# List of top-scoring protein chains for t2k-100-30-alpha 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 1qmzB 259 3.16e-02 1vin a.74.1.1 18338 a.74.1.1 18339 1vin 268 5.23e-02 1vin a.74.1.1 18354 a.74.1.1 18355 1ku0A 388 1.17e-01 1a48 306 2.74e-01 1a48 d.143.1.1 41590 1fo1A 271 3.47e-01 1fo1A c.10.2.3 30869 d.58.7.2 39213 1jkw 323 3.63e-01 1jkw a.74.1.1 18356 a.74.1.1 18357 1i3dA 146 4.89e-01 a.1.1.2 61587 1huqA 164 6.89e-01 1byuA c.37.1.8 32020 1lqvA 193 7.83e-01 1kxu 333 8.92e-01 1jkw a.74.1.1 18358 a.74.1.1 18359 1mrp 309 9.86e-01 1mrp c.94.1.1 35796 1jjoC 261 1.03e+00 1qm9A 198 1.20e+00 1qm9A d.58.7.1 39207 d.58.7.1 39208 2cgpA 210 1.50e+00 2cgpA a.4.5.4 16102 b.82.3.2 28141 1d8wA 426 1.62e+00 1de5A c.1.15.2 29394 1kbqA 273 1.86e+00 c.23.5.3 68391 2gar 212 1.90e+00 2gar c.65.1.1 34161 1d4aA 273 1.94e+00 1d4aA c.23.5.3 31219 1fsu 492 1.94e+00 1auk c.76.1.2 35032 1d3yA 301 1.98e+00 1d3yA e.12.1.1 43252 1cx4A 305 1.98e+00 b.82.3.2 59099 b.82.3.2 59100 1cleA 534 2.04e+00 1thg c.69.1.17 34771 1bu2A 229 2.35e+00 1bu2A a.74.1.1 18360 a.74.1.1 18361 1iciA 256 2.35e+00 1iciA c.31.1.5 62266 1garA 212 2.35e+00 2gar c.65.1.1 34162 1booA 323 3.34e+00 1booA c.66.1.11 34248 1g6gA 127 3.45e+00 1g6gA b.26.1.2 23916 1au1A 166 3.53e+00 1ifa a.26.1.3 16889 1ntr 124 3.55e+00 1dbwA c.23.1.1 31092 1irdB 146 3.74e+00 a.1.1.2 66287 1qumA 285 3.75e+00 1qumA c.1.15.1 29393 1qtwA 285 4.13e+00 1qumA c.1.15.1 29392 1larA 575 4.42e+00 1larA c.45.1.2 32693 c.45.1.2 32694 1l4aD 87 4.57e+00 1iwhB 146 4.92e+00 1spgA 144 5.01e+00 1abwA a.1.1.2 15409 1kqfC 217 5.50e+00 1g3gA 164 5.58e+00 1g6gA b.26.1.2 23918 1hw5A 210 5.78e+00 2cgpA a.4.5.4 16098 b.82.3.2 28137 1dxtB 147 5.79e+00 1abwA a.1.1.2 15450 1babB 146 5.95e+00 1abwA a.1.1.2 15414 1zpdA 568 6.14e+00 1zpdA c.31.1.3 31741 c.36.1.1 31785 c.36.1.1 31786 1jkxA 212 6.15e+00 c.65.1.1 66813 1ki0A 253 7.08e+00 1de5A 426 7.26e+00 1de5A c.1.15.2 29402 1qopB 396 7.58e+00 2tysB c.79.1.1 35270 1jjtA 228 7.63e+00 1a7tA d.157.1.1 63139 1i36A 264 7.66e+00 1j6nA 303 7.83e+00 1qqfA 277 7.92e+00 1c3d a.102.4.4 18875 1dvoA 152 8.01e+00 1dvoA a.136.1.1 19623 3rabA 169 8.02e+00 1ctqA c.37.1.8 32018 1bksB 397 8.04e+00 2tysB c.79.1.1 35285 1tl2A 236 8.11e+00 1tl2A b.67.1.1 27541 1dd6A 228 8.13e+00 1a7tA d.157.1.1 42054 1l0wA 580 8.41e+00 1qu9A 128 8.57e+00 1qu9A d.79.1.1 39755 1qu9C 128 8.57e+00 1qu9A d.79.1.1 39757 1btkA 169 8.62e+00 1btkA b.55.1.1 26959 1khdA 345 8.65e+00 1a8o 70 8.97e+00 1a8o a.28.3.1 16953 1bd3A 243 9.05e+00 1bd3A c.61.1.1 34098 1gxqA 106 9.75e+00 1d1nA 99 9.89e+00 1d1nA b.43.3.1 25718 1f82A 424 9.99e+00 1f82A d.92.1.7 40307 1de6A 426 1.01e+01 1de5A c.1.15.2 29398 1d0qA 103 1.04e+01 1d0qA g.41.3.2 45208 1psdA 409 1.07e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1fhjB 146 1.08e+01 1abwA a.1.1.2 59838 1gcvA 140 1.11e+01 1cg5B a.1.1.2 15410 1ksfX 