# 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 1ju2A 536 1.70e-02 c.3.1.2 77169 d.16.1.1 77170 1trb 320 1.28e-01 1trb c.3.1.5 30529 c.3.1.5 30530 1qopB 396 2.57e-01 2tysB c.79.1.1 35270 1f3lA 321 2.75e-01 1g6q2 c.66.1.6 59630 1f60A 458 3.06e-01 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1j0aA 325 3.10e-01 c.79.1.1 83871 1chuA 540 3.17e-01 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1gal 583 3.90e-01 1gpeA c.3.1.2 30386 d.16.1.1 37950 1jztA 246 5.50e-01 c.104.1.1 63319 2pfkA 320 6.84e-01 3pfk c.89.1.1 35577 1pwhA 327 6.84e-01 1qhoA 686 6.93e-01 1cxlA b.1.18.2 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1ng4A 390 7.98e-01 c.3.1.2 85666 d.16.1.3 85667 1gpeA 587 8.31e-01 1gpeA c.3.1.2 30387 d.16.1.1 37951 1pj5A 830 1.06e+00 1jnyA 435 1.08e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 4pfk 319 1.11e+00 3pfk c.89.1.1 35582 1dpgA 485 1.16e+00 1dpgA c.2.1.3 30074 d.81.1.5 39989 1k1xA 659 1.35e+00 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1pamA 686 1.44e+00 1cxlA b.1.18.2 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1eiwA 111 1.45e+00 1eiwA c.23.3.1 31130 1p5jA 372 1.58e+00 1gsoA 431 1.66e+00 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1ii7A 333 1.72e+00 1ii7A d.159.1.4 62415 1v4vA 376 1.93e+00 1fl2A 310 2.16e+00 1hyuA c.3.1.5 59869 c.3.1.5 59870 3pmgA 561 2.33e+00 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1afwA 393 2.36e+00 1afwA c.95.1.1 35900 c.95.1.1 35901 1gesA 450 2.44e+00 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1ha3A 405 2.91e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1kgsA 225 2.99e+00 a.4.6.1 68596 c.23.1.1 68597 1kdgA 546 3.14e+00 c.3.1.2 77337 d.16.1.1 77338 1hdkA 141 3.25e+00 b.29.1.3 65807 6ldh 330 3.26e+00 3ldh c.2.1.5 30161 d.162.1.1 42128 1f6dA 376 3.28e+00 1f6dA c.87.1.3 35467 1hyeA 313 3.37e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1qrrA 394 3.41e+00 1qrrA c.2.1.2 29824 1d2eA 397 3.65e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1rcuA 195 3.74e+00 1ooeA 236 3.79e+00 c.2.1.2 87196 1s0uA 408 3.94e+00 1d2sA 170 3.99e+00 1d2sA b.29.1.4 24221 1inlA 296 4.07e+00 c.66.1.17 66220 1ps9A 671 4.19e+00 1fecA 490 4.24e+00 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1uirA 314 4.47e+00 1r9gA 216 4.58e+00 1kq3A 376 4.65e+00 e.22.1.2 68790 1lcl 142 4.67e+00 1lcl b.29.1.3 24216 1nzhA 282 4.76e+00 1gy8A 397 4.78e+00 c.2.1.2 83376 1jg1A 235 4.78e+00 c.66.1.7 66661 1ojaA 520 4.97e+00 1exmA 405 5.01e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1o0wA 252 5.55e+00 a.149.1.1 80751 d.50.1.1 80752 1g291 372 5.75e+00 1g291 3grs 478 5.95e+00 3grs c.3.1.5 30441 c.3.1.5 30442 d.87.1.1 40152 1kshB 152 6.40e+00 b.1.18.8 72915 1rliA 184 6.59e+00 1ei9A 279 6.62e+00 1ei9A c.69.1.13 34713 1uhvA 500 6.68e+00 1bu8A 452 6.70e+00 1gpl b.12.1.2 23647 c.69.1.19 34795 1kqzA 273 6.92e+00 c.1.8.5 68844 1kssA 571 6.94e+00 a.138.1.3 72928 c.3.1.4 72929 d.168.1.1 