3.66e+01 2sniI d.40.1.1 38570 1ab5A 125 3.66e+01 3chy c.23.1.1 31056 1bmqA 167 3.67e+01 1pauA c.17.1.1 30998 3uagA 437 3.68e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1gxjA 186 3.73e+01 d.215.1.1 70707 1yr1A 119 3.78e+01 1gz6A 319 3.79e+01 c.2.1.2 76410 1c3jA 351 3.85e+01 1c3jA c.87.1.1 35459 1rpxA 230 3.90e+01 1rpxA c.1.2.2 28536 1ws6A 171 3.90e+01 1jysA 242 3.91e+01 c.56.2.1 77216 6rxn 46 3.92e+01 1rb9 g.41.5.1 45222 1ibcA 194 3.98e+01 1pauA c.17.1.1 30997 1pb1A 416 4.03e+01 c.77.1.1 88014 1fukA 165 4.08e+01 1fukA c.37.1.19 32409 8rxnA 52 4.08e+01 1rb9 g.41.5.1 45215 1kv8A 216 4.08e+01 c.1.2.3 73054 2acvA 463 4.10e+01 1n40A 396 4.11e+01 a.104.1.1 79977 1rb9 53 4.12e+01 1rb9 g.41.5.1 45214 1s8fA 177 4.12e+01 c.37.1.8 105370 1tqzA 133 4.13e+01 1q6oA 216 4.15e+01 c.1.2.3 95986 1jkfA 533 4.17e+01 c.2.1.3,d.81.1.3 71700,71701 1uw4A 91 4.21e+01 d.58.7.4 100071 1wmbA 260 4.22e+01 1se4 239 4.22e+01 3seb b.40.2.2,d.15.6.1 25187,37776 1m4vA 204 4.23e+01 b.40.2.2,d.15.6.1 74459,74460 1vh7A 265 4.25e+01 c.1.2.1 100646 1ysjA 404 4.28e+01 1cxvA 164 4.39e+01 1ck7A d.92.1.11 40404 1vsrA 136 4.39e+01 1vsrA c.52.1.15 33332 1rwxA 178 4.44e+01 1esgA 213 4.46e+01 1bam c.52.1.3 33286 1ha9A 34 4.52e+01 1ha9A g.3.2.1 60876 1nmoA 247 4.62e+01 c.135.1.1 91980 1brfA 53 4.62e+01 1rb9 g.41.5.1 45236 7icd 416 4.63e+01 1iso c.77.1.1 35072 1bq8A 54 4.65e+01 1rb9 g.41.5.1 45237 1s7zA 117 4.65e+01 a.159.3.1 98715 1y81A 138 4.66e+01 1g6sA 427 4.70e+01 1eps d.68.2.2 39584 1bkcA 255 4.72e+01 1bkcA d.92.1.10 40331 2cbf 234 4.73e+01 1cbf c.90.1.1 35588 1ax4A 467 4.74e+01 1ax4A c.67.1.2 34391 1bam 213 4.77e+01 1bam c.52.1.3 33285 1ffkU 91 4.82e+01 1ffkU d.29.1.1 38458 1hc8A 76 4.87e+01 a.4.7.1 70963 1iso 416 4.94e+01 1iso c.77.1.1 35065 1vqoX 92 5.03e+01 1vrvA 101 5.17e+01 1bkcI 256 5.22e+01 1bkcA d.92.1.10 40334 1lea 84 5.24e+01 1lea a.4.5.2 16085 2aq5A 402 5.26e+01 2cs3A 93 5.28e+01 1uzmA 247 5.35e+01 1g5aA 628 5.39e+01 b.71.1.1,c.1.8.1 65152,65153 1jrmA 104 5.57e+01 d.206.1.1 67136 1yhtA 367 5.59e+01 1wxaA 116 5.69e+01 1ehaA 558 5.81e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1efuA 385 5.82e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 2bgu 351 5.83e+01 1c3jA c.87.1.1 35460 2ddfA 257 5.85e+01 1oz9A 150 5.86e+01 d.92.1.15 93808 1ipiA 123 5.97e+01 c.52.1.18 66255 2b67A 204 6.00e+01 1du3A 130 6.01e+01 1d4vA g.24.1.1,g.24.1.1,g.24.1.1 44927,44928,44929 1ciqA 40 6.02e+01 2sniI d.40.1.1 38576 1nzaA 103 6.02e+01 d.58.5.2 86444 1hjzA 192 6.04e+01 c.50.1.2 83520 1zmaA 118 6.09e+01 2f06A 144 6.10e+01 2b6cA 220 6.11e+01 1qopB 396 6.13e+01 2tysB c.79.1.1 35270 1gmxA 108 6.18e+01 c.46.1.3 65355 1vhuA 211 6.18e+01 c.50.1.2 100703 3seb 238 6.18e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1bd8 156 6.20e+01 1bd8 d.211.1.1 19157 1jjuA 489 6.23e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 1fcyA 236 6.27e+01 2lbd a.123.1.1 19282 1uae 419 6.28e+01 1uae d.68.2.2 39574 1dq3A 454 6.29e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1k8kB 394 6.37e+01 c.55.1.1 68307 1a50B 396 6.39e+01 2tysB c.79.1.1 35280 1cbf 285 6.46e+01 1cbf c.90.1.1 35587 1j4wA 174 6.51e+01 d.51.1.1,d.51.1.1 71529,71530 1fshA 105 6.52e+01 1fshA a.4.5.31 60006 1c0aA 585 6.53e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1dzlA 