# List of top-scoring protein chains for t04-100-30-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 1q5qA 259 5.71e-02 d.153.1.4 -11433 1e3dB 542 5.80e-01 1h2rL e.18.1.1 59189 1rypG 244 9.62e-01 d.153.1.4 41938 1mdwA 328 1.01e+00 d.3.1.3 84934 1o8bA 219 1.02e+00 unknown_sccs 81180 d.58.40.1 81181 1e19A 314 2.23e+00 1b7bA c.73.1.1 34967 1914 232 2.38e+00 1914 d.49.1.1 83028 d.49.1.1 83029 1dhkB 223 2.42e+00 1led b.29.1.1 24157 1mp8A 281 2.62e+00 d.144.1.7 -11361 1r62A 160 2.67e+00 1pysA 350 3.03e+00 1pysA d.104.1.1 40775 1ubkL 534 3.06e+00 e.18.1.1 88422 1i7nA 309 3.27e+00 c.30.1.5 83681 d.142.1.3 83682 1h2rL 534 3.34e+00 1h2rL e.18.1.1 43298 1b7yA 350 3.67e+00 1pysA d.104.1.1 40776 1q1rA 431 3.75e+00 c.3.1.5 -6048 c.3.1.5 -6049 d.87.1.1 -10502 1fiqC 763 3.80e+00 1fiqC d.41.1.1 38588 d.133.1.1 41418 1rypC 244 3.84e+00 1rypC d.153.1.4 41934 1s72Q 96 4.14e+00 1dysA 348 4.16e+00 1bvwA c.6.1.1 30669 1v97A 1332 4.19e+00 1q6hA 224 4.23e+00 d.26.1.1 -9487 1q8iA 783 4.34e+00 c.55.3.5 -7635 e.8.1.1 -11885 1rvkA 382 4.71e+00 c.1.11.2 -5568 d.54.1.1 -9826 1ntvA 152 4.80e+00 b.55.1.2 86168 1jj2P 95 4.89e+00 1ffkN b.34.5.1 63101 1qpcA 279 5.08e+00 1fgkA d.144.1.7 41685 1dgfA 497 5.56e+00 1cf9A e.5.1.1 42782 1h4pA 408 5.68e+00 c.1.8.3 -5314 1r6jA 82 5.80e+00 b.36.1.1 -3732 1odzA 386 5.86e+00 c.1.8.3 86889 1oyeA 1049 6.12e+00 d.58.44.1 87587 d.58.44.1 87588 d.58.44.1 87589 d.58.44.1 87590 d.225.1.1 87591 d.225.1.1 87592 f.35.1.1 87593 f.35.1.1 87594 1j9yA 385 6.26e+00 1j9yA c.1.8.3 62791 1nbwA 607 6.44e+00 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1k6wA 426 6.82e+00 b.92.1.2 68236 c.1.9.5 68237 2shpA 525 7.09e+00 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1nteA 82 7.16e+00 b.36.1.1 86163 1fo4A 1332 7.24e+00 a.56.1.1 17910 d.15.4.2 37695 d.41.1.1 38586 d.87.2.1 40227 d.133.1.1 41416 d.145.1.3 41758 1j6pA 418 7.54e+00 b.92.1.4 77089 c.1.9.9 77090 1rypB 250 7.64e+00 1rypB d.153.1.4 41933 1r6wA 322 7.94e+00 c.1.11.2 -5563 d.54.1.1 -9821 1e4fT 419 8.15e+00 1e4fT c.55.1.1 33453 c.55.1.1 33454 1p1mA 406 8.28e+00 b.92.1.4 87696 c.1.9.9 87697 1jx4A 352 8.77e+00 unknown_sccs -10188 unknown_sccs -11898 1pkp 150 8.80e+00 1pkp d.14.1.1 37551 d.50.1.2 38787 1k5nA 276 9.06e+00 b.1.1.2 77266 d.19.1.1 77267 1omrA 201 9.80e+00 a.39.1.5 -854 2trxA 108 9.87e+00 1thx c.47.1.1 32719 3fruA 269 9.96e+00 1agdA b.1.1.2 20657 d.19.1.1 38150 1nu5A 370 1.02e+01 c.1.11.2 -5565 d.54.1.1 -9823 1bqyA 234 1.05e+01 5ptp b.47.1.2 26332 1euvA 221 1.09e+01 1euvA d.3.1.7 37133 1mkmA 249 1.11e+01 a.4.5.33 79242 d.110.2.2 79243 1p8xA 344 1.12e+01 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1a05A 358 1.17e+01 1cnzA c.77.1.1 35059 1lla 628 1.20e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1eejA 216 1.21e+01 1eejA