# List of top-scoring protein chains for t2k-100-30-str2 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 1gm6A 175 4.53e-02 b.60.1.1 70272 1d8iA 311 1.13e-01 1d8iA d.63.1.1 39541 1d8hA 311 1.39e-01 1d8iA d.63.1.1 39544 1v8cA 168 4.02e-01 1cjxA 357 4.06e-01 1cjxA d.32.1.3 38516 d.32.1.3 38517 1hn2A 159 7.30e-01 b.60.1.1 65890 1gt1A 159 7.31e-01 1lfpA 249 1.01e+00 e.39.1.1 73885 1eguA 731 1.03e+00 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.5.2 24423 1ew3A 159 1.17e+00 1mup b.60.1.1 27114 1n7oA 721 1.27e+00 a.102.3.2 80259 b.24.1.1 80260 b.30.5.2 80261 1sqc 631 1.32e+00 2sqcA a.102.4.2 18858 a.102.4.2 18859 1o4sA 389 1.50e+00 c.67.1.1 86620 1k3eA 156 1.59e+00 d.198.1.1 68103 1ukkA 142 1.86e+00 1ex2A 189 2.11e+00 1ex2A c.51.4.2 33225 1obpA 159 2.26e+00 1obpA b.60.1.1 27092 1ewqA 765 2.65e+00 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1aw0 72 2.73e+00 1aw0 d.58.17.1 39342 2sqcA 631 2.74e+00 2sqcA a.102.4.2 18854 a.102.4.2 18855 1f1xA 322 2.82e+00 d.32.1.3 83208 d.32.1.3 83209 1p9vA 310 3.15e+00 d.21.1.2 88007 d.21.1.2 88008 1sdjA 310 3.15e+00 1gtdA 85 3.23e+00 d.58.45.1 76344 1lngA 87 3.42e+00 d.201.1.1 74045 1czaN 917 3.46e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1lxkA 721 3.80e+00 a.102.3.2 74331 b.24.1.1 74332 b.30.5.2 74333 1ax4A 467 3.83e+00 1ax4A c.67.1.2 34391 1psdA 409 4.31e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1lgtA 297 4.40e+00 d.32.1.3 77956 d.32.1.3 77957 1dgkN 917 4.49e+00 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1hkbA 917 4.59e+00 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1iq4A 179 4.60e+00 1iq4A d.77.1.1 62641 1r9cA 139 4.81e+00 9apiA 347 4.82e+00 1ovaA e.1.1.1 42630 1atiA 505 5.86e+00 1atiA c.51.1.1 33196 d.104.1.1 40745 1ik9A 213 6.16e+00 b.59.1.1 66176 h.1.11.1 66177 1ks2A 219 6.36e+00 c.35.1.2 72908 d.58.40.1 72909 1a3yA 149 6.60e+00 1obpA b.60.1.1 27110 1o8bA 219 6.68e+00 c.35.1.2 81180 d.58.40.1 81181 1bh5A 183 6.83e+00 1qipA d.32.1.1 38476 1f1uA 323 6.90e+00 d.32.1.3 83200 d.32.1.3 83201 1dzkA 157 7.17e+00 1obpA b.60.1.1 27096 1qwdA 177 7.18e+00 1rwsA 77 7.69e+00 1lkdA 297 7.69e+00 d.32.1.3 78059 d.32.1.3 78060 1nh8A 304 7.95e+00 c.94.1.1 80507 d.58.5.3 80508 1atiB 505 8.30e+00 1atiA c.51.1.1 33197 d.104.1.1 40746 1qipA 183 8.42e+00 1qipA d.32.1.1 38470 1ukuA 102 8.71e+00 1pkhA 204 8.90e+00 1hkcA 917 9.06e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1qtoA 122 9.23e+00 1bylA d.32.1.2 38494 1guzA 310 9.25e+00 c.2.1.5 65586 d.162.1.1 65587 1p8kZ 254 9.26e+00 1nd4A 264 1.01e+01 1oghA 204 1.04e+01 b.85.4.1 86994 2eifA 136 1.05e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1lkzA 219 1.06e+01 c.35.1.2 73991 d.58.40.1 73992 1k47A 337 1.09e+01 d.14.1.5 72040 d.58.26.4 72041 1tgoA 773 1.11e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1kr4A 125 1.12e+01 d.58.5.2 72889 1vokA 200 1.20e+01 1ytbA d.129.1.1 41242 d.129.1.1 41243 1ri5A 298 1.20e+01 1qnaA 200 1.21e+01 1ytbA d.129.1.1 41226 d.129.1.1 41227 1ytbB 