505 6.57e+01 1dzlA b.121.6.1 23586 1rf6A 427 6.60e+01 d.68.2.2 97366 1skz 119 6.60e+01 1skz g.3.15.1,g.3.15.1 44366,44367 1o26A 232 6.63e+01 d.207.1.1 86566 2gaxA 135 6.67e+01 1k87A 669 6.74e+01 a.176.1.1,c.1.23.2 77286,77287 1s1fA 406 6.80e+01 1jbgA 109 6.80e+01 a.6.1.3 66480 3bamA 213 6.80e+01 1bam c.52.1.3 33288 2cdcA 366 6.83e+01 1zpxA 23 6.85e+01 1nu0A 138 6.86e+01 c.55.3.8 92165 1jj2W 91 6.91e+01 1ffkU d.29.1.1 63108 1innA 166 6.92e+01 1j98A d.185.1.2 62608 1jpmA 366 7.00e+01 c.1.11.2,d.54.1.1 67031,67032 1hc7A 477 7.03e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1vjeA 166 7.03e+01 d.185.1.2 100807 1s72X 92 7.06e+01 d.29.1.1 105343 1snyA 267 7.10e+01 c.2.1.2 105833 1nh1A 330 7.10e+01 e.45.1.1 91871 1eh9A 558 7.14e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 1xtzA 264 7.15e+01 2bvfA 459 7.20e+01 1n13B 113 7.20e+01 1uouA 474 7.23e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 8ohm 435 7.25e+01 1heiA c.37.1.14,c.37.1.14 32469,32470 1gcoA 261 7.29e+01 1ybvA c.2.1.2 29884 1geeA 261 7.36e+01 c.2.1.2 90509 1z6aA 500 7.37e+01 1blxA 326 7.38e+01 1hcl d.144.1.7 41596 1eh2 106 7.40e+01 1eh2 a.39.1.6 17339 1z02A 446 7.44e+01 1acp 77 7.61e+01 1acp a.28.1.1 16931 1dx8A 70 7.70e+01 1rb9 g.41.5.1 45243 1hybA 181 7.70e+01 1f9aA c.26.1.3 61399 1v54K 56 7.79e+01 f.23.5.1 100332 1iseA 185 7.83e+01 d.67.3.1 90691 2bh1A 250 7.83e+01 1adjA 421 7.83e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 2f5xA 312 7.84e+01 1at1A 310 7.84e+01 3csuA c.78.1.1,c.78.1.1 35168,35169 1fe0A 68 7.88e+01 1cc8A d.58.17.1 39345 1d5mC 239 7.88e+01 3seb b.40.2.2,d.15.6.1 25185,37774 1h5vA 304 7.91e+01 c.1.8.3 70898 1yh1A 359 7.91e+01 1a2n 419 7.92e+01 1uae d.68.2.2 39575 1ar61 302 7.92e+01 1pov1 1vjoA 393 7.92e+01 c.67.1.3 100827 1a1vA 476 7.94e+01 1heiA c.37.1.14,c.37.1.14 32467,32468 1al21 302 7.95e+01 1pov1 1acmA 310 7.99e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 1a3h 300 8.09e+01 7a3hA c.1.8.3 28819 1evhA 112 8.12e+01 1evhA b.55.1.4 26997 2f2hA 773 8.15e+01 1rhcA 330 8.17e+01 c.1.16.3 97468 1xsjA 778 8.18e+01 1j0fA 100 8.31e+01 c.47.1.14 90739 1jceA 344 8.32e+01 c.55.1.1,c.55.1.1 62876,62877 1dtjA 76 8.32e+01 1dt4A d.51.1.1 38800 1yp5A 58 8.35e+01 2tysB 397 8.36e+01 2tysB c.79.1.1 35272 1a1uA 35 8.40e+01 a.53.1.1 17863 1gxrA 337 8.41e+01 b.69.4.1 70722 1e6mA 128 8.43e+01 3chy c.23.1.1 31039 1ej2A 181 8.47e+01 1f9aA c.26.1.3 59414 1edt 271 8.48e+01 2ebn c.1.8.5 28993 7a3hA 303 8.48e+01 7a3hA c.1.8.3 28817 1o4vA 183 8.49e+01 c.23.8.1 86628 1wbhA 214 8.51e+01 2c0aA 214 8.51e+01 1ctn 540 8.52e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1yxmA 303 8.55e+01 1ew4A 106 8.59e+01 1ew4A d.82.2.1 40023 1ja9A 274 8.60e+01 c.2.1.2 62817 1htwA 158 8.70e+01 c.37.1.18 71083 1hqi 90 8.72e+01 1hqi d.137.1.1 41454 1fsu 492 8.74e+01 1auk c.76.1.2 35032 1k9tA 540 8.76e+01 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 1h4vB 421 8.79e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1ar71 302 8.79e+01 1pov1 1edqA 540 8.80e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1ecpA 238 8.84e+01 1ecpA c.56.2.1 33775 1dt4A 73 8.87e+01 1dt4A d.51.1.1 38799 1hxs1 302 8.89e+01 2a2pA 129 8.91e+01 1to2I 64 8.92e+01 1enj 138 8.94e+01 2end a.18.1.1 16401 1hrhA 136 9.00e+01 1rthA c.55.3.1 33577