# 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 1lq9A 112 1.04e-07 d.58.4.3 78129 1iujA 106 2.06e-07 unknown_sccs -9953 1q8bA 105 5.87e-04 unknown_sccs -9958 1q4rA 112 1.74e-03 d.58.4.4 -9943 1qysA 106 4.25e-03 unknown_sccs -13432 1q53A 112 1.53e-02 d.58.4.4 -9944 1cvjA 190 1.60e-02 1cvjB d.58.7.1 39191 d.58.7.1 39192 1fjcA 96 5.44e-02 1fjcA d.58.7.1 39212 1j5yA 187 5.45e-02 a.4.5.1 71592 d.94.2.1 71593 1cnt1 187 8.67e-02 1cnt3 1p8xA 344 9.85e-02 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1jmtA 104 1.22e-01 d.58.7.3 63180 1o0uA 429 2.32e-01 c.118.1.1 80743 1v02A 565 2.47e-01 1fjeB 175 2.61e-01 1fj7A d.58.7.1 39210 d.58.7.1 39211 1bm9A 122 2.75e-01 1bm9A a.4.5.7 16116 1qb0A 211 2.80e-01 1c25 c.46.1.1 32699 1j0wA 103 3.81e-01 b.55.1.2 -4364 1edt 271 5.70e-01 2ebn c.1.8.5 28993 1o6uA 403 7.33e-01 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1cbg 490 7.33e-01 1e70M c.1.8.4 28933 1bn6A 294 7.94e-01 1bn6A c.69.1.8 34678 1e44B 96 8.47e-01 1e44B b.101.1.1 59220 1fxlA 167 9.39e-01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1shdA 107 1.08e+00 1fmk d.93.1.1 40440 1a99A 344 1.14e+00 1pot c.94.1.1 35812 1sek 378 1.18e+00 1sek e.1.1.1 42675 1d0nA 729 1.19e+00 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1g8kA 825 1.22e+00 1g8jA b.52.2.2 26920 c.81.1.1 35328 1eny 268 1.36e+00 1eny c.2.1.2 29910 1v7oA 165 1.49e+00 unknown_sccs -10249 1a4iA 301 1.51e+00 1a4iA c.2.1.7 30278 c.58.1.2 33926 1f2fA 104 1.51e+00 1fmk d.93.1.1 40455 1zid 268 1.55e+00 1eny c.2.1.2 29911 1umhA 184 1.61e+00 unknown_sccs -3127 1aye 401 1.68e+00 1aye c.56.5.1 33824 d.58.3.1 39065 1h49A 512 1.70e+00 c.1.8.4 83477 1g8jA 825 1.71e+00 1g8jA b.52.2.2 26924 c.81.1.1 35332 1cnt3 187 1.72e+00 1cnt3 1e55A 512 1.75e+00 1e70M c.1.8.4 28934 1cqwA 295 1.76e+00 1b6g c.69.1.8 34679 1bn7A 294 1.77e+00 1bn6A c.69.1.8 34677 1f47B 144 1.82e+00 1f46A d.129.4.1 59645 1diaA 306 1.82e+00 1a4iA c.2.1.7 30280 c.58.1.2 33928 1dtdA 303 1.82e+00 1aye c.56.5.1 33823 1h9dB 134 1.95e+00 2jhbA b.54.1.1 60822 1o60A 292 1.97e+00 c.1.10.4 -5549 1sviA 195 2.01e+00 1f7wA 144 2.17e+00 1f46A d.129.4.1 59679 1ubeA 349 2.20e+00 c.37.1.11 88412 d.48.1.1 88413 1fi4A 416 2.23e+00 1fi4A d.14.1.5 59847 d.58.26.2 59848 1a4iB 301 2.26e+00 1a4iA c.2.1.7 30279 c.58.1.2 33927 1g60A 260 2.30e+00 c.66.1.11 70151 1cx0A 95 2.31e+00 1urnA d.58.7.1 39158 1b7fA 168 2.39e+00 1b7fA d.58.7.1 39169 d.58.7.1 39170 1o4rA 108 2.49e+00 d.93.1.1 -10624 1e50B 134 2.55e+00 2jhbA b.54.1.1 59245 1cvjB 190 2.58e+00 1cvjB d.58.7.1 39193 d.58.7.1 39194 1urnA 97 2.62e+00 1urnA d.58.7.1 39153 1f4kA 122 2.65e+00 1bm9A a.4.5.7 59646 