# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-scores 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 1mk4A 157 3.08e-03 d.108.1.1 84979 2fe7A 166 8.25e-02 1tiqA 180 1.38e-01 d.108.1.1 107010 1kt8A 365 2.91e-01 e.17.1.1 77531 1cjwA 166 3.24e-01 1cjwA d.108.1.1 40818 2coiA 386 3.34e-01 1y1uA 585 3.43e-01 2d4pA 141 3.47e-01 1kuxA 207 3.48e-01 d.108.1.1 73021 2fl4A 149 4.50e-01 1vqzA 341 4.71e-01 1ekfA 365 8.53e-01 1ekfA e.17.1.1 59445 2fsrA 195 1.02e+00 2vil 126 1.08e+00 2vil d.109.1.1 40830 2a1hA 365 1.19e+00 1ktaA 365 1.19e+00 e.17.1.1 77533 1twyA 290 1.26e+00 2ge3A 170 1.29e+00 1yr0A 175 1.56e+00 1ne9A 335 1.57e+00 d.108.1.4,d.108.1.4 91839,91840 2ganA 190 1.84e+00 1v7rA 186 2.13e+00 c.51.4.1 100482 1wwzA 159 2.39e+00 2gwnA 452 4.24e+00 1z5nA 242 4.26e+00 1z5oA 242 4.26e+00 1tfuA 157 4.35e+00 c.26.1.3 106859 1jl0A 334 4.91e+00 1jenA d.156.1.1 63155 1xmxA 385 4.92e+00 1zo0A 126 4.98e+00 1g4uS 383 5.01e+00 1g4uS a.24.11.1,c.45.1.2 16643,32691 1kb9A 431 5.16e+00 d.185.1.1,d.185.1.1 77311,77312 1s3zA 165 5.43e+00 d.108.1.1 105250 1nslA 184 5.69e+00 d.108.1.1 86137 1jysA 242 6.12e+00 c.56.2.1 77216 2fh1A 344 6.25e+00 1p8xA 344 6.31e+00 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1d7cA 190 6.39e+00 1d7bA b.1.9.1 22309 1dc1A 323 6.58e+00 1dc1A c.52.1.11 33321 1vchA 175 6.73e+00 1sg4A 260 7.36e+00 1a4sA 503 7.58e+00 1bpwA c.82.1.1 35361 1jwgA 147 7.61e+00 a.118.9.2 71911 1ezvA 430 7.64e+00 1be3A d.185.1.1,d.185.1.1 59541,59542 1ujkA 147 7.69e+00 a.118.9.2 99457 1mho 88 8.43e+00 1b4cA a.39.1.2 17171 1yqtA 538 8.49e+00 1glv 303 9.02e+00 1gsa c.30.1.3,d.142.1.1 31721,41480 1gegA 256 9.16e+00 1ybvA c.2.1.2 29888 1konA 249 9.40e+00 e.39.1.1 72823 1o0sA 605 9.76e+00 c.2.1.7,c.58.1.3 86540,86541 1wmaA 276 9.92e+00 1i39A 225 9.95e+00 1ekeA c.55.3.1 61585 1h1lA 481 1.01e+01 c.92.2.3 70851 1bxsA 501 1.02e+01 1bpwA c.82.1.1 35357 1vs0A 310 1.04e+01 1wn5A 130 1.07e+01 1mioA 534 1.11e+01 1qguA c.92.2.3 35601 1kyoA 430 1.14e+01 d.185.1.1,d.185.1.1 73249,73250 1eyqA 222 1.18e+01 1eypA d.36.1.1 38534 1g4wR 383 1.18e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 2gaeA 346 1.19e+01 1jpmA 366 1.21e+01 c.1.11.2,d.54.1.1 67031,67032 1tkkA 366 1.26e+01 c.1.11.2,d.54.1.1 107089,107090 1i7nA 309 1.26e+01 c.30.1.5,d.142.1.3 83681,83682 1ulyA 192 1.28e+01 1o04A 500 1.29e+01 c.82.1.1 86508 1eypA 222 1.32e+01 1eypA d.36.1.1 38536 1b4cA 92 1.36e+01 1b4cA a.39.1.2 17169 1b16A 254 1.36e+01 1b16A c.2.1.2 29875 1af7 274 1.38e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1p3dA 475 1.41e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1sbyA 254 1.47e+01 1jepA 222 1.53e+01 d.36.1.1 66612 1xxqA 161 1.54e+01 2hvm 273 1.54e+01 1cnv c.1.8.5 28985 1oj4A 283 1.59e+01 d.14.1.5,d.58.26.5 93083,93084 1ag8A 499 1.59e+01 1bpwA c.82.1.1 35341 1pz1A 333 1.61e+01 c.1.7.1 95390 1gqyA 475 1.62e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1kqzA 