c.47.1.9 33057 d.17.3.1 38071 1f35A 162 1.22e+01 1f35A b.94.1.1 59628 1rg9A 383 1.22e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1js8A 394 1.24e+01 a.86.1.1 67219 b.112.1.1 67220 1qyaA 307 1.28e+01 1qhfA 240 1.29e+01 1qhfA c.60.1.1 33960 1dlwA 116 1.32e+01 1dlyA a.1.1.1 14982 1fzoA 274 1.33e+01 1agdA b.1.1.2 60155 d.19.1.1 60156 1h2kA 349 1.33e+01 b.82.2.6 76572 1ec7A 446 1.36e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1azpA 66 1.41e+01 1azpA b.34.13.1 37467 1ub0A 258 1.44e+01 c.72.1.2 88394 1lr0A 129 1.45e+01 d.212.1.1 74213 1kkoA 413 1.46e+01 c.1.11.2 68675 d.54.1.1 68676 1r4pB 70 1.47e+01 b.40.2.1 -3887 1mucA 373 1.47e+01 1mucA c.1.11.2 29236 d.54.1.1 38880 1pieA 419 1.51e+01 d.14.1.5 -9075 unknown_sccs -10120 1rec 201 1.51e+01 1rec a.39.1.5 17326 1l3lA 234 1.62e+01 a.4.6.2 73541 d.110.5.1 73542 1g3qA 237 1.65e+01 1hyqA c.37.1.10 60237 1fhuA 320 1.67e+01 1fhuA c.1.11.2 29234 d.54.1.1 38878 1te5A 257 1.69e+01 1lk2A 274 1.69e+01 b.1.1.2 -2610 d.19.1.1 -9365 1gk9B 557 1.71e+01 1e3aB 560 1.72e+01 1ajqB 1awqA 164 1.73e+01 2cpl b.62.1.1 27461 1hrhA 136 1.77e+01 1rthA c.55.3.1 33577 1ryp1 222 1.77e+01 1ryp1 2cpl 165 1.78e+01 2cpl b.62.1.1 27420 1ctt 294 1.80e+01 1ctt c.97.1.1 36022 c.97.1.1 36023 1auvA 311 1.80e+01 1auvA c.30.1.5 31723 d.142.1.3 41558 1jh6A 189 1.81e+01 d.61.1.1 66707 1r0pA 312 1.81e+01 d.144.1.7 -11377 1kjvA 284 1.82e+01 b.1.1.2 77421 d.19.1.1 77422 1i7qA 519 1.82e+01 1qdlA d.161.1.1 61901 1oltA 457 1.82e+01 unknown_sccs -5688 1a9xB 379 1.85e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1awsA 164 1.89e+01 2cpl b.62.1.1 27431 1trkA 680 1.93e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1h6zA 913 1.99e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1tkiA 321 2.08e+01 1tkiA d.144.1.7 41638 1s68A 249 2.10e+01 unknown_sccs -11253 7taa 478 2.10e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1p1lA 102 2.12e+01 d.58.5.2 87695 1k0iA 394 2.12e+01 c.3.1.2 67942 d.16.1.2 67943 1e79H 146 2.12e+01 1e79H a.2.10.1 15721 b.93.1.1 28438 3tgl 269 2.16e+01 3tgl c.69.1.17 34733 1jfmA 174 2.17e+01 d.19.1.1 66640 1omwA 689 2.19e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1onwA 390 2.22e+01 b.92.1.7 87172 c.1.9.13 87173 1gpuA 680 2.26e+01 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1uyrA 737 2.29e+01 c.14.1.4 -6258 c.14.1.4 -6259 1squA 155 2.31e+01 unknown_sccs -10229 1jnrB 150 2.31e+01 d.58.1.5 66969 1qd1A 325 2.37e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1gmyA 261 2.38e+01 d.3.1.1 76236 1rxxA 421 2.42e+01 unknown_sccs -10982 1qh3A 260 2.44e+01 1qh5A d.157.1.2 42059 1jv4A 162 2.46e+01 b.60.1.1 67343 1qh5A 260 2.47e+01 1qh5A d.157.1.2 42057 1rypH 205 2.47e+01 d.153.1.4 41876 1ton 235 2.51e+01 5ptp b.47.1.2 26307 1l7aA 318 2.54e+01 