72930 1d3cA 686 6.99e+00 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721 1q9iA 571 7.11e+00 1jl3A 139 7.27e+00 c.44.1.1 66826 1nhp 447 7.30e+00 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1m6iA 493 7.49e+00 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1s3iA 310 7.71e+00 1vddA 228 7.86e+00 1nhs 447 7.95e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1e39A 571 7.97e+00 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1jrrA 382 8.13e+00 e.1.1.1 63256 1f5fA 205 8.15e+00 1d2sA b.29.1.4 24222 1ou0A 207 8.45e+00 1eokA 290 8.47e+00 1eokA c.1.8.5 28991 1ek6A 348 8.53e+00 1xel c.2.1.2 29800 1uqxA 113 9.68e+00 1ig3A 263 9.76e+00 1ig3A b.82.6.1 62358 c.100.1.1 62359 1jae 471 9.80e+00 1smd b.71.1.1 27773 c.1.8.1 28760 1k5jA 124 9.80e+00 b.121.3.1 68201 1s3eA 520 1.00e+01 1sr9A 644 1.02e+01 1rj8A 164 1.03e+01 1pswA 348 1.08e+01 c.87.1.7 88287 1a9xB 379 1.09e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1cf2O 337 1.09e+01 1b7gO c.2.1.3 29994 d.81.1.1 39909 1i24A 404 1.10e+01 c.2.1.2 83663 1kewA 361 1.11e+01 c.2.1.2 68544 1q7fA 286 1.14e+01 2cuaA 135 1.15e+01 2cuaA b.6.1.2 23039 1ju3A 583 1.16e+01 b.18.1.13 67300 c.69.1.21 67301 1kqfA 1015 1.17e+01 b.52.2.2 72871 c.81.1.1 72872 1pmi 440 1.17e+01 1pmi b.82.1.3 28114 3il8 72 1.22e+01 1tvxA d.9.1.1 37356 1qhdA 398 1.27e+01 1qhdA a.115.1.2 63324 b.19.1.1 63325 4pgaA 337 1.32e+01 4pgaA c.88.1.1 35565 1dhs 344 1.32e+01 1dhs c.31.1.1 31727 2fcr 173 1.36e+01 1rcf c.23.5.1 31151 1o9wA 177 1.39e+01 b.2.3.5 86713 1oi7A 288 1.41e+01 c.2.1.8 87049 c.23.4.1 87050 1srrA 124 1.45e+01 1dz3A c.23.1.1 31110 1b5qA 472 1.50e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1e2tA 284 1.50e+01 1e2tA d.3.1.5 37121 1nofA 383 1.52e+01 1lj8A 493 1.55e+01 a.100.1.9 78033 c.2.1.6 78034 1nnsA 326 1.56e+01 c.88.1.1 85910 1a3k 137 1.57e+01 1a3k b.29.1.3 24218 1l3iA 192 1.58e+01 c.66.1.22 77676 1t82A 155 1.62e+01 1lk5A 229 1.77e+01 c.35.1.2 73960 d.58.40.1 73961 1o1yA 239 1.77e+01 c.23.16.1 86554 2hgsA 474 1.78e+01 2hgsA c.30.1.4 31722 d.142.1.6 75997 1je6A 275 1.79e+01 b.1.1.2 71638 d.19.1.1 71639 4pep 326 1.81e+01 1smrA b.50.1.2 26843 1d7yA 408 1.86e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1j9lA 247 1.86e+01 c.106.1.1 62762 1cb8A 678 1.88e+01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1f2vA 219 1.93e+01 1f2vA c.23.17.1 59627 1bg6 359 1.94e+01 1bg6 a.100.1.5 18810 c.2.1.6 30214 1mvoA 136 1.99e+01 c.23.1.1 79513 7taa 478 2.02e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1fp2A 352 2.06e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 2aaa 484 2.07e+01 7taa b.71.1.1 27777 c.1.8.1 28764 1ehiA 377 2.09e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1i1nA 226 2.12e+01 c.66.1.7 71102 1a04A 215 2.17e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1ift 263 2.23e+01 1mrj d.165.1.1 42211 1q1rA 431 2.26e+01 1ivnA 190 2.27e+01 c.23.10.5 83719 1reoA 486 2.29e+01 1rybA 212 2.32e+01 1lt8A 406 