273 1.70e+01 c.1.8.5 68844 1p7gA 222 1.71e+01 a.2.11.1,d.44.1.1 94223,94224 1bpwA 503 1.72e+01 1bpwA c.82.1.1 35365 2plc 274 1.72e+01 2plc c.1.18.2 29614 1p0hA 318 1.73e+01 d.108.1.1 93866 1hu4A 288 1.73e+01 1hu4A 1a8s 273 1.74e+01 1brt c.69.1.12 34710 1n5dA 288 1.75e+01 c.2.1.2 80030 1r0pA 312 1.76e+01 d.144.1.7 96734 2vik 126 1.77e+01 2vil d.109.1.1 40829 1je0A 236 1.81e+01 c.56.2.1 66581 1px5A 349 1.82e+01 a.160.1.2,d.218.1.6 95277,95278 1d7bA 186 1.83e+01 1d7bA b.1.9.1 22307 1kqyA 273 1.86e+01 c.1.8.5 68843 1zosA 230 1.90e+01 2aj6A 159 1.93e+01 1np8A 159 1.93e+01 a.39.1.8 92022 1yz1A 174 1.96e+01 1aod 289 1.98e+01 2plc c.1.18.2 29615 1dmr 823 2.04e+01 1dmr b.52.2.2,c.81.1.1 26904,35312 1gsa 316 2.05e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 2c5kT 95 2.06e+01 2g5cA 281 2.10e+01 1zy9A 564 2.14e+01 1f3aA 222 2.17e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1sqhA 312 2.20e+01 d.108.1.5 98966 1xmtA 103 2.21e+01 2ghpA 292 2.22e+01 1a4uA 254 2.24e+01 1b16A c.2.1.2 29878 2ae0X 345 2.25e+01 1gw5S 142 2.26e+01 d.110.4.2 70633 1uh5A 329 2.34e+01 c.2.1.2 107840 1qo7A 394 2.37e+01 1qo7A c.69.1.11 34697 1alvA 173 2.40e+01 1alvA a.39.1.8 17370 2bswA 146 2.41e+01 1xtlA 175 2.44e+01 1xtmA 175 2.46e+01 1s6cA 183 2.47e+01 a.39.1.5 98594 1xo0A 324 2.53e+01 1yksA 440 2.54e+01 1h3qA 140 2.57e+01 d.110.4.3 76652 1cne 270 2.57e+01 1ndh b.43.4.2,c.25.1.1 25661,31551 4crxA 322 2.58e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1crxA 322 2.61e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 1yemA 179 2.64e+01 1j8yF 297 2.64e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1pwxA 254 2.64e+01 c.2.1.2 95262 2bmfA 451 2.64e+01 1mhqA 148 2.71e+01 a.118.9.2 84973 1jykA 254 2.74e+01 c.68.1.13 67458 4mbp 370 2.80e+01 4mbp c.94.1.1 35777 1exqA 154 2.81e+01 1b9dA c.55.3.2 33646 1zmtA 254 2.84e+01 1nzaA 103 2.95e+01 d.58.5.2 86444 1qdlA 422 2.96e+01 1qdlA d.161.1.1 42088 1li5B 461 3.08e+01 a.27.1.1,c.26.1.1 73914,73915 1qguA 478 3.09e+01 1qguA c.92.2.3 35625 2cy2A 174 3.15e+01 2gyqA 175 3.21e+01 1b6bA 174 3.22e+01 1cjwA d.108.1.1 40819 1yx0A 159 3.28e+01 2arzA 247 3.29e+01 1cnv 299 3.30e+01 1cnv c.1.8.5 28989 1bc5A 269 3.31e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1lw7A 365 3.34e+01 c.26.1.3,c.37.1.1 74295,74296 1vhsA 175 3.36e+01 d.108.1.1 100698 1rxyA 253 3.37e+01 c.56.2.1 98065 1g6zA 70 3.37e+01 1g6zA b.34.13.2 60321 1qh8A 478 3.38e+01 1qguA c.92.2.3 35633 1u0mA 382 3.42e+01 c.95.1.2,c.95.1.2 107557,107558 1sfxA 109 3.43e+01 a.4.5.50 105505 16pk 415 3.47e+01 16pk c.86.1.1 35454 1h1nA 305 3.51e+01 c.1.8.3 70855 1lx7A 253 3.53e+01 c.56.2.1 74329 1whxA 111 3.54e+01 1d3uB 201 3.62e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1uxoA 192 3.64e+01 c.69.1.31 108121 1wqaA 455 3.68e+01 1vkmA 297 3.69e+01 c.138.1.1 108670 1ytvA 366 3.83e+01 1amoA 615 3.88e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1aj5A 