1g7vA 284 2.65e+00 1d9eA c.1.10.4 60335 1isaA 192 2.67e+00 1avmA a.2.11.1 15731 d.44.1.1 38724 1iscA 192 2.68e+00 1avmA a.2.11.1 15733 d.44.1.1 38726 1d9eA 284 2.69e+00 1d9eA c.1.10.4 29195 3pbgA 468 2.70e+00 1e70M c.1.8.4 28951 1h2vZ 156 2.91e+00 d.58.7.1 76595 1g19A 350 2.91e+00 2reb c.37.1.11 32284 d.48.1.1 38770 1pbgA 468 3.03e+00 1e70M c.1.8.4 28946 1g7eA 122 3.08e+00 1g7eA c.47.1.7 33055 1f46A 140 3.14e+00 1f46A d.129.4.1 59643 1eikA 77 3.16e+00 1eikA d.78.1.1 39751 1b3tA 147 3.18e+00 1b3tA d.58.8.1 39228 1vjtA 483 3.19e+00 c.2.1.5 -5941 d.162.1.2 -11508 1c25 161 3.25e+00 1c25 c.46.1.1 32698 1shbA 104 3.26e+00 1fmk d.93.1.1 40425 1mwqA 101 3.36e+00 unknown_sccs -9962 1g0cA 364 3.37e+00 7a3hA c.1.8.3 60165 1shaA 104 3.45e+00 1fmk d.93.1.1 40424 1yprA 125 3.49e+00 3nul d.110.1.1 40888 1mo9A 523 3.55e+00 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1iibA 106 3.73e+00 1iibA c.44.2.1 32648 1tca 317 3.88e+00 1tca c.69.1.17 34726 1qpbA 563 3.89e+00 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 2u1a 88 4.00e+00 2u1a d.58.7.1 39164 1g01A 364 4.02e+00 7a3hA c.1.8.3 60161 2jhbA 143 4.17e+00 2jhbA b.54.1.1 26950 1egzA 291 4.23e+00 7a3hA c.1.8.3 28828 1o0pA 104 4.54e+00 d.58.7.1 86535 1ehiA 377 4.61e+00 1iow c.30.1.2 31716 d.142.1.1 41484 1fzdA 201 4.65e+00 3fib d.171.1.1 42484 1ro2A 216 4.71e+00 unknown_sccs -11391 1esgA 213 4.87e+00 1bam c.52.1.3 33286 1bam 213 4.87e+00 1bam c.52.1.3 33285 1jclA 260 4.90e+00 c.1.10.1 66501 1p1xA 260 5.07e+00 2scuB 388 5.19e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1cg2A 393 5.22e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 1ro0A 216 5.49e+00 unknown_sccs -11390 1bix 287 5.56e+00 1bix d.151.1.1 41781 1l9vA 317 6.27e+00 d.13.2.1 73760 d.216.1.1 73761 1d2kA 392 6.31e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 1pvdA 537 6.36e+00 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1ub1A 133 6.58e+00 d.10.1.3 -8969 1m5oC 100 6.60e+00 d.58.7.1 78654 1qfxA 460 6.62e+00 1qfxA c.60.1.2 33994 1pydA 556 6.62e+00 1zpdA c.31.1.3 31735 c.36.1.5 31773 c.36.1.9 31774 3sxlA 184 6.67e+00 1b7fA d.58.7.1 39173 d.58.7.1 39174 1js3A 486 6.75e+00 c.67.1.6 67215 1b06A 210 6.82e+00 1avmA a.2.11.1 15740 d.44.1.1 38737 1ll7A 392 6.82e+00 c.1.8.5 78085 d.26.3.1 78086 1q7sA 117 6.88e+00 unknown_sccs -7522 1vhiA 142 6.92e+00 1b3tA d.58.8.1 39230 1qk9A 92 7.10e+00 1qk9A d.10.1.3 37485 5gcnA 166 7.28e+00 1yghA d.108.1.1 40807 1bjx 110 7.28e+00 1bjx c.47.1.2 32774 2bjxA 110 7.28e+00 1bjx c.47.1.2 32776 1c4kA 730 7.46e+00 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 8rucI 123 7.57e+00 1rboC d.73.1.1 39629 