# 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 1mkiA 330 1.67e-53 e.3.1.2 84994 1i2sA 282 1.44e-04 e.3.1.1 71104 4blmA 265 3.17e-04 1btl e.3.1.1 42721 1iysA 262 1.79e-03 e.3.1.1 -11760 1ghpA 258 2.91e-03 1btl e.3.1.1 60520 1bza 262 3.38e-03 1btl e.3.1.1 42701 1e25A 282 1.53e-02 1e25A e.3.1.1 42731 1bueA 265 3.35e-02 1btl e.3.1.1 42727 2sqcA 631 5.86e-02 2sqcA a.102.4.2 18854 a.102.4.2 18855 1ei5A 520 6.27e-02 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1bsg 266 6.60e-02 1btl e.3.1.1 42729 1ermA 263 1.14e-01 1btl e.3.1.1 42690 1btl 263 1.23e-01 1btl e.3.1.1 42691 1ouvA 273 1.43e-01 a.118.18.1 -1586 1n9bA 265 1.57e-01 e.3.1.1 85463 1klxA 138 1.67e-01 a.118.18.1 77440 1m40A 263 1.86e-01 e.3.1.1 74437 1hzoA 271 1.91e-01 e.3.1.1 71092 1j1jA 240 2.02e-01 a.118.16.1 -1637 1g6aA 271 2.08e-01 1btl e.3.1.1 42704 1ci9A 392 4.28e-01 e.3.1.1 64767 1is1A 185 4.59e-01 d.67.3.1 83704 1top 162 4.81e-01 1ncx a.39.1.5 17223 2bltA 361 5.18e-01 1gceA e.3.1.1 42739 1rgzA 363 5.33e-01 e.3.1.1 -11771 1ga0A 364 5.77e-01 1gceA e.3.1.1 60410 1pi4A 358 6.09e-01 e.3.1.1 -11774 1fsyA 358 6.40e-01 1gceA e.3.1.1 60016 1uw4B 248 6.87e-01 unknown_sccs -1560 1odoA 408 7.19e-01 a.104.1.1 -1463 1fw9A 164 7.83e-01 1fw9A d.190.1.1 60059 1pjjA 271 9.00e-01 1nnjA 271 9.24e-01 a.156.1.2 80669 b.113.1.1 80670 g.39.1.8 80671 1uocA 289 9.78e-01 unknown_sccs -7671 1jfbA 404 1.12e+00 a.104.1.1 66624 1oshA 232 1.14e+00 a.123.1.1 -1697 1fcyA 236 1.22e+00 2lbd a.123.1.1 19282 1l1zA 274 1.24e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1f24A 402 1.34e+00 1rom a.104.1.1 18953 4crxA 322 1.53e+00 4crxA a.60.9.1 18095 d.163.1.1 42155 1gpr 162 1.53e+00 1gpr b.84.3.1 28267 1mtyD 512 1.65e+00 1mhyD a.25.1.2 16742 1mp1A 111 1.67e+00 unknown_sccs -996 1r2zA 274 1.83e+00 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1o7eA 276 1.86e+00 e.3.1.1 -11766 1auiB 169 1.88e+00 1auiB a.39.1.5 17325 1pd21 199 1.97e+00 1pd21 1uch 230 2.02e+00 1uch d.3.1.6 37129 1l8bA 190 2.29e+00 d.86.1.1 73683 1l0gA 358 2.58e+00 e.3.1.1 73400 1q5dA 419 2.65e+00 a.104.1.1 -1454 1euvA 221 2.69e+00 1euvA d.3.1.7 37133 1vi9A 299 2.87e+00 c.72.1.5 -8393 1ej1A 190 3.00e+00 1ejhA d.86.1.1 40144 1q7fA 286 3.35e+00 unknown_sccs -4599 1nj4A 363 3.67e+00 b.105.1.1 80545 e.3.1.1 80546 1r9dA 787 3.92e+00 1rgyA 360 3.99e+00 e.3.1.1 -11768 1ezvD 245 4.20e+00 1be3D a.3.1.3 59546 f.23.11.1 59547 1ne9A 335 4.30e+00 d.108.1.4 -10805 d.108.1.4 -10806 1cqqA 180 4.34e+00 1cqqA b.47.1.4 26422 1teaA 299 4.48e+00 1k82A 268 4.48e+00 a.156.1.2 75866 b.113.1.1 75867 g.39.1.8 75868 1eca 136 4.54e+00 1flp a.1.1.2 15209 1qq5A 253 4.59e+00 1qq5A c.108.1.1 43327 1ca1 370 4.64e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1dpjA 329 4.94e+00 1smrA b.50.1.2 26828 1qmeA 702 5.05e+00 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1qb2A 109 5.13e+00 1qb2A a.36.1.1 17125 1qq7A 253 5.26e+00 1qq5A c.108.1.1 43329 1mo9A 523 5.30e+00 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1g3mA 