173 3.91e+01 1alvA a.39.1.8 17367 2b5gA 171 3.94e+01 1wduA 245 3.98e+01 d.151.1.1 109286 1fjgC 239 4.05e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1vg8A 207 4.11e+01 c.37.1.8 108606 1ml8A 134 4.11e+01 d.227.1.2 85013 1e2wA 251 4.14e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1a3wA 500 4.18e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27060,29288,33142 1anf 370 4.19e+01 4mbp c.94.1.1 35776 1kbuA 349 4.22e+01 a.60.9.1,d.163.1.1 72284,72285 1hfbA 370 4.23e+01 c.1.10.4 76706 1va4A 279 4.24e+01 c.69.1.12 108458 1y37A 304 4.25e+01 1skyE 473 4.42e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18314,26479,32359 1ris 101 4.47e+01 1ris d.58.14.1 39314 1prxA 224 4.48e+01 1prxA c.47.1.10 33076 1mpb 370 4.50e+01 4mbp c.94.1.1 35780 1e8oB 106 4.57e+01 1914 d.49.1.1 38775 1l6rA 227 4.58e+01 c.108.1.10 77768 3crxA 343 4.59e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 2aobA 99 4.66e+01 1yvkA 163 4.70e+01 1i4nA 251 4.72e+01 c.1.2.4 71114 1bl3A 160 4.73e+01 1b9dA c.55.3.2 33655 1aisB 200 4.80e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1khyA 148 4.88e+01 a.174.1.1 77410 1broA 277 4.94e+01 1brt c.69.1.12 34700 1prxB 224 4.99e+01 1prxA c.47.1.10 33077 1qg8A 255 4.99e+01 1qg8A c.68.1.1 34505 1iufA 144 5.00e+01 a.4.1.7,a.4.1.7 71439,71440 1kaeA 434 5.00e+01 c.82.1.2 72247 1k75A 434 5.02e+01 c.82.1.2 68253 1gdoA 240 5.02e+01 1gdoA 2giyA 191 5.04e+01 1bam 213 5.05e+01 1bam c.52.1.3 33285 2be4A 272 5.08e+01 1p3qQ 54 5.16e+01 a.5.2.4 87748 1amk 251 5.34e+01 1amk c.1.1.1 28503 2gh1A 301 5.35e+01 1a8uA 277 5.36e+01 1brt c.69.1.12 34703 1n55A 251 5.37e+01 c.1.1.1 80007 1t95A 240 5.38e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1t6aA 126 5.39e+01 d.129.8.1 106555 1dcjA 81 5.44e+01 1dcjA d.68.3.3 59115 1ehyA 294 5.49e+01 1ehyA c.69.1.11 34693 1e5dA 402 5.52e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 2if1 126 5.58e+01 2if1 d.64.1.1 39547 2c3zA 222 5.59e+01 1j8mF 297 5.60e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2f9fA 177 5.61e+01 1je3A 97 5.61e+01 d.68.3.3 71637 1b04A 318 5.63e+01 1b04A d.142.2.2 41579 1ni9A 338 5.74e+01 e.7.1.2 85739 1dioB 224 5.75e+01 1dioB c.51.3.1 33219 1dik 874 5.78e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1d0nA 729 5.82e+01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 1kyhA 276 5.84e+01 c.72.1.4 73222 1wdnA 226 5.84e+01 1lst c.94.1.1 35816 1w78A 422 5.89e+01 1eexB 224 5.91e+01 1dioB c.51.3.1 33213 1httA 423 5.92e+01 1adjA c.51.1.1,d.104.1.1 33178,40727 1mwpA 96 6.00e+01 1mwpA d.170.2.1 42453 1ocsA 162 6.03e+01 d.189.1.1 92776 1aq3A 129 6.09e+01 1msc d.85.1.1 40079 1tuaA 191 6.17e+01 d.51.1.1,d.51.1.1 107321,107322 1xt8A 292 6.26e+01 1ad3A 452 6.34e+01 1ad3A c.82.1.1 35335 2c27A 315 6.35e+01 1a1vA 476 6.38e+01 1heiA c.37.1.14,c.37.1.14 32467,32468 2ms2A 129 6.42e+01 1msc d.85.1.1 40049 1b0uA 262 6.56e+01 1b0uA