1rboC 123 7.58e+00 1rboC d.73.1.1 39634 1k3eA 156 7.68e+00 d.198.1.1 68103 1qd1A 325 7.78e+00 1qd1A d.58.34.1 39493 d.58.34.1 39494 1cnt2 187 7.82e+00 1cnt3 1h70A 255 7.84e+00 1h70A d.126.1.3 60711 1gqeA 365 7.90e+00 e.38.1.1 70351 1h5wA 309 8.07e+00 e.27.1.1 65635 1ordA 730 8.39e+00 1ordA c.23.1.4 31274 c.67.1.5 34503 d.125.1.1 41124 1jae 471 8.67e+00 1smd b.71.1.1 27773 c.1.8.1 28760 2ptd 298 8.91e+00 2plc c.1.18.2 29605 1va4A 279 9.14e+00 1ez0A 510 9.22e+00 1eyyA c.82.1.1 35385 1n13B 113 9.82e+00 1vjzA 341 9.91e+00 c.1.8.3 -5318 1j27A 102 9.96e+00 unknown_sccs -10116 1m4jA 142 1.06e+01 d.109.1.2 78602 1mb4A 370 1.08e+01 c.2.1.3 78908 d.81.1.1 78909 1pgx 83 1.08e+01 2igd d.15.7.1 37823 1igd 61 1.09e+01 2igd d.15.7.1 37822 2igd 61 1.09e+01 2igd d.15.7.1 37821 1on0A 158 1.09e+01 d.108.1.1 87095 1ufhA 180 1.11e+01 d.108.1.1 88485 1j6uA 469 1.11e+01 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1mup 166 1.12e+01 1mup b.60.1.1 27133 1e6qM 501 1.13e+01 1e70M c.1.8.4 28920 1cb2A 365 1.14e+01 1bvwA c.6.1.1 30661 3bamA 213 1.18e+01 1bam c.52.1.3 33288 1fsu 492 1.20e+01 1auk c.76.1.2 35032 3bamB 213 1.21e+01 1bam c.52.1.3 33289 1bag 425 1.23e+01 1bag b.71.1.1 27720 c.1.8.1 28707 1miuA 738 1.23e+01 a.170.1.1 79153 a.171.1.1 79154 b.40.4.3 79155 b.40.4.3 79156 b.40.4.3 79157 1e4mM 501 1.25e+01 1e70M c.1.8.4 59226 1e70M 501 1.25e+01 1e70M c.1.8.4 28926 1nw8A 319 1.26e+01 c.66.1.11 86292 1uuqA 440 1.27e+01 c.1.8.3 -5321 1ltqA 301 1.28e+01 c.108.1.9 78208 c.37.1.1 78209 1mkeA 152 1.30e+01 b.55.1.4 79231 1c4zA 358 1.31e+01 1c4zA d.148.1.1 41766 1e4iA 447 1.32e+01 1e70M c.1.8.4 59225 1pyaB 228 1.32e+01 1pyaB 1g7cB 94 1.32e+01 1b64 d.58.12.1 39308 1im8A 244 1.33e+01 c.66.1.14 66212 1mp9A 198 1.33e+01 a.74.1.2 -1127 a.74.1.2 -1128 1oef 24 1.36e+01 j.39.1.1 46299 1jv4A 162 1.37e+01 b.60.1.1 67343 1lk5A 229 1.39e+01 unknown_sccs 73960 d.58.40.1 73961 1i06A 180 1.41e+01 1mup b.60.1.1 27131 1df3A 162 1.43e+01 1mup b.60.1.1 27134 1i05A 180 1.45e+01 1mup b.60.1.1 27130 1eyyA 510 1.48e+01 1eyyA c.82.1.1 35389 1qjwA 365 1.48e+01 1bvwA c.6.1.1 30657 1bhgA 613 1.48e+01 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1fgyA 127 1.49e+01 1faoA b.55.1.1 26976 1ijgA 309 1.54e+01 1fouA e.27.1.1 62493 1irf 112 1.55e+01 2irfG a.4.5.23 16192 1ibvB 229 1.56e+01 1eg2A 319 1.57e+01 1eg2A c.66.1.11 34249 1q1oA 98 1.58e+01 d.15.2.2 -9172 1gk8I 140 1.60e+01 d.73.1.1 65242 1qy1A 174 1.60e+01 b.60.1.1 -4445 1gy8A 397 1.61e+01 c.2.1.2 83376 1mml 265 1.62e+01 1mml e.8.1.2 43015 1di0A 158 1.67e+01 1di0A c.16.1.1 30957 1chmA 401 1.67e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 