294 5.42e+00 c.37.1.5 83268 1fs0E 138 5.46e+00 1aqt a.2.10.1 59997 b.93.1.1 59998 1qv1A 195 5.64e+00 a.39.1.5 -830 1jx4A 352 5.80e+00 unknown_sccs -10188 unknown_sccs -11898 1d5rA 324 5.83e+00 1d5rA b.7.1.1 23181 c.45.1.1 32697 1uldA 150 6.07e+00 b.29.1.3 -3423 1qwlA 505 6.29e+00 e.5.1.1 -11823 1dlyA 164 6.41e+00 1dlyA a.1.1.1 14983 1nkqA 259 6.59e+00 1au1A 166 6.64e+00 1ifa a.26.1.3 16889 1keaA 221 6.76e+00 a.96.1.2 68491 1m6sA 347 6.79e+00 c.67.1.1 78701 1jg8A 347 6.90e+00 1jg8A c.67.1.1 62946 1uwzA 136 6.95e+00 1el4A 195 6.99e+00 1ej3A a.39.1.5 59453 1pysA 350 7.07e+00 1pysA d.104.1.1 40775 1o0wA 252 7.33e+00 a.149.1.1 80751 d.50.1.1 80752 1abv 134 7.41e+00 1abv a.70.1.1 18317 1p5sA 203 7.43e+00 a.40.1.1 -900 1ci3M 249 7.44e+00 1hcz b.2.6.1 22480 b.84.2.2 28266 1js8A 394 7.60e+00 a.86.1.1 67219 b.112.1.1 67220 1regX 122 7.65e+00 1regX d.58.27.1 39406 1eonA 245 8.14e+00 1rvaA c.52.1.2 33238 1rvaA 244 8.16e+00 1rvaA c.52.1.2 33240 1e0bA 68 8.21e+00 1e0bA b.34.13.2 37476 1nzoA 363 8.34e+00 b.105.1.1 -2933 e.3.1.1 -11784 1j1iA 296 8.48e+00 c.69.1.10 83977 1k38A 254 8.52e+00 e.3.1.1 84303 1ngvA 534 8.63e+00 c.111.1.2 85698 1g6oA 330 8.65e+00 1g6oA c.37.1.11 32430 1jrrA 382 8.76e+00 e.1.1.1 63256 1rfzA 168 8.86e+00 unknown_sccs -1206 1pbv 195 9.32e+00 1pbv a.118.3.1 19179 1e7uA 961 9.60e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1p9qC 256 9.64e+00 1fm9D 272 9.65e+00 2prgA a.123.1.1 19313 1n27A 96 9.83e+00 b.34.9.2 -3585 1omhA 293 9.92e+00 unknown_sccs -10527 1vrtA 560 9.99e+00 1rthA c.55.3.1 33574 e.8.1.2 43023 3rp2A 224 1.01e+01 1a7s b.47.1.2 26298 1hvbA 349 1.02e+01 3pte e.3.1.1 42686 1cby 259 1.02e+01 1cby d.103.1.1 40705 1yghA 164 1.02e+01 1yghA d.108.1.1 40802 16pk 415 1.04e+01 16pk c.86.1.1 35454 1korA 400 1.04e+01 c.26.2.1 72824 d.210.1.1 72825 1kb9D 246 1.05e+01 a.3.1.3 77317 f.23.11.1 77318 1cdcA 99 1.05e+01 1cdcA b.1.1.1 19746 1ls6A 295 1.05e+01 c.37.1.5 -7026 1iyhA 198 1.08e+01 a.45.1.1 83790 c.47.1.5 83791 1m7sA 484 1.10e+01 e.5.1.1 74574 2gdm 153 1.10e+01 2gdm a.1.1.2 15212 1v74A 107 1.12e+01 unknown_sccs -9319 1kjqA 391 1.13e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1b7yA 350 1.14e+01 1pysA d.104.1.1 40776 1sx5A 244 1.14e+01 c.52.1.2 -7551 1c44A 123 1.15e+01 1qndA d.106.1.1 40795 1lj8A 493 1.17e+01 a.100.1.9 78033 c.2.1.6 78034 1hm6A 346 1.17e+01 1avc a.65.1.1 18147 1oyeA 1049 1.17e+01 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 1eyzA 392 1.18e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1ku1A 230 1.19e+01 a.118.3.1 72996 1aa7A 158 1.19e+01 1aa7A a.95.1.1 18741 1np3A 338 1.20e+01 a.100.1.2 85946 c.2.1.6 85947 1wdcB 156 1.23e+01 1wdcB a.39.1.5 17302 1kktA 511 1.24e+01 a.102.2.1 68687 1ek8A 185 1.27e+01 1ek8A d.67.3.1 59444 1tluA 130 1.30e+01 1n83A 270 1.33e+01 a.123.1.1 80276 1csh 435 1.33e+01 1csh a.103.1.1 18880 1dq3A 454 1.34e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1bo1A 416 1.34e+01 1bo1A