180 1.21e+01 1ytbA d.129.1.1 41278 d.129.1.1 41279 1qqsA 174 1.22e+01 1nglA b.60.1.1 27143 1hbkA 94 1.22e+01 1aca a.11.1.1 60887 1rfmA 344 1.24e+01 1qovH 260 1.24e+01 6prcH b.41.1.1 25464 f.23.10.1 43457 1ytbA 180 1.25e+01 1ytbA d.129.1.1 41276 d.129.1.1 41277 1fa8A 135 1.25e+01 1qipA d.32.1.1 38486 1f9zA 135 1.28e+01 1qipA d.32.1.1 38484 1ejdA 419 1.30e+01 1uae d.68.2.2 39576 1han 297 1.31e+01 1han d.32.1.3 38506 d.32.1.3 38507 1rzhH 260 1.35e+01 1kw3B 292 1.35e+01 d.32.1.3 77549 d.32.1.3 77550 1uae 419 1.36e+01 1uae d.68.2.2 39574 1i4uA 181 1.41e+01 b.60.1.1 61732 1e4fT 419 1.42e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1fuiA 591 1.47e+01 1fuiA b.43.2.1 25674 c.85.1.1 35444 1tbaB 180 1.48e+01 1ytbA d.129.1.1 41286 d.129.1.1 41287 1l6rA 227 1.53e+01 c.108.1.10 77768 1ecfA 504 1.57e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1gdgA 293 1.58e+01 1jflA 228 1.59e+01 c.78.2.1 71656 c.78.2.1 71657 1bv8A 138 1.60e+01 1ayoA b.2.4.1 22430 1bu8A 452 1.60e+01 1gpl b.12.1.2 23647 c.69.1.19 34795 1l3iA 192 1.65e+01 c.66.1.22 77676 1f52A 468 1.67e+01 1lgr d.15.9.1 37839 d.128.1.1 41169 1iv3A 152 1.68e+01 d.79.5.1 76828 1pgtA 210 1.70e+01 1pgtA a.45.1.1 17515 c.47.1.5 32809 1jyhA 157 1.71e+01 d.60.1.3 71956 1irxA 523 1.71e+01 a.97.1.2 71378 c.26.1.1 71379 1dcoA 104 1.72e+01 1dcpA d.74.1.1 39680 1esgA 213 1.72e+01 1bam c.52.1.3 33286 1h91A 180 1.72e+01 b.60.1.1 60805 1oz9A 150 1.74e+01 1ystH 260 1.74e+01 6prcH b.41.1.1 25482 f.23.10.1 43511 1bd2D 204 1.74e+01 1tcrA b.1.1.1 20622 b.1.1.2 21557 1dhy 292 1.75e+01 1han d.32.1.3 38504 d.32.1.3 38505 1ah6 220 1.86e+01 1yer d.122.1.1 41094 1gw5S 142 1.88e+01 d.110.4.2 70633 1f5sA 211 1.88e+01 1f5sA c.108.1.4 59656 1jjyA 636 1.89e+01 1jjyA e.26.1.2 63141 1j97A 211 1.89e+01 1f5sA c.108.1.4 62753 1qgvA 142 1.95e+01 1qgvA c.47.1.8 33056 1dcpA 104 1.96e+01 1dcpA d.74.1.1 39672 1b04A 318 1.98e+01 1b04A d.142.2.2 41579 1hnnA 282 1.99e+01 c.66.1.15 65895 1vioA 243 2.00e+01 1l7mA 211 2.03e+01 c.108.1.4 73664 1ksiA 642 2.03e+01 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1ksyA 154 2.05e+01 d.89.1.2 72948 1ecsA 126 2.06e+01 1ecsA d.32.1.2 59407 1k8wA 327 2.08e+01 b.122.1.1 83094 d.58.35.2 68317 d.58.35.2 83095 1b3qA 379 2.12e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1qhaA 917 2.12e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1h70A 255 2.13e+01 1h70A d.126.1.3 60711 1l0lA 446 2.13e+01 d.185.1.1 84482 d.185.1.1 84483 1h4rA 314 2.14e+01 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1c0aA 585 2.15e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1e8cA 498 2.15e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1rhs 296 2.15e+01 1rhs c.46.1.2 32703 c.46.1.2 32704 1f1sA 814 2.19e+01 a.102.3.2 64928 b.1.18.2 64929 b.24.1.1 64930 b.30.5.2 64931 1itg 166 2.22e+01 1b9dA c.55.3.2 33661 2cpgA 45 2.25e+01 2cpgA a.43.1.2 17455 1fu1A 203 2.25e+01 1fu1B b.59.1.1 27076 h.1.11.1 45630 1ksiB 642 2.27e+01 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1n6zA 