c.37.1.12 32370 1zhvA 134 6.58e+01 1ddgA 374 6.62e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1fm2A 169 6.62e+01 1fm2A d.153.1.2 59877 1ukcA 522 6.66e+01 c.69.1.17 107911 1wz7A 111 6.67e+01 1igs 248 6.73e+01 1a53 c.1.2.4 28565 2bfwA 200 6.74e+01 1si2A 149 6.74e+01 b.34.14.1 105569 1po5A 476 6.76e+01 a.104.1.1 94963 1b25A 619 6.77e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1ro5A 201 6.77e+01 d.108.1.3 105023 2c71A 216 6.80e+01 1din 236 6.83e+01 1din c.69.1.9 34682 1jenA 267 6.89e+01 1jenA 1bs9 207 6.96e+01 1bs9 c.69.1.30 31330 1g66A 207 6.96e+01 1bs9 c.69.1.30 31329 1juk 248 6.97e+01 1a53 c.1.2.4 28567 1u6mA 199 6.98e+01 2cjpA 328 7.06e+01 1rro 108 7.12e+01 1a75A a.39.1.4 17195 1z7mA 344 7.13e+01 1xewX 182 7.21e+01 2faoA 309 7.22e+01 1mjfA 281 7.24e+01 c.66.1.17 79198 1th8A 145 7.24e+01 d.122.1.3 106908 1k3fA 253 7.25e+01 c.56.2.1 68105 1wkbA 810 7.33e+01 1or0A 160 7.37e+01 d.153.1.2 93445 1uwoA 92 7.39e+01 4icb a.39.1.2 17174 1nksA 194 7.44e+01 1nksA c.37.1.1 31886 1mc0A 368 7.44e+01 d.110.2.1,d.110.2.1 78937,78938 1pl3A 186 7.47e+01 b.1.9.1 88158 1vl2A 421 7.51e+01 c.26.2.1,d.210.1.1 108708,108709 1k3sA 113 7.59e+01 d.198.1.1 68120 1zvdA 380 7.59e+01 1dk5A 322 7.70e+01 1dk5A a.65.1.1 18192 1s4iA 175 7.71e+01 1zoiA 276 7.73e+01 1cqqA 180 7.74e+01 1cqqA b.47.1.4 26422 1s1eA 224 7.75e+01 1a6dA 545 7.75e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 1fdi 715 7.78e+01 2napA b.52.2.2,c.81.1.1 26918,35326 1qq2A 199 7.95e+01 1qq2A c.47.1.10 33064 1d4xG 126 7.95e+01 1d0nA d.109.1.1 59109 1preA 470 7.97e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1cpzA 68 7.97e+01 1aw0 d.58.17.1 39351 2gx9A 129 7.98e+01 1yagG 125 7.98e+01 1d0nA d.109.1.1 40846 1nm1G 125 8.00e+01 d.109.1.1 80653 1ggvA 232 8.01e+01 1din c.69.1.9 34683 1aa6 715 8.02e+01 2napA b.52.2.2,c.81.1.1 26916,35324 1914 232 8.02e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1ryaA 160 8.07e+01 d.113.1.5 105122 1nd7A 374 8.08e+01 d.148.1.1 91817 1brt 277 8.09e+01 1brt c.69.1.12 34699 1t44G 147 8.15e+01 d.109.1.1 106395 1fcdC 174 8.21e+01 1fcdC a.3.1.4,a.3.1.4 15966,15967 2axcA 264 8.25e+01 1ii7A 333 8.29e+01 1ii7A d.159.1.4 62415 1w1hA 151 8.34e+01 2fp8A 322 8.38e+01 1tfr 305 8.42e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1i4wA 353 8.42e+01 c.66.1.24 66028 1qs2A 401 8.44e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 1vqoW 154 8.56e+01 1ovqA 138 8.59e+01 c.55.3.8 93607 1srqA 341 8.61e+01 e.55.1.1 105967 1wnfA 328 8.77e+01 1m6jA 261 8.80e+01 c.1.1.1 78693 1a53 247 8.80e+01 1a53 c.1.2.4 28564 2fnoA 248 8.81e+01 2aqlA 173 8.82e+01 1gzqA 300 8.83e+01 b.1.1.2,d.19.1.1 70818,70819 1raxA 115 8.84e+01 1lfdA d.15.1.5 37626 1ejdA 419 8.89e+01 1uae d.68.2.2 39576 2sfa 191 8.90e+01 1qq4A b.47.1.1 25815 1fn9A 365 8.94e+01 1fn9A d.196.1.1 59894 1zbqA 327 8.95e+01 2iv2X 715 8.97e+01 1nu5A 370 8.97e+01 c.1.11.2,d.54.1.1 92183,92184