d.143.1.2 41591 1jtkA 136 1.36e+01 c.97.1.1 71862 1nrfA 262 1.36e+01 e.3.1.1 -11780 1jpzA 473 1.37e+01 a.104.1.1 67069 1n1jA 93 1.40e+01 a.22.1.3 79813 1r8sE 203 1.41e+01 a.118.3.1 -1579 1n91A 108 1.44e+01 d.206.1.1 80326 1qazA 351 1.46e+01 1qazA a.102.3.1 18848 4tmkA 213 1.46e+01 5tmpA c.37.1.1 31930 1spgA 144 1.48e+01 1abwA a.1.1.2 15409 1efnB 152 1.48e+01 1efnB d.102.1.1 40699 1e8yA 966 1.49e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 2ae2A 260 1.51e+01 1bdb c.2.1.2 29945 1jihA 531 1.51e+01 unknown_sccs -10212 unknown_sccs -11922 1rthA 560 1.52e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1tvfA 369 1.54e+01 1t95A 240 1.55e+01 1ex2A 189 1.56e+01 1ex2A c.51.4.2 33225 1aquA 297 1.60e+01 1aquA c.37.1.5 31942 1ik9A 213 1.61e+01 b.59.1.1 66176 h.1.11.1 66177 1p9bA 442 1.62e+01 c.37.1.10 -7115 1uouA 474 1.64e+01 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1ornA 226 1.64e+01 a.96.1.1 87342 2hlcA 230 1.65e+01 5ptp b.47.1.2 26074 1sig 339 1.66e+01 1sig a.177.1.1 19068 1ad4A 266 1.70e+01 1aj2 c.1.21.1 29670 1b25A 619 1.73e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1np7A 489 1.74e+01 a.99.1.1 80677 c.28.1.1 80678 1m3qA 317 1.74e+01 a.96.1.3 -1288 d.129.1.2 -11006 1dp0A 1023 1.75e+01 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1go2A 304 1.75e+01 b.43.4.2 76243 c.25.1.1 76244 1jz8A 1023 1.77e+01 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.5.1 67833 c.1.8.3 67834 1dgfA 497 1.78e+01 1cf9A e.5.1.1 42782 1ivyA 452 1.79e+01 1ivyA c.69.1.5 34654 1dxrL 273 1.81e+01 6prcL f.26.1.1 43431 1furA 467 1.81e+01 1furA a.127.1.1 19403 1hjrA 158 1.82e+01 1hjrA c.55.3.6 33727 1ogiA 303 1.82e+01 b.43.4.2 -4042 c.25.1.1 -6587 1ad1A 266 1.84e+01 1aj2 c.1.21.1 29668 1que 303 1.87e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1p2xA 159 1.92e+01 1v93A 296 1.94e+01 c.1.23.1 -5654 1rec 201 1.96e+01 1rec a.39.1.5 17326 1dfoA 417 1.98e+01 1bj4A c.67.1.4 34480 1k8kG 151 1.99e+01 a.118.13.1 68313 1gjnA 153 2.00e+01 a.1.1.2 70191 1oaiA 59 2.00e+01 a.5.2.3 81255 1mucA 373 2.03e+01 1mucA c.1.11.2 29236 d.54.1.1 38880 1ok8A 394 2.03e+01 b.1.18.4 -2737 f.10.1.1 -12384 1cc1L 498 2.03e+01 1h2rL e.18.1.1 43301 1brwA 433 2.04e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1squA 155 2.04e+01 unknown_sccs -10229 1aj8A 371 2.05e+01 1aj8A a.103.1.1 18900 5eau 548 2.05e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1mun 225 2.09e+01 1mun a.96.1.2 18744 1s4kA 120 2.09e+01 1gdoA 240 2.09e+01 1gdoA d.153.1.1 41804 1otgA 125 2.10e+01 1otgA d.80.1.2 39831 1m93C 41 2.14e+01 1mtyG 162 2.14e+01 1mtyG a.23.3.1 16498 1k8tA 510 2.15e+01 e.41.1.1 68316 1q0rA 298 2.19e+01 unknown_sccs -8330 1lvwA 295 2.22e+01 c.68.1.6 84723 1nrvA 105 2.24e+01 d.93.1.1 86126 1cqxA 403 2.27e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1ukgA 252 2.28e+01 b.29.1.1 -3390 1n3oA 252 2.30e+01 b.29.1.1 79967 1f44A 324 2.30e+01 a.60.9.1 64982 d.163.1.1 64983 1iu4A 331 2.34e+01 d.3.1.8 71430 