# List of top-scoring protein chains for t2k-100-30-str2-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 2ny1B 184 6.88e-02 b.1.1.1,b.1.1.3 138764,138765 3cbnA 151 2.27e-01 2dyuA 334 1.22e+00 1cdy 178 1.43e+00 1cdy 2uxyA 341 1.52e+00 1iwmA 186 2.68e+00 b.125.1.2 83758 1z9nA 177 2.87e+00 2obtA 327 2.90e+00 1z4vA 532 3.00e+00 1pzsA 208 3.26e+00 b.1.8.1 104397 3cswA 285 3.58e+00 1x3cA 73 3.75e+00 g.37.1.1 121660 3cniA 156 3.81e+00 2hm7A 310 3.92e+00 1u4nA 310 4.20e+00 c.69.1.2 113021 2hzqA 174 5.56e+00 1um5H 217 5.89e+00 b.1.1.1,b.1.1.2 113302,113303 1ru0A 105 6.29e+00 d.74.1.1 111937 2apsA 162 6.31e+00 1yaiA b.1.8.1 22298 2hf2A 283 6.96e+00 2pa6A 427 7.13e+00 1z9pA 155 7.34e+00 1w6tA 444 7.62e+00 c.1.11.1,d.54.1.1 120670,120671 1xtmA 175 8.01e+00 1rlmA 271 8.35e+00 c.108.1.10 111860 2hft 218 8.40e+00 1boy 2hftA 218 8.40e+00 b.1.2.1,b.1.2.1 21951,21952 2gysA 419 9.03e+00 b.1.2.1,b.1.2.1,b.1.2.1,b.1.2.1 135865,135866,135867,135868 1qa1A 554 9.10e+00 1tyv b.80.1.6 28047 1qq1A 559 9.10e+00 1tyv b.80.1.6 28041 2rmpA 361 9.14e+00 2rmpA b.50.1.2 26825 1qfjA 232 9.28e+00 1qfjA b.43.4.2,c.25.1.1 25655,31545 2qklA 127 9.33e+00 1z6jT 211 9.46e+00 b.1.2.1,b.1.2.1 124527,124528 1d2eA 397 9.47e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1rloA 271 9.52e+00 c.108.1.10 111864 2ix2A 249 1.05e+01 1tyvA 554 1.14e+01 b.80.1.6 28038 1tyv 542 1.14e+01 1tyv 2aqqA 164 1.15e+01 2aqpA 164 1.17e+01 1boy 219 1.24e+01 1boy 1danT 80 1.24e+01 1boy b.1.2.1 21953 1dt9A 437 1.27e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1jj2A 239 1.30e+01 1rl2A b.34.5.3,b.40.4.5 63084,63085 1yaiA 151 1.30e+01 1yaiA b.1.8.1 22289 1gmuA 143 1.36e+01 b.107.1.1,d.58.38.1 65335,65336 2uubL 135 1.36e+01 b.40.4.5 139943 2hr0A 645 1.38e+01 2aqmA 154 1.42e+01 2eklA 313 1.43e+01 1dlcA 584 1.43e+01 b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 3c1mA 473 1.47e+01 1xtlA 175 1.48e+01 1eysH 259 1.50e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 1iz6A 138 1.51e+01 b.34.5.2,b.40.4.5 76976,76977 2fymA 431 1.53e+01 c.1.11.1,d.54.1.1 134379,134380 1oi0A 124 1.54e+01 c.97.3.1 93045 2hx0A 154 1.54e+01 d.290.1.3 136830 1ddzA 496 1.64e+01 1ddzA c.53.2.1,c.53.2.1 33372,33373 2dscA 212 1.64e+01 2al1A 436 1.67e+01 c.1.11.1,d.54.1.1 126949,126950 1vkyA 347 1.67e+01 e.53.1.1 108696 1uj6A 227 1.69e+01 c.124.1.4,d.58.40.1 107898,107899 2al2A 436 1.72e+01 c.1.11.1,d.54.1.1 126953,126954 3c0fB 91 1.72e+01 1o20A 427 1.76e+01 c.82.1.1 86556 2dg1A 333 1.78e+01 b.68.6.1 131493 1mkmA 249 1.80e+01 a.4.5.33,d.110.2.2 79242,79243 2axwA 134 1.85e+01 1uzxA 169 1.92e+01 d.20.1.2 100238 1oneA 436 1.93e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1mdaH 368 1.96e+01 2bbkH b.69.2.1 27637 1tf6A 190 