# List of top-scoring protein chains for t2k-100-30-o_sep-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 2chgA 226 1.79e-02 1elqA 390 4.77e-02 1elqA c.67.1.3 34436 1eluB 390 6.01e-02 1elqA c.67.1.3 34435 1yb2A 275 7.13e-02 1eluA 390 7.72e-02 1elqA c.67.1.3 34434 1w34A 304 1.47e-01 1qh0A 295 1.87e-01 b.43.4.2,c.25.1.1 68891,68892 1go2A 304 1.88e-01 b.43.4.2,c.25.1.1 76243,76244 2bmwA 304 2.23e-01 1que 303 2.46e-01 1fnc b.43.4.2,c.25.1.1 25647,31537 1ogiA 303 2.47e-01 b.43.4.2,c.25.1.1 92914,92915 2bsaA 303 2.49e-01 1yb5A 351 2.81e-01 1c2pA 576 3.12e-01 1quvA e.8.1.4 43117 1ytlA 174 3.60e-01 1b2rA 304 3.68e-01 1fnc b.43.4.2,c.25.1.1 25648,31538 1zd9A 188 4.14e-01 1ecfB 504 4.17e-01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1jb9A 316 4.39e-01 1fnc b.43.4.2,c.25.1.1 62840,62841 1wgbA 159 4.49e-01 1yoaA 159 4.65e-01 1ecfA 504 4.76e-01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1gtdA 85 4.82e-01 d.284.1.1 76344 1j5sA 463 4.87e-01 c.1.9.8 71580 1mh1 186 6.46e-01 1eesA c.37.1.8 32002 1v7pC 200 6.51e-01 c.62.1.1 108408 1o5hA 214 6.72e-01 a.191.1.1 92497 2a9kA 187 7.52e-01 1vg8A 207 7.88e-01 c.37.1.8 108606 1tx4B 178 7.99e-01 1ctqA c.37.1.8 32045 1e5pA 151 8.30e-01 1bj7 b.60.1.1 59272 1aoxA 203 1.01e+00 1aoxA c.62.1.1 34151 1zelA 298 1.02e+00 2c2hA 192 1.10e+00 2fi9A 128 1.11e+00 1x11A 172 1.15e+00 1x11A b.55.1.2 26985 1c3oB 382 1.17e+00 1c3oB c.8.3.1,c.23.16.1 30744,31421 1a9xB 379 1.19e+00 1c3oB c.8.3.1,c.23.16.1 30732,31409 1kmqA 184 1.27e+00 c.37.1.8 84412 1c30B 382 1.30e+00 c.8.3.1,c.23.16.1 30736,31413 1fnb 314 1.39e+00 1fnc b.43.4.2,c.25.1.1 25628,31518 1u8zA 168 1.39e+00 1k87A 669 1.47e+00 a.176.1.1,c.1.23.2 77286,77287 1tqyB 415 1.53e+00 c.95.1.1,c.95.1.1 107247,107248 1r5tA 142 1.59e+00 c.97.1.1 104812 1fnd 314 1.64e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 1cs0B 382 1.70e+00 1c3oB c.8.3.1,c.23.16.1 30740,31417 1dfaA 454 1.82e+00 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 1bx1A 314 1.82e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1jkmA 358 1.94e+00 1jkmA c.69.1.2 34633 2aq4A 434 2.03e+00 2a35A 215 2.04e+00 2liv 344 2.17e+00 2liv c.93.1.1 35708 1qv9A 283 2.21e+00 c.127.1.1 96356 1xccA 220 2.26e+00 1rhcA 330 2.38e+00 c.1.16.3 97468 1nf3A 195 2.41e+00 c.37.1.8 85594 2fbhA 146 2.55e+00 1g5cA 170 2.55e+00 1g5cA c.53.2.1 60264 1a8p 258 2.58e+00 1fdr b.43.4.2,c.25.1.1 25654,31544 1yt3A 375 2.61e+00 2axyA 73 3.03e+00 1mzhA 225 3.07e+00 c.1.10.1 79698 1azsC 388 3.08e+00 1cipA a.66.1.1,c.37.1.8 18203,32086 2evwX 166 3.32e+00 1v8gA 329 