758 1.15e+01 1fpzA 212 1.16e+01 1fpzA c.45.1.1 59976 1obwA 175 1.20e+01 2prd b.40.5.1 25416 1crl 534 1.23e+01 1thg c.69.1.17 34765 1krhA 338 1.26e+01 1jakA 512 1.32e+01 c.1.8.6 66472 d.92.2.1 66473 1hp5A 512 1.34e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1qvbA 481 1.34e+01 1qvbA c.1.8.4 28983 1dysA 348 1.34e+01 1bvwA c.6.1.1 30669 1k2eA 156 1.35e+01 1hp4A 512 1.38e+01 1hp4A c.1.8.6 61111 d.92.2.1 61112 1f83A 425 1.39e+01 1f82A d.92.1.7 40306 1fg7A 356 1.42e+01 1gewA c.67.1.1 59819 1qlpA 394 1.42e+01 1ovaA e.1.1.1 42628 1g99A 408 1.43e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1d7qA 143 1.46e+01 1d7qA b.40.4.5 25331 1qqiA 104 1.49e+01 1opc a.4.6.1 16233 1ci6B 63 1.58e+01 1ci6B h.1.3.1 45549 1kit 757 1.61e+01 1kit b.29.1.8 24272 b.29.1.8 24273 b.68.1.1 27616 1ehiA 377 1.64e+01 1iow c.30.1.2 31716 d.142.1.1 41484 2tysB 397 1.65e+01 2tysB c.79.1.1 35272 1ii7A 333 1.68e+01 1ii7A d.159.1.4 62415 1e5eA 404 1.70e+01 1ibjA c.67.1.3 59265 1f5mA 180 1.70e+01 1f5mB d.110.2.1 40895 1e0tA 470 1.75e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1gewA 356 1.77e+01 1gewA c.67.1.1 60470 1g8fA 511 1.84e+01 1g8fA b.58.1.2 60348 c.26.1.5 60349 c.37.1.15 60350 1edzA 320 1.86e+01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1pmi 440 1.91e+01 1pmi b.82.1.3 28114 1qk3A 233 1.92e+01 1qk3A c.61.1.1 34031 1bw0A 416 1.98e+01 1bw0A c.67.1.1 34385 1bmx 31 1.99e+01 1bmx j.47.1.1 46326 1lddA 74 2.00e+01 1e39A 571 2.04e+01 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1in6A 334 2.07e+01 1hqcA a.4.5.11 62601 c.37.1.13 62602 1qs2A 401 2.12e+01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1de4C 640 2.16e+01 1cx8B a.48.2.1 17779 c.8.4.1 30760 c.56.5.5 33848 1f5mB 180 2.17e+01 1f5mB d.110.2.1 40896 1i7dA 659 2.19e+01 1d6mA e.10.1.1 61886 1qdlA 422 2.21e+01 1qdlA d.161.1.1 42088 1cx8B 639 2.22e+01 1cx8B a.48.2.1 17783 c.8.4.1 30764 c.56.5.5 33852 1j5pA 253 2.22e+01 1itf 165 2.25e+01 1b5l a.26.1.3 16899 1fioA 196 2.26e+01 1fioA a.47.2.1 17773 1ifa 158 2.30e+01 1ifa a.26.1.3 16892 1iwgA 1053 2.31e+01 1jw3A 140 2.33e+01 d.208.1.1 67373 2prd 174 2.34e+01 2prd b.40.5.1 25435 1i40A 175 2.39e+01 b.40.5.1 66024 1exkA 79 2.46e+01 1exkA g.54.1.1 45384 4mbp 370 2.47e+01 4mbp c.94.1.1 35777 1dusA 194 2.49e+01 1dusA c.66.1.4 34182 1skyE 473 2.49e+01 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1ee9A 320 2.50e+01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1ktgA 138 2.56e+01 1kyoA 430 2.57e+01 2wsyB 396 2.60e+01 2tysB c.79.1.1 35288 1k26A 156 2.64e+01 1j58A 385 2.65e+01 1aorA 605 2.67e+01 1b25A a.110.1.1 19042 d.152.1.1 41794 1qa7B 217 2.67e+01 1havA b.47.1.4 26426 1iam 185 2.67e+01 1zxq b.1.1.3 21653 b.1.1.4 21689 1io2A 213 2.68e+01 1ekeA c.55.3.1 62612 2arcA 164 2.69e+01 2arcA b.82.4.1 28148 1d4xG 126 2.71e+01 1d0nA d.109.1.1 59109 1gcvB 136 2.71e+01 1cg5B a.1.1.2 