1.97e+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 2co7B 221 1.98e+01 2fliA 220 2.01e+01 c.1.2.2 133714 1b88A 114 2.03e+01 1tcrA b.1.1.1 20608 1o12A 376 2.03e+01 b.92.1.5,c.1.9.10 80758,80759 1oalA 151 2.06e+01 b.1.8.1 86739 2bvcA 486 2.06e+01 d.15.9.1,d.128.1.1 129243,129244 1olrA 224 2.07e+01 b.29.1.11 93330 4enl 436 2.07e+01 4enl 1gvhA 396 2.12e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1yh2A 175 2.23e+01 d.20.1.1 123158 2oynA 146 2.26e+01 3cnqP 80 2.27e+01 3bm4A 210 2.31e+01 1s4iA 175 2.35e+01 1xaoA 121 2.39e+01 1hl9A 449 2.39e+01 b.71.1.3,c.1.8.11 90650,90651 1dlfL 113 2.45e+01 8fabA b.1.1.1 20382 2r0hA 164 2.52e+01 3c26A 266 2.54e+01 2qh0A 138 2.55e+01 2f4wA 187 2.56e+01 d.20.1.1 132958 1ikpA 613 2.57e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1ush 550 2.64e+01 1ush 1b3cA 64 2.66e+01 1aho g.3.7.1 44121 2cg4A 152 2.70e+01 a.4.5.32,d.58.4.2 130417,130418 2oqkA 117 2.71e+01 1zxuA 217 2.72e+01 d.23.1.2 125796 1qftA 175 2.72e+01 1qftA b.60.1.1 27151 1k4iA 233 2.72e+01 d.115.1.2 72056 2oizA 361 2.73e+01 2agyA 361 2.73e+01 1rypH 205 2.77e+01 d.153.1.4 41876 1pm3A 78 2.78e+01 b.41.1.2 94889 2i24N 121 2.78e+01 1fzyA 149 2.81e+01 d.20.1.1 65072 1vqoA 240 2.83e+01 b.34.5.3,b.40.4.5 120361,120362 2q4mA 217 2.91e+01 d.23.1.2 139870 1a21A 219 2.93e+01 1boy b.1.2.1,b.1.2.1 21967,21968 2o4uX 334 2.94e+01 1gsjA 258 3.04e+01 c.73.1.2 70397 1rd5A 262 3.04e+01 c.1.2.4 111772 2d73A 738 3.12e+01 1o7iA 119 3.14e+01 b.40.4.3 86642 2bsaA 303 3.15e+01 b.43.4.2,c.25.1.1 129078,129079 1s21A 206 3.16e+01 d.166.1.4 105222 2o5nA 319 3.17e+01 1i5pA 633 3.18e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 2bcqA 335 3.18e+01 a.60.6.1,a.60.12.1,d.218.1.2 128304,128305,128306 1bkb 136 3.19e+01 1bkb 1bkbA 136 3.19e+01 b.34.5.2,b.40.4.5 24609,25341 2z4tA 514 3.22e+01 1y8xA 160 3.23e+01 d.20.1.1 122769 2ntiA 249 3.26e+01 2ifeA 100 3.27e+01 1tig d.68.1.1 39567 1xsoA 150 3.28e+01 1mfmA b.1.8.1 22273 1shwB 181 3.28e+01 b.18.1.4 105563 1rztA 331 3.30e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1nqbA 256 3.31e+01 1mfa b.1.1.1,b.1.1.1 20042,20043 1iyxA 432 3.34e+01 c.1.11.1,d.54.1.1 83815,83816 3by7A 100 3.39e+01 1oaqH 121 3.40e+01 b.1.1.1 92707 2i75A 320 3.41e+01 2asuB 234 3.43e+01 2f1lA 187 3.45e+01 b.41.1.4,b.43.3.4 132780,132781 1qhlA 227 3.46e+01 1qhlA c.37.1.12 32382 2fn9A 290 3.50e+01 2imqX 282 3.52e+01 1si6X 282 3.52e+01 d.151.1.2 118968 1wosA 364 3.53e+01 b.44.2.1,d.250.1.1 109468,109469 1yudA 170 3.54e+01 b.82.1.16 124046 2cwsA 237 3.56e+01 1qh0A 295 3.58e+01 b.43.4.2,c.25.1.1 68891,68892 1dmhA 311 3.64e+01 1dmhA b.3.6.1 22633 1u7iA 136 3.65e+01 d.32.1.7 107724 3b77A 193 3.65e+01 1fx5A 242 3.67e+01 1led b.29.1.1 24135 1ogiA 303 3.71e+01 b.43.4.2,c.25.1.1 