3.55e+00 a.46.2.1,c.27.1.1 100505,100506 1an0A 190 3.55e+00 1ctqA c.37.1.8 32066 1aqcA 172 3.57e+00 1x11A b.55.1.2 26983 1fnc 314 3.85e+00 1fnc b.43.4.2,c.25.1.1 25627,31517 1yckA 175 3.87e+00 1f6bA 198 3.92e+00 c.37.1.8 64986 1iqpA 327 3.93e+00 a.80.1.1,c.37.1.20 62649,62650 1s7hA 200 3.94e+00 d.58.48.2 105349 3fib 249 3.97e+00 3fib d.171.1.1 42455 1qg0A 308 4.26e+00 1fnc b.43.4.2,c.25.1.1 25639,31529 1qd1A 325 4.30e+00 1qd1A d.58.34.1,d.58.34.1 39493,39494 2azpA 318 4.35e+00 1i0lA 221 4.35e+00 c.61.1.1 71096 1ip9A 85 4.58e+00 1ip9A d.15.2.2 62638 2fibA 269 4.66e+00 3fib d.171.1.1 42457 1lqtA 456 4.80e+00 c.3.1.1,c.4.1.1 74198,74199 2c31A 568 4.80e+00 1wn2A 121 4.82e+00 1fib 269 4.92e+00 3fib d.171.1.1 42456 1icwA 72 5.07e+00 1tvxA d.9.1.1 37357 1z15A 344 5.25e+00 1hkkA 364 5.36e+00 c.1.8.5,d.26.3.1 90634,90635 2fpqA 444 5.43e+00 1uarA 285 5.55e+00 c.46.1.2,c.46.1.2 107762,107763 2apqA 139 5.61e+00 1ewkA 490 5.64e+00 1ewkA c.93.1.1 35712 2f2lX 167 5.80e+00 1s99A 200 5.80e+00 8abp 306 5.93e+00 8abp c.93.1.1 35647 1i7nA 309 5.93e+00 c.30.1.5,d.142.1.3 83681,83682 2flsA 132 6.08e+00 1agp 166 6.09e+00 1ctqA c.37.1.8 31985 2pii 112 6.14e+00 2pii d.58.5.1 39071 1abe 306 6.14e+00 8abp c.93.1.1 35648 5abp 306 6.19e+00 8abp c.93.1.1 35651 1sgvA 316 6.54e+00 b.122.1.1,d.265.1.2 98858,98859 1jkmB 361 6.73e+00 1jkmA c.69.1.2 34634 2bo4A 397 6.73e+00 1jztA 246 7.01e+00 c.104.1.1 63319 1t3cA 421 7.01e+00 d.92.1.7 106343 1mwvA 714 7.23e+00 a.93.1.3,a.93.1.3 85161,85162 1a4rA 191 7.41e+00 1ctqA c.37.1.8 32063 821p 166 7.47e+00 1ctqA c.37.1.8 31969 1jdpA 441 7.72e+00 c.93.1.1 62906 1mjgM 729 7.74e+00 e.26.1.3 79204 1z98A 281 7.94e+00 1bap 306 7.95e+00 8abp c.93.1.1 35654 1ogsA 497 7.97e+00 b.71.1.2,c.1.8.3 86997,86998 1hyeA 313 8.41e+00 2cmd c.2.1.5,d.162.1.1 61400,61401 1hfc 169 8.59e+00 1hfc d.92.1.11 40335 1jeoA 180 8.65e+00 c.80.1.3 66611 1c25 161 8.65e+00 1c25 c.46.1.1 32698 1scuA 288 8.70e+00 2scuA c.2.1.8,c.23.4.1 30307,31135 1v5vA 401 8.71e+00 1yoeA 322 8.79e+00 1b3tA 147 8.98e+00 1b3tA d.58.8.1 39228 2eryA 172 9.01e+00 1es9A 232 9.19e+00 1wab c.23.10.3 31340 1udsA 255 9.22e+00 d.14.1.4,d.101.1.1 99219,99220 1p1mA 406 9.29e+00 b.92.1.4,c.1.9.9 87696,87697 2faoA 309 9.30e+00 1pvvA 315 9.40e+00 c.78.1.1,c.78.1.1 95190,95191 1tc1A 220 9.56e+00 1tc1A c.61.1.1 34083 1ivhA 394 9.57e+00 3mdeA a.29.3.1,e.6.1.1 16608,42869 1tc5A 194 9.84e+00 c.110.1.1 106752 1sk4A 163 9.99e+00 d.118.1.1 105664 1w3uA 362 1.01e+01 1t3lA 337 1.01e+01 b.34.2.1,c.37.1.1 106358,106359 1fzqA 181 1.02e+01 1hurA c.37.1.8 32060 