1ako 268 1.70e+01 1ako d.151.1.1 41779 1rgxA 114 1.70e+01 1colA 204 1.72e+01 1a87 f.1.1.1 43378 1ucdA 190 1.75e+01 1bk7A 190 1.75e+01 1bk7A d.124.1.1 41121 1ovnA 248 1.76e+01 a.71.1.1 -1096 c.47.1.7 -7477 1ucaA 190 1.78e+01 d.124.1.1 88462 1edqA 540 1.79e+01 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 1k9tA 540 1.80e+01 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1dioB 224 1.82e+01 1dioB c.51.3.1 33219 1a8s 273 1.83e+01 1brt c.69.1.12 34710 1ctn 540 1.85e+01 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1a3h 300 1.89e+01 7a3hA c.1.8.3 28819 7a3hA 303 1.89e+01 7a3hA c.1.8.3 28817 1l3kA 196 1.91e+01 d.58.7.1 73539 d.58.7.1 73540 1eexB 224 1.92e+01 1dioB c.51.3.1 33213 1jcjA 260 1.95e+01 c.1.10.1 66499 1o7nB 194 2.01e+01 d.17.4.4 81164 2fmr 65 2.01e+01 2fmr d.51.1.1 38808 1eg9B 194 2.04e+01 1ndoB d.17.4.4 38120 1lylA 504 2.06e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1ff9A 450 2.07e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1akz 223 2.08e+01 3eugA c.18.1.1 31007 1forL 210 2.08e+01 8fabA b.1.1.1 19988 b.1.1.2 21044 1ndoB 194 2.09e+01 1ndoB d.17.4.4 38121 1sspE 223 2.11e+01 3eugA c.18.1.1 31009 1jl0A 334 2.12e+01 1jenA d.156.1.1 63155 1jenA 267 2.16e+01 1jenA 1htwA 158 2.16e+01 c.37.1.18 71083 1rkuA 206 2.17e+01 unknown_sccs -6823 1krhA 338 2.19e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1mszA 86 2.20e+01 d.68.7.1 79428 1ptmA 329 2.21e+01 unknown_sccs -8456 1pls 113 2.22e+01 1pls b.55.1.1 26965 1bob 320 2.22e+01 1bob d.108.1.1 40816 1lt8A 406 2.24e+01 c.1.26.1 78186 1h5vA 304 2.26e+01 c.1.8.3 70898 1q7zA 566 2.32e+01 c.1.21.2 -5638 c.1.26.1 -5666 1r8hA 87 2.32e+01 d.58.8.1 -10041 1tufA 434 2.35e+01 1a48 306 2.36e+01 1a48 d.143.1.1 41590 1v1aA 309 2.38e+01 c.72.1.1 -8400 1uedA 406 2.39e+01 a.104.1.1 -1459 1btkB 169 2.40e+01 1btkA b.55.1.1 26960 3c2c 112 2.41e+01 1ycc a.3.1.1 15885 1acc 735 2.42e+01 1acc f.11.1.1 43828 1trkA 680 2.43e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1p27B 106 2.44e+01 d.58.7.1 -10020 1egxA 115 2.45e+01 1evhA b.55.1.4 27000 1k9dA 679 2.48e+01 c.1.8.10 77292 d.92.2.2 77293 1iv0A 98 2.49e+01 unknown_sccs -7667 1kp9B 287 2.52e+01 c.66.1.18 68734 1svy 114 2.55e+01 1svy d.109.1.1 40831 1gpuA 680 2.62e+01 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1ufaA 520 2.64e+01 unknown_sccs -421 unknown_sccs -6065 1kpgA 287 2.68e+01 c.66.1.18 68735 1mwpA 96 2.68e+01 1mwpA d.170.2.1 42453 1hi9A 274 2.69e+01 1hi9A c.99.1.1 61063 1b73A 254 2.75e+01 1b74A c.78.2.1 35266 c.78.2.1 35267 3cbh 365 2.76e+01 1bvwA c.6.1.1 30665 1uroA 367 2.76e+01 1uroA c.1.22.1 29675 1f53A 84 2.76e+01 