c.69.1.25 77772 1i05A 180 2.59e+01 1mup b.60.1.1 27130 1dypA 271 2.59e+01 1dypA b.29.1.2 24185 1ukuA 102 2.62e+01 d.58.5.2 -9992 1a8q 274 2.70e+01 1brt c.69.1.12 34702 1fxjA 331 2.71e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1pbe 394 2.71e+01 1pbe c.3.1.2 30338 d.16.1.2 37869 1k38A 254 2.76e+01 e.3.1.1 84303 1i06A 180 2.77e+01 1mup b.60.1.1 27131 2bltA 361 2.80e+01 1gceA e.3.1.1 42739 1h9sA 140 2.85e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1ovnA 248 2.86e+01 a.71.1.1 -1096 c.47.1.7 -7477 1hbzA 498 2.87e+01 1cf9A e.5.1.1 60937 1ufbA 127 2.87e+01 a.24.16.3 -635 2napA 723 2.87e+01 2napA b.52.2.2 26926 c.81.1.1 35334 1by2 119 2.91e+01 1by2 d.170.1.1 42452 1q3eA 207 2.95e+01 b.82.3.2 -4922 2phlA 397 2.96e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1lx7A 253 2.97e+01 c.56.2.1 74329 1ew2A 513 2.97e+01 1b8jA c.76.1.1 59525 1uox 296 2.99e+01 1uox 1r4uA 301 3.01e+01 d.96.1.4 -10709 d.96.1.4 -10710 1m6eX 359 3.05e+01 unknown_sccs -8071 1dkzA 219 3.07e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1j1nA 492 3.08e+01 c.94.1.1 83978 1nvmB 312 3.10e+01 c.2.1.3 86251 d.81.1.1 86252 1rxyA 253 3.12e+01 c.56.2.1 -7834 1jpmA 366 3.13e+01 c.1.11.2 67031 d.54.1.1 67032 1ep0A 185 3.14e+01 1dzrA b.82.1.1 28080 1byqA 228 3.26e+01 1yer d.122.1.1 41100 1oe4A 247 3.26e+01 c.18.1.3 86895 1gweA 503 3.29e+01 e.5.1.1 70667 1uwvA 433 3.32e+01 unknown_sccs -3950 unknown_sccs -8107 1qqsA 174 3.34e+01 1nglA b.60.1.1 27143 1hh1A 143 3.35e+01 1gefA c.52.1.18 61036 1tfe 145 3.36e+01 1tfe d.43.1.1 38680 1h7mA 102 3.40e+01 d.79.3.1 83485 1im8A 244 3.42e+01 c.66.1.14 66212 1eaf 243 3.42e+01 1eaf c.43.1.1 32617 1s6yA 450 3.44e+01 1fs0E 138 3.49e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1hq0A 295 3.50e+01 1hzgA d.194.1.1 61122 1fltV 98 3.54e+01 1vpfA g.17.1.1 44751 1rgzA 363 3.54e+01 e.3.1.1 -11771 1p7tA 731 3.54e+01 c.1.13.1 -5600 1lrzA 426 3.56e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1adjA 421 3.61e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1ga0A 364 3.65e+01 1gceA e.3.1.1 60410 1erjA 393 3.65e+01 1erjA b.69.4.1 27660 1o6uA 403 3.67e+01 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1onxA 390 3.69e+01 b.92.1.7 87176 c.1.9.13 87177 1mla 309 3.74e+01 1mla c.19.1.1 31031 d.58.23.1 39383 1nm8A 616 3.75e+01 c.43.1.3 85872 c.43.1.3 85873 1q0vA 81 3.76e+01 j.105.1.1 -13401 1gw5S 142 3.77e+01 d.110.4.2 70633 1nzhA 282 3.84e+01 d.151.1.2 -11398 1ihoA 283 3.85e+01 1ihoA c.26.1.4 62390 1i7kA 179 3.86e+01 1u9aA d.20.1.1 61889 1mpxA 615 3.87e+01 b.18.1.13 85041 c.69.1.21 85042 1bgp 309 3.90e+01 1bgp a.93.1.1 18690 1jkeA 145 3.93e+01 c.110.1.1 66791 1h4vB 421 3.94e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1vfrA 218 3.95e+01 1vfrA d.90.1.1 40247 1f2tB 148 4.00e+01 1f2tB