1ixmA 192 1.02e+01 1ixmA d.123.1.1 41114 1xfkA 336 1.07e+01 1guzA 310 1.08e+01 c.2.1.5,d.162.1.1 65586,65587 1dpb 243 1.08e+01 1eaf c.43.1.1 32618 1v54A 514 1.08e+01 f.24.1.1 100321 2fn4A 181 1.09e+01 1s8fA 177 1.09e+01 c.37.1.8 105370 1d6mA 653 1.11e+01 1d6mA e.10.1.1 43248 1wmsA 177 1.11e+01 c.37.1.8 109414 1zwwA 256 1.11e+01 2bjvA 265 1.14e+01 2axtT 32 1.16e+01 1jvwA 167 1.16e+01 d.26.1.1 71907 1gydB 315 1.17e+01 b.67.2.1 70751 1j5vA 351 1.18e+01 c.72.1.1 71585 1t0hB 224 1.20e+01 c.37.1.1 106208 1mbxC 106 1.22e+01 d.45.1.2 78929 2atxA 194 1.23e+01 1sviA 195 1.24e+01 c.37.1.8 106048 1gyhA 318 1.24e+01 b.67.2.1 70757 5p21 166 1.25e+01 1ctqA c.37.1.8 31966 1se0A 116 1.27e+01 g.52.1.1 98814 1sfnA 246 1.27e+01 b.82.1.11 105496 1wf3A 301 1.27e+01 2f1fA 164 1.27e+01 1n6eA 1071 1.29e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1ctqA 166 1.29e+01 1ctqA c.37.1.8 31965 1i76A 163 1.30e+01 1hfc d.92.1.11 61877 1guaA 167 1.31e+01 1ctqA c.37.1.8 32013 1bt4A 362 1.32e+01 1bjnA c.67.1.4 34468 1ro7A 259 1.34e+01 c.130.1.1 97667 1cipA 353 1.35e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 2ax3A 502 1.36e+01 2b5oA 402 1.36e+01 1v71A 323 1.38e+01 1wab 232 1.38e+01 1wab c.23.10.3 31341 1h6hA 143 1.39e+01 d.189.1.1 65681 1vgvA 384 1.39e+01 c.87.1.3 100608 1uj2A 252 1.43e+01 c.37.1.6 99452 2a6aA 218 1.43e+01 1svsA 353 1.45e+01 c.37.1.8 106051 1pil 112 1.46e+01 2pii d.58.5.1 39072 2occA 514 1.46e+01 2occA f.24.1.1 43518 1of5A 221 1.49e+01 d.17.4.2 86933 1usmA 80 1.50e+01 d.74.1.1 99876 1xtqA 177 1.51e+01 1vk8A 106 1.51e+01 d.58.48.1 108636 1chrA 370 1.52e+01 1mucA c.1.11.2,d.54.1.1 29252,38896 1ukgA 252 1.54e+01 b.29.1.1 99489 2gjsA 176 1.56e+01 1vdeA 454 1.56e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 2afbA 351 1.60e+01 1yyaA 250 1.62e+01 1whxA 111 1.64e+01 1xahA 354 1.65e+01 1kum 108 1.66e+01 1kum b.3.1.1 22525 1vddA 228 1.68e+01 e.49.1.1 108519 1k32A 1045 1.68e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1gt7A 274 1.68e+01 c.74.1.1 70398 2fh7A 595 1.69e+01 1qg3A 195 1.70e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1tag 324 1.72e+01 1cipA a.66.1.1,c.37.1.8 18197,32080 2bl0C 142 1.73e+01 1z0jA 170 1.73e+01 1j6pA 418 1.76e+01 b.92.1.4,c.1.9.9 77089,77090 1gmuA 143 1.77e+01 b.107.1.1,d.58.38.1 65335,65336 2c0rA 362 1.77e+01 1m1fA 110 1.81e+01 b.34.6.2 78401 1zuwA 272 1.84e+01 1edoA 244 1.85e+01 1ybvA c.2.1.2 29896 1r6oC 106 1.86e+01 1d2nA 272 1.87e+01 1d2nA c.37.1.20 32428 1zzkA 82 1.90e+01 1l9gA 192 1.91e+01 c.18.1.2 84568 1r5rA 119 1.92e+01 a.39.2.1 97104 1quvA 578 