1f53A b.11.1.4 23632 1jpaA 312 2.78e+01 d.144.1.7 67011 1i6kA 328 2.81e+01 c.26.1.1 66040 1tkaA 678 2.83e+01 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 1r3sA 367 2.84e+01 c.1.22.1 -5648 1pk6B 132 2.85e+01 b.22.1.1 -3290 1es4A 262 2.87e+01 1skf e.3.1.1 42683 1l8nA 679 2.88e+01 c.1.8.10 84564 d.92.2.2 84565 1itwA 741 2.89e+01 c.77.1.2 76793 1twdA 256 2.92e+01 1urrA 102 2.96e+01 1avpA 204 2.97e+01 1avpA d.3.1.7 37132 1qb7A 236 2.98e+01 1qb7A c.61.1.1 34087 2irfG 113 3.00e+01 2irfG a.4.5.23 16185 1vhmA 195 3.03e+01 d.110.2.1 -10828 1qvbA 481 3.06e+01 1qvbA c.1.8.4 28983 1mkmA 249 3.07e+01 a.4.5.33 79242 d.110.2.2 79243 1n82A 331 3.08e+01 c.1.8.3 -5306 1otgA 125 3.10e+01 1otgA d.80.1.2 39831 1ve9A 347 3.11e+01 c.4.1.2 -6056 d.16.1.3 -9214 1ddwA 120 3.11e+01 1evhA b.55.1.4 27001 1bg0 356 3.12e+01 1qh4A a.83.1.1 18476 d.128.1.2 41211 1on3A 523 3.13e+01 c.14.1.4 87107 c.14.1.4 87108 1lvmA 229 3.16e+01 b.47.1.3 78243 1aapA 58 3.18e+01 1bpi g.8.1.1 44543 1j5uA 136 3.20e+01 d.208.1.1 71584 2prd 174 3.23e+01 2prd b.40.5.1 25435 1tux 301 3.23e+01 1taxA c.1.8.3 28907 1pvuA 154 3.23e+01 3pviA c.52.1.6 33306 1tr1A 447 3.26e+01 1e70M c.1.8.4 28957 1fo5A 85 3.28e+01 1fo5A c.47.1.1 59922 1pyfA 312 3.29e+01 c.1.7.1 -5251 1t2aA 375 3.29e+01 c.2.1.2 -5764 1fmk 452 3.30e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.7 41690 1sy3A 184 3.33e+01 1oen 540 3.33e+01 1ayl c.91.1.1 64750 c.109.1.1 64751 1an9A 340 3.36e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1aa8A 347 3.39e+01 1an9A 1mjgM 729 3.39e+01 e.26.1.3 79204 1s7jA 262 3.40e+01 d.21.1.2 -9424 1oaoC 729 3.41e+01 e.26.1.3 86746 1obdA 306 3.41e+01 d.143.1.1 86767 1ly1A 181 3.43e+01 c.37.1.1 74334 1usmA 80 3.45e+01 d.74.1.1 -10334 1cb0A 283 3.46e+01 1cb0A c.56.2.1 33790 1mjhA 162 3.51e+01 1mjhA c.26.2.4 31639 1icxA 155 3.55e+01 d.129.3.1 71191 1knt 58 3.60e+01 1bpi g.8.1.1 44538 3pviA 157 3.60e+01 3pviA c.52.1.6 33300 1cuk 203 3.60e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1sb8A 352 3.62e+01 1atiA 505 3.64e+01 1atiA c.51.1.1 33196 d.104.1.1 40745 1uc8A 280 3.67e+01 unknown_sccs -6718 unknown_sccs -11230 1koiA 184 3.72e+01 b.60.1.1 68725 1erxA 184 3.74e+01 1np1A b.60.1.1 27164 1f60B 94 3.77e+01 1b64 d.58.12.1 39307 1atiB 505 3.77e+01 1atiA c.51.1.1 33197 d.104.1.1 40746 1s2dA 167 3.79e+01 c.23.14.1 -6469 1af7 274 3.80e+01 1af7 a.58.1.1 17928 c.66.1.8 34203 1dciA 275 3.81e+01 1dciA c.14.1.3 30918 1jndA 420 3.81e+01 c.1.8.5 71757 d.26.3.1 71758 1ps9A 671 3.88e+01 c.1.4.1 -5206 3minB 522 3.92e+01 1qguB c.92.2.3 35606 1obbA 480 3.93e+01 c.2.1.5 86760 d.162.1.2 86761 1n2zA 245 3.94e+01 c.92.2.2 79865