2.35e+01 c.1.26.1 78186 1pjr 724 2.37e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 3ladA 476 2.39e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1ktbA 405 2.39e+01 b.71.1.1 72960 c.1.8.1 72961 1wab 232 2.41e+01 1wab c.23.10.3 31341 1es9A 232 2.43e+01 1wab c.23.10.3 31340 1pk6C 129 2.43e+01 1dcfA 136 2.45e+01 1dcfA c.23.1.2 31124 1h7wA 1025 2.46e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1gteA 1025 2.50e+01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1brwA 433 2.54e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1o0uA 429 2.55e+01 c.118.1.1 80743 1m2dA 110 2.56e+01 c.47.1.11 78476 1g2iA 166 2.58e+01 1g2iA c.23.16.2 31438 1el5A 389 2.59e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1r64A 481 2.61e+01 1aqm 453 2.63e+01 1smd b.71.1.1 27717 c.1.8.1 28704 1ewkA 490 2.64e+01 1ewkA c.93.1.1 35712 1mkfA 382 2.64e+01 b.116.1.1 79232 1lv7A 257 2.65e+01 c.37.1.20 78232 1sek 378 2.69e+01 1sek e.1.1.1 42675 1g94A 448 2.74e+01 b.71.1.1 65169 c.1.8.1 65170 1i7qB 193 2.74e+01 1qdlB c.23.16.1 61902 1uq5A 263 2.82e+01 1ca1 370 2.87e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1rl2A 137 2.91e+01 1rl2A b.34.5.3 24610 b.40.4.5 25342 1qmgA 524 2.93e+01 1qmgA a.100.1.2 18785 c.2.1.6 30182 1j1yA 136 2.95e+01 1scuA 288 3.02e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1ne2A 200 3.02e+01 c.66.1.32 85586 1nni1 174 3.02e+01 1fsoA 139 3.08e+01 1rhoA b.1.18.8 60007 1esmA 316 3.13e+01 1esmA c.37.1.6 31953 2hvm 273 3.13e+01 1cnv c.1.8.5 28985 1lqvA 193 3.14e+01 d.19.1.1 74206 1m0wA 491 3.15e+01 c.30.1.4 78363 d.142.1.6 78364 1iyeA 309 3.17e+01 e.17.1.1 83786 1uctA 218 3.18e+01 b.1.1.4 88467 b.1.1.4 88468 1d3gA 367 3.18e+01 1d3gA c.1.4.1 28600 1uebA 184 3.23e+01 1qyaA 307 3.24e+01 1r5jA 337 3.24e+01 1mjfA 281 3.32e+01 c.66.1.17 79198 1egaA 301 3.38e+01 1egaA c.37.1.8 32150 d.52.3.1 38836 1ff9A 450 3.42e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1sfp 114 3.46e+01 1sfp b.23.1.1 23895 1f37A 110 3.47e+01 1f37A c.47.1.11 33088 1e25A 282 3.50e+01 1e25A e.3.1.1 42731 1php 394 3.54e+01 16pk c.86.1.1 35452 1gp1A 198 3.54e+01 1gp1A c.47.1.10 33059 1b7gO 340 3.54e+01 1b7gO c.2.1.3 29992 d.81.1.1 39907 1i1kA 309 3.55e+01 1daaA e.17.1.1 61533 1oxcA 114 3.61e+01 1kjqA 391 3.62e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1ukz 203 3.65e+01 1zin c.37.1.1 31840 1k7hA 476 3.74e+01 c.76.1.1 72101 1garA 212 3.76e+01 2gar c.65.1.1 34162 1t2dA 322 3.76e+01 1uj2A 252 3.79e+01 1crzA 403 3.81e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1kk1A 410 3.88e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1qs1A 462 3.89e+01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1v7rA 186 3.90e+01 1gsmA 210 3.92e+01 b.1.1.4 65535 b.1.1.4 65536 1o7jA 327 3.92e+01 c.88.1.1 81140 1sdjA 310 3.93e+01 1mxtA 504 3.96e+01 c.3.1.2 79671 d.16.1.1 79672 1gbg 214 3.96e+01 1axkA b.29.1.2 24171 1n4wA 504 3.98e+01 1h30A 422 3.98e+01 b.29.1.4 76604 b.29.1.4 76605