1.93e+01 1quvA e.8.1.4 43119 1n3oA 252 1.95e+01 b.29.1.1 79967 1c0aA 585 1.95e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1lxjA 104 1.97e+01 d.58.48.1 84736 1w23A 360 1.99e+01 2bjdA 101 2.01e+01 1e01A 48 2.04e+01 1e01A 1kpgA 287 2.05e+01 c.66.1.18 68735 1f6dA 376 2.05e+01 1f6dA c.87.1.3 35467 1a85A 158 2.09e+01 1hfc d.92.1.11 40355 1gx5A 536 2.09e+01 e.8.1.4 70682 1z06A 189 2.12e+01 2g2cA 167 2.13e+01 1o69A 394 2.15e+01 c.67.1.4 92560 1r3eA 309 2.16e+01 b.122.1.1,d.265.1.2 96907,96908 1oaoC 729 2.17e+01 e.26.1.3 86746 1bzsA 165 2.17e+01 1hfc d.92.1.11 40348 1wb0A 445 2.19e+01 1nsf 273 2.23e+01 1d2nA c.37.1.20 32429 1zsqA 528 2.23e+01 1w30A 201 2.25e+01 1a8l 226 2.25e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 2g84A 197 2.25e+01 1dfoA 417 2.27e+01 1bj4A c.67.1.4 34480 1csjA 531 2.28e+01 1quvA e.8.1.4 43120 1lg2A 365 2.28e+01 c.1.8.5,d.26.3.1 77950,77951 2gf9A 189 2.30e+01 2bv5A 282 2.32e+01 1y88A 199 2.33e+01 1hizA 379 2.34e+01 c.1.8.3 65841 2f5xA 312 2.42e+01 1oi7A 288 2.43e+01 c.2.1.8,c.23.4.1 87049,87050 1snnA 227 2.49e+01 d.115.1.2 105821 1a44 185 2.50e+01 1a44 b.17.1.1 23704 1gveA 327 2.50e+01 c.1.7.1 70597 1im4A 221 2.52e+01 e.8.1.7 62581 1h75A 81 2.52e+01 1h75A c.47.1.1 60716 1fdr 248 2.55e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1g6gA 127 2.58e+01 1g6gA b.26.1.2 23916 1ykiA 217 2.59e+01 1u9cA 224 2.59e+01 1tvjA 166 2.61e+01 1qpxA 218 2.62e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1rnd 124 2.62e+01 7rsa d.5.1.1 37178 1ujqA 305 2.63e+01 c.1.12.7 99463 1a79A 171 2.66e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1vljA 407 2.71e+01 e.22.1.2 108832 2h0eA 121 2.72e+01 1e0gA 48 2.73e+01 1e01A d.7.1.1 37325 1ve3A 227 2.73e+01 1umkA 275 2.74e+01 1howA 373 2.74e+01 1hcl d.144.1.7 41679 1u0jA 267 2.75e+01 c.37.1.20 107546 7rsa 124 2.75e+01 7rsa d.5.1.1 37165 1ge9A 184 2.77e+01 1dd5A d.67.3.1 60463 1bjoA 360 2.79e+01 1bjnA c.67.1.4 34471 1jy1A 464 2.79e+01 d.136.1.3,d.136.1.3 67438,67439 1gpuA 680 2.80e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1ojrA 274 2.80e+01 c.74.1.1 93147 1rztA 331 2.81e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 2scuA 288 2.81e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1npdA 288 2.86e+01 c.2.1.7,c.58.1.5 80681,80682 1hm5A 558 2.88e+01 c.80.1.2 76717 1r85A 379 2.90e+01 c.1.8.3 104839 1kjnA 157 2.91e+01 c.115.1.1 72614 2cvjA 180 2.93e+01 1as0 353 2.94e+01 1cipA a.66.1.1,c.37.1.8 18212,32095 2dbsA 90 2.97e+01 1c9oA 66 2.98e+01 1mjc b.40.4.5 25325 1nh1A 330 3.02e+01 e.45.1.1 91871 1fds 327 