# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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.soe.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 2bngA