92914,92915 1rxxA 421 3.71e+01 d.126.1.4 98061 1w4sA 174 3.73e+01 2jmkA 111 3.73e+01 2bmwA 304 3.75e+01 b.43.4.2,c.25.1.1 128815,128816 1gs5A 258 3.76e+01 c.73.1.2 70395 1v0aA 178 3.78e+01 b.18.1.30 119815 1o5uA 101 3.79e+01 b.82.1.8 92518 1fjgL 135 3.81e+01 1fjfL b.40.4.5 25346 1ypyA 184 3.85e+01 2vl7A 540 3.87e+01 2ak4E 245 3.89e+01 1w34A 304 3.90e+01 b.43.4.2,c.25.1.1 120620,120621 1gwyA 175 3.92e+01 b.97.1.1 83356 2ooiA 162 3.97e+01 2ia2A 265 4.02e+01 1zc3B 113 4.05e+01 b.55.1.1 124881 1dp0A 1023 4.05e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 1jz8A 1023 4.05e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 2p3yA 491 4.12e+01 1jmsA 381 4.12e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1xgyH 219 4.16e+01 b.1.1.2 121985 1b2rA 304 4.24e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1p42A 270 4.35e+01 d.14.1.7,d.14.1.7 87754,87755 2e27H 126 4.36e+01 1konA 249 4.36e+01 e.39.1.1 72823 1wgsA 133 4.44e+01 b.34.13.3 114622 1ywhA 313 4.49e+01 1c5cH 215 4.50e+01 1igtB b.1.1.1,b.1.1.2 20475,21439 1ao7D 204 4.57e+01 1tcrA b.1.1.1 20623 1sq2N 113 4.64e+01 b.1.1.1 105881 1tjgH 237 4.65e+01 b.1.1.1,b.1.1.2 112446,112447 2b3gA 123 4.66e+01 b.40.4.3 127786 1kw3B 292 4.69e+01 d.32.1.3,d.32.1.3 77549,77550 1qz8A 113 4.73e+01 b.140.1.1 96619 1o6dA 163 4.74e+01 c.116.1.3 92567 2rkuA 294 4.77e+01 1kb5A 115 4.78e+01 1tvdA b.1.1.1 20611 2go3A 267 4.82e+01 d.14.1.7,d.14.1.7 135422,135423 1cqxA 403 4.83e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1tf3A 92 4.91e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45057,45058,45059 1lzlA 323 4.92e+01 c.69.1.2 78306 1ixmA 192 4.92e+01 1ixmA d.123.1.1 41114 1ovaA 386 4.93e+01 1ovaA e.1.1.1 42619 1hqlA 257 4.95e+01 b.29.1.1 65907 1n3lA 372 4.96e+01 c.26.1.1 79966 2akzA 439 4.96e+01 c.1.11.1,d.54.1.1 126944,126945 2ejwA 332 4.97e+01 1tt8A 164 5.02e+01 d.190.1.1 112635 1hp1A 516 5.06e+01 d.114.1.1,d.159.1.2 70976,70977 2yyoA 171 5.10e+01 2p10A 286 5.11e+01 1htqA 477 5.11e+01 d.15.9.1,d.128.1.1 71035,71036 2p9rA 102 5.16e+01 2j5uA 255 5.17e+01 1dfuP 94 5.18e+01 1dfuP b.53.1.1 26936 1go2A 304 5.22e+01 b.43.4.2,c.25.1.1 76243,76244 1snnA 227 5.22e+01 d.115.1.2 105821 1gkkA 297 5.25e+01 c.69.1.2 65248 2a8jA 420 5.34e+01 1tp9A 162 5.34e+01 c.47.1.10 119306 2bsfA 176 5.42e+01 1rl5A 60 5.44e+01 1kjvA 284 5.47e+01 b.1.1.2,d.19.1.1 77421,77422 2owbA 335 5.50e+01 1jeqB 565 5.50e+01 1jeqB b.131.1.2,c.62.1.4 90368,90369 1zd0A 150 5.52e+01 d.329.1.1 124927 3cbwA 353 5.54e+01 2viuB 175 5.56e+01 1hgeB h.3.1.1 45676 1oc2A 348 5.56e+01 c.2.1.2 92765 2z84A 218 5.57e+01 1wk8A 194 5.58e+01 1hgeB 175 5.60e+01 1hgeB h.3.1.1 45680 2a74A 643 5.61e+01 1mvpA 124 5.65e+01 2rspB b.50.1.1 26775 1bev1 281 5.72e+01 1aym1 1hvc 