3.02e+01 1fds c.2.1.2 29838 1qmhA 347 3.02e+01 1qmhA c.47.2.1,d.68.2.1 33082,39568 1i7pA 274 3.06e+01 b.43.4.2,c.25.1.1 66048,66049 1ze3D 125 3.06e+01 1ky3A 182 3.08e+01 c.37.1.8 73193 1mu7A 485 3.09e+01 d.136.1.3,d.136.1.3 79475,79476 2gnoA 305 3.15e+01 1b7aA 186 3.16e+01 1a44 b.17.1.1 23705 2gm5A 139 3.17e+01 1a1s 314 3.18e+01 1othA c.78.1.1,c.78.1.1 35258,35259 1d5cA 162 3.23e+01 1ctqA c.37.1.8 32021 1mho 88 3.26e+01 1b4cA a.39.1.2 17171 1pt6A 213 3.27e+01 c.62.1.1 95091 1y51A 88 3.29e+01 1aje 194 3.33e+01 1ctqA c.37.1.8 32071 1wdkC 390 3.33e+01 c.95.1.1,c.95.1.1 109258,109259 1hmy 327 3.34e+01 6mhtA c.66.1.26 34229 1qc5A 192 3.34e+01 1aoxA c.62.1.1 34147 1i7dA 659 3.39e+01 1d6mA e.10.1.1 61886 1fcqA 350 3.43e+01 c.1.8.9 65006 1e08D 88 3.45e+01 i.4.1.1 45915 1f60B 94 3.48e+01 1b64 d.58.12.1 39307 2f2lA 167 3.49e+01 1hkhA 279 3.50e+01 c.69.1.12 90628 1i5rA 327 3.51e+01 c.2.1.2 83668 1cfpA 92 3.52e+01 1b4cA a.39.1.2 17172 1bncB 449 3.55e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28237,31644,41489 1icrA 217 3.55e+01 1vfrA d.90.1.1 62274 1eagA 342 3.56e+01 1eagA b.50.1.2 26826 1x1oA 286 3.62e+01 1fqtA 112 3.62e+01 1fqtA b.33.1.1 24441 1aua 296 3.64e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1eaf 243 3.65e+01 1eaf c.43.1.1 32617 1t6nA 220 3.66e+01 c.37.1.19 106576 1aqjA 421 3.66e+01 2admA c.66.1.27 34242 1oeyA 83 3.67e+01 d.15.2.2 92800 1ptf 88 3.68e+01 1ptf d.94.1.1 40549 1cvrA 435 3.69e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1u8sA 192 3.70e+01 d.58.18.5,d.58.18.5 107737,107738 1sjiA 350 3.71e+01 1kbpA 432 3.77e+01 4kbpA b.1.12.1,d.159.1.1 22349,42068 2bijA 305 3.77e+01 1w25A 459 3.78e+01 1j0aA 325 3.81e+01 c.79.1.1 83871 1kutA 230 3.82e+01 d.143.1.1 73017 1in0A 163 3.83e+01 d.58.49.1,d.58.49.1 83694,83695 1aoeA 192 3.86e+01 1aoeA c.71.1.1 34923 1dqrA 557 3.87e+01 1dqrA c.80.1.2 35305 1b4bA 71 3.91e+01 1b4aA d.74.2.1 39718 1nbwA 607 3.96e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 2a0mA 316 3.96e+01 1vchA 175 3.97e+01 2a5vA 213 3.99e+01 1utuA 108 4.03e+01 1yksA 440 4.04e+01 1wywA 230 4.07e+01 1fvrA 327 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1hv8A c.37.1.19,c.37.1.19 32405,32406 1j27A 102 8.64e+01 d.58.50.1 90778 1w9hA 427 8.72e+01 1jkgA 140 8.72e+01 d.17.4.2 66795 1qltA 560 8.77e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 1euhA 475 8.79e+01 1euhA c.82.1.1 35369 2ki5A 366 8.82e+01 1qhiA c.37.1.1 31862 1o26A 232 8.85e+01 d.207.1.1 86566 1lylA 504 8.86e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 2aeeA 211 8.95e+01