105 2.30e+01 d.74.5.1 85369 1ry9A 145 2.31e+01 1d3uB 201 2.32e+01 1aisB a.74.1.2 18386 a.74.1.2 18387 1fu1B 203 2.32e+01 1fu1B b.59.1.1 27077 h.1.11.1 45631 1gh9A 71 2.36e+01 1gh9A g.41.6.1 45266 1iu9A 111 2.37e+01 1su8A 636 2.50e+01 1jbeA 128 2.52e+01 3chy c.23.1.1 62845 1dgsA 667 2.55e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1f93A 104 2.56e+01 1dcpA d.74.1.1 39688 1ng6A 148 2.59e+01 a.182.1.1 85670 1j1tA 233 2.63e+01 1ecfB 504 2.66e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1i7qA 519 2.69e+01 1qdlA d.161.1.1 61901 1aym3 238 2.72e+01 1aym3 1e6mA 128 2.80e+01 3chy c.23.1.1 31039 1k3yA 221 2.81e+01 a.45.1.1 77245 c.47.1.5 77246 1mpyA 307 2.81e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1q5yA 85 2.81e+01 1qysA 106 2.81e+01 1iznA 286 2.82e+01 e.43.1.1 83847 1e5pA 151 2.84e+01 1bj7 b.60.1.1 59272 2dln 306 2.84e+01 1iow c.30.1.2 31715 d.142.1.1 41483 1jpmA 366 2.87e+01 c.1.11.2 67031 d.54.1.1 67032 1r69 69 2.87e+01 1r69 a.35.1.2 17028 1cye 129 2.95e+01 3chy c.23.1.1 31077 1ewjA 126 2.97e+01 1ecsA d.32.1.2 59526 1k3fA 253 3.01e+01 c.56.2.1 68105 1oxxK 353 3.05e+01 1o26A 232 3.05e+01 d.207.1.1 86566 1inp 400 3.06e+01 1inp e.7.1.1 42972 1f1zA 273 3.14e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1jc4A 148 3.21e+01 1jc4A d.32.1.4 62863 1bdo 80 3.22e+01 1bdo b.84.1.1 28214 1b7yA 350 3.23e+01 1pysA d.104.1.1 40776 1dlyA 164 3.23e+01 1dlyA a.1.1.1 14983 1ej5A 107 3.23e+01 1ej5A a.68.1.1 18268 1szwA 379 3.25e+01 1q9uA 130 3.26e+01 1j6uA 469 3.30e+01 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 3chy 128 3.31e+01 3chy c.23.1.1 31038 1kafA 108 3.39e+01 d.199.1.1 68372 1gx1A 160 3.40e+01 d.79.5.1 70675 1si7A 369 3.40e+01 1feuA 206 3.41e+01 1feuA b.53.1.1 59801 1dk4A 252 3.42e+01 1dk4A e.7.1.1 42970 1go3F 107 3.44e+01 a.60.8.2 65407 1gseA 221 3.53e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1gqoX 143 3.53e+01 c.23.13.1 76317 1bgp 309 3.56e+01 1bgp a.93.1.1 18690 1mc3A 296 3.56e+01 c.68.1.6 78943 1oxsC 353 3.57e+01 b.40.6.3 87519 c.37.1.12 87520 1k3lA 221 3.58e+01 a.45.1.1 77229 c.47.1.5 77230 1hcnA 92 3.63e+01 1hcnA g.17.1.4 44809 1tdj 514 3.63e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1pv9A 348 3.64e+01 1nnmA 652 3.65e+01 1pg4A 652 3.65e+01 e.23.1.1 88067 1quqA 129 3.65e+01 1quqA b.40.4.3 25303 1iba 101 3.65e+01 1iba d.95.1.1 40567 1gefA 123 3.71e+01 1gefA c.52.1.18 60465 1h72C 296 3.72e+01 d.14.1.5 60712 d.58.26.1 60713 1ap8 213 3.73e+01 1ap8 d.86.1.1 40151 1i06A 180 3.74e+01 1mup b.60.1.1 27131 1rkqA 282 3.75e+01 1imuA 107 3.81e+01 d.204.1.1 66218 1dk8A 147 3.81e+01 1agrE a.91.1.1 18548 1lgr 468 3.85e+01 1lgr d.15.9.1 37837 d.128.1.1 41167 2lgsA 468 3.87e+01 1lgr d.15.9.1 37838 d.128.1.1 41168 1cqmA 101 3.88e+01 1ris d.58.14.1 39321 1dp3A 55 3.94e+01 1dp3A a.55.1.2 59128 1fsz 372 3.95e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 5p21 166 3.98e+01 1ctqA c.37.1.8 31966 1fseA 74 4.00e+01 1fseA a.4.6.2 60000 3bamA 213 4.00e+01 1bam c.52.1.3 33288