203 5.72e+01 1hvc 1mzyA 333 5.77e+01 b.6.1.3,b.6.1.3 103848,103849 2e27L 119 5.96e+01 1esoA 154 5.98e+01 b.1.8.1 22293 1jjfA 268 6.02e+01 c.69.1.2 66765 1eagA 342 6.02e+01 1eagA b.50.1.2 26826 1wb4A 297 6.06e+01 c.69.1.2 120827 1xtoA 311 6.07e+01 d.157.1.6 116030 2iw0A 254 6.08e+01 c.6.2.3 137737 1mgpA 313 6.09e+01 c.119.1.1 79098 1fltX 95 6.12e+01 1fltX b.1.1.4 21765 1y4wA 518 6.13e+01 b.29.1.19,b.67.2.3 116470,116471 1kdgA 546 6.18e+01 c.3.1.2,d.16.1.1 77337,77338 3cmsA 323 6.19e+01 b.50.1.2 26865 1fwkA 296 6.19e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1ifrA 121 6.22e+01 b.1.16.1 71203 2a8mA 420 6.25e+01 1dqqB 210 6.29e+01 1igtB b.1.1.1,b.1.1.2 20421,21391 1wmvA 54 6.33e+01 1wba 175 6.38e+01 1wba 1wbaA 175 6.38e+01 b.42.4.1 25591 2petA 231 6.40e+01 2i5gA 325 6.42e+01 1ituA 369 6.46e+01 c.1.9.7 71423 1zjaA 557 6.48e+01 2id4A 503 6.50e+01 b.18.1.20,c.41.1.1 137265,137266 1vluA 468 6.54e+01 c.82.1.1 108864 2jtmA 60 6.58e+01 2in1A 175 6.58e+01 d.20.1.4 137521 1ok7A 366 6.66e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 2ghsA 326 6.70e+01 b.68.6.1 135209 1ad9B 219 6.76e+01 1gc1H b.1.1.1,b.1.1.2 20215,21227 1zt1A 277 6.85e+01 1xccA 220 6.85e+01 c.47.1.10 115113 1xf1A 926 6.85e+01 2g76A 335 6.87e+01 2pulA 397 6.87e+01 2o20A 332 6.89e+01 1bec 238 6.90e+01 1bec 1jndA 420 6.95e+01 c.1.8.5,d.26.3.1 71757,71758 1x1oA 286 6.97e+01 2icjA 233 7.01e+01 1ikoP 178 7.03e+01 b.6.1.5 71243 1zuoA 186 7.07e+01 d.20.1.1 125680 1qtyT 101 7.10e+01 1fltX b.1.1.4 21769 1h5bA 113 7.17e+01 1tvdA b.1.1.1 60638 3d9aH 210 7.17e+01 1aipA 405 7.19e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1z7wA 322 7.19e+01 c.79.1.1 124674 2ft0A 235 7.22e+01 1ncwH 222 7.24e+01 b.1.1.1,b.1.1.2 85555,85556 1vhsA 175 7.29e+01 d.108.1.1 100698 2j01P 150 7.29e+01 2qmlA 198 7.30e+01 1ngzB 220 7.31e+01 b.1.1.1,b.1.1.2 80502,80503 2ichA 335 7.33e+01 2rspA 124 7.36e+01 2rspB b.50.1.1 26771 1bglA 1023 7.37e+01 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 1r64A 481 7.37e+01 b.18.1.20,c.41.1.1 97140,97141 1zmoA 244 7.40e+01 1h4uA 265 7.41e+01 1h4uA d.22.1.2,g.3.11.5 60622,60623 1ooeA 236 7.45e+01 c.2.1.2 87196 2re7A 134 7.49e+01 2yzqA 282 7.54e+01 2j59M 168 7.54e+01 2fo3A 125 7.58e+01 d.20.1.1 133868 3czbA 351 7.59e+01 1xneA 113 7.59e+01 b.122.1.6 115579 2df8A 325 7.61e+01 1bob 320 7.66e+01 1bob 1bobA 320 7.66e+01 d.108.1.1 40816 1f8xA 157 7.68e+01 1f8xA c.23.14.1 31397 1ypcI 64 7.70e+01 2sniI d.40.1.1 38570 1azvA 153 7.70e+01 1mfmA b.1.8.1 22247 1k7jA 206 7.71e+01 d.115.1.1 72103 2p4oA 306 7.76e+01 2e5fA 325 7.82e+01 2g1lA 104 7.87e+01 b.26.1.2 134520 2polA 366 7.88e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1dcoA 104 7.97e+01 1dcpA d.74.1.1 39680 2pmvA 399 7.98e+01