15589 1dmhA 311 2.72e+01 1dmhA b.3.6.1 22633 1jeqB 565 2.74e+01 1jeqB e.31.1.2 62922 1jeyB 565 2.77e+01 1jeqB e.31.1.2 62925 1cl7I 82 2.81e+01 1igtB 1kssA 571 2.86e+01 2arcB 164 2.87e+01 2arcA b.82.4.1 28149 1cf3A 583 2.88e+01 1gpeA c.3.1.2 30385 d.16.1.4 37949 1toh 343 2.88e+01 4pah d.178.1.1 42573 1btkB 169 2.91e+01 1btkA b.55.1.1 26960 1m1cA 680 2.93e+01 1anf 370 2.93e+01 4mbp c.94.1.1 35776 1lvaA 258 2.94e+01 1i50C 318 2.95e+01 d.74.3.1 61756 d.181.1.1 61757 1irk 306 2.98e+01 1fmk d.144.1.2 41703 1eyyA 510 2.99e+01 1eyyA c.82.1.1 35389 2sas 185 3.04e+01 2sas a.39.1.5 17258 1itm 130 3.06e+01 1rcb a.26.1.2 16858 1ez0A 510 3.07e+01 1eyyA c.82.1.1 35385 1eo6A 117 3.10e+01 1eo6A d.15.1.3 37609 1jj2P 95 3.12e+01 1ffkN b.34.5.1 63101 1sek 378 3.16e+01 1sek e.1.1.1 42675 1h89A 64 3.19e+01 h.1.3.1 65724 1b37B 472 3.23e+01 1b37B c.3.1.2 30390 d.16.1.5 37954 1b5qA 472 3.24e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1opy 131 3.27e+01 1opy d.17.4.3 38113 1ecl 597 3.29e+01 1ecl e.10.1.1 43238 1ezvA 430 3.30e+01 1be3A d.185.1.1 59541 d.185.1.1 59542 1jrkA 156 3.30e+01 1g3qA 237 3.31e+01 1hyqA c.37.1.10 60237 1mfiA 114 3.31e+01 1dptA d.80.1.3 39856 1cx8A 639 3.32e+01 1cx8B a.48.2.1 17782 c.8.4.1 30763 c.56.5.5 33851 1g72B 69 3.37e+01 4aahB a.137.2.1 19627 1b37A 472 3.37e+01 1b37B c.3.1.2 30389 d.16.1.5 37953 1g8pA 350 3.37e+01 1g8pA c.37.1.13 60376 1aj8A 371 3.38e+01 1aj8A a.103.1.1 18900 1ffkQ 119 3.44e+01 1ffkQ b.34.5.1 24605 1j7nB 776 3.47e+01 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1rmi 160 3.48e+01 1ifa a.26.1.3 16891 1ffkN 95 3.51e+01 1ffkN b.34.5.1 24606 1h4wA 224 3.54e+01 b.47.1.2 65622 1khbA 625 3.54e+01 c.91.1.1 68606 c.109.1.1 68607 1tyv 542 3.57e+01 1tyv b.80.1.6 28038 1dtgA 334 3.60e+01 1nnt c.94.1.2 35896 1axkA 394 3.60e+01 1axkA b.29.1.2 24181 b.29.1.11 24315 1fohA 664 3.65e+01 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1noyA 388 3.66e+01 1clqA c.55.3.5 33713 1kwsA 261 3.70e+01 1efiD 103 3.72e+01 3chbD b.40.2.1 24870 1a8e 329 3.75e+01 1cb6A c.94.1.2 35888 1dmmA 131 3.78e+01 1opy d.17.4.3 38114 1aijL 281 3.80e+01 6prcL f.2.1.2 43461 1hjbA 87 3.81e+01 1hjbA h.1.3.1 61073 1hml 142 3.82e+01 3lzt d.2.1.2 36598 1f9zA 135 3.82e+01 1qipA d.32.1.1 38484 1ea2A 131 3.84e+01 d.17.4.3 64860 1jj2S 119 3.86e+01 1ffkQ b.34.5.1 63104 1nozA 388 3.87e+01 1clqA c.55.3.5 33715 1djrD 103 3.90e+01 3chbD b.40.2.1 24865 1preB 470 3.90e+01 1preA d.169.1.2 42438 f.8.1.1 43825 1oasA 322 3.90e+01 1oasA c.79.1.1 35293 1dlwA 116 3.92e+01 1dlyA a.1.1.1 14982 1hdfA 102 3.94e+01 1ag4 b.11.1.1 23627 1fa8A 135 3.94e+01 1qipA d.32.1.1 38486 1c4kA 730 3.97e+01 1ordA c.23.7.1 31273 c.67.1.5 34502 d.125.1.1 41123 1qr4B 186 3.98e+01 1qr4B b.1.2.1 21988 b.1.2.1 21989 1pyaA 81 3.99e+01 1pyaA d.155.1.1 42026 1a0sP 413 4.00e+01 1a0tP f.4.3.2 43797 1c24A 263 4.00e+01 1c24A d.127.1.1 41148