1ggzA 148 2.40e+01 a.39.1.5 70176 1fu1A 203 2.41e+01 1fu1B b.59.1.1 27076 h.1.11.1 45630 1ako 268 2.46e+01 1ako d.151.1.1 41779 1dc1A 323 2.47e+01 1dc1A c.52.1.11 33321 1dceB 331 2.51e+01 1dceB a.102.4.3 18872 1hf8A 289 2.52e+01 1hg5A unknown_sccs -399 unknown_sccs -1628 1lylA 504 2.53e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1su8A 636 2.55e+01 e.26.1.2 -12015 1lvfA 110 2.61e+01 a.47.2.1 74280 1iazA 179 2.62e+01 1iazA b.97.1.1 62131 1jjyA 636 2.63e+01 1jjyA 1q44A 326 2.65e+01 c.37.1.5 -7037 1dwtA 153 2.69e+01 1a6m a.1.1.2 15190 1jf2A 195 2.69e+01 1ej3A a.39.1.5 62930 1v4eA 299 2.72e+01 a.128.1.1 -1781 1ka2A 499 2.72e+01 d.92.1.5 77305 1vduA 172 2.73e+01 unknown_sccs -1651 1uc8A 280 2.74e+01 unknown_sccs -6718 unknown_sccs -11230 3pte 349 2.86e+01 3pte e.3.1.1 42687 1rmd 116 2.86e+01 1rmd g.37.1.1 45025 g.44.1.1 45322 1n2fA 142 2.89e+01 d.227.1.1 79853 1up8A 598 2.90e+01 a.111.1.2 -1480 1qb5D 99 2.91e+01 b.40.2.1 88357 1qnjA 240 2.93e+01 5ptp b.47.1.2 26238 1pjpA 226 2.94e+01 5ptp b.47.1.2 26301 2ahjA 206 2.98e+01 2ahjA d.149.1.1 41772 1e3dB 542 3.00e+01 1h2rL e.18.1.1 59189 1h8eA 510 3.03e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1nrgA 261 3.03e+01 b.45.1.1 80694 3ertA 261 3.04e+01 3erdA a.123.1.1 19292 1bh9B 89 3.05e+01 1bh9B a.22.1.3 16485 1pwgA 349 3.05e+01 1q59A 172 3.07e+01 f.1.4.1 -12062 1nq7A 244 3.10e+01 a.123.1.1 -1682 1q87A 221 3.14e+01 unknown_sccs -12028 1f2tB 148 3.18e+01 1f2tB 1eljA 381 3.19e+01 4mbp c.94.1.1 35791 1o57A 291 3.20e+01 unknown_sccs -249 c.61.1.1 -7960 1qgrA 876 3.23e+01 1qgrA a.118.1.1 19119 1q2wA 308 3.26e+01 b.47.1.4 88355 1fqtA 112 3.27e+01 1fqtA b.33.1.1 24441 1r5qA 102 3.27e+01 unknown_sccs -965 1n7oA 721 3.28e+01 a.102.3.2 80259 b.24.1.1 80260 b.30.5.2 80261 1iapA 211 3.30e+01 a.91.1.1 62119 1i0aA 466 3.35e+01 1auwA a.127.1.1 61479 1nn6A 228 3.36e+01 b.47.1.2 85893 1eguA 731 3.37e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.5.2 24423 1nxuA 333 3.43e+01 c.122.1.1 86389 1m6kA 251 3.43e+01 e.3.1.1 78695 1on2A 142 3.48e+01 a.4.5.24 87103 a.76.1.1 87104 1ayaA 101 3.50e+01 1qadA d.93.1.1 40460 1cf9A 753 3.51e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1gttA 429 3.54e+01 d.177.1.1 70529 d.177.1.1 70530 1lehA 364 3.54e+01 1bw9A c.2.1.7 30268 c.58.1.1 33916 1i7oA 429 3.58e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1k7wA 468 3.58e+01 a.127.1.1 72130 1na3A 91 3.59e+01 k.38.1.1 85481 1tiiD 99 3.62e+01 1tiiD b.40.2.1 24965 1e79A 510 3.65e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 2shpA 525 3.71e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1k0dA 260 3.72e+01 a.45.1.1 67930 c.47.1.5 67931 1unnC 115 3.83e+01 unknown_sccs -10216 1m0wA 491 3.87e+01 c.30.1.4 78363 d.142.1.6 78364 1h6zA 913 3.88e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1je8A 82 3.90e+01 a.4.6.2 77108 1kkhA 317 3.91e+01 d.14.1.5 72645 d.58.26.3 72646 1h8bA 75 3.95e+01 a.39.1.7 60736 1hy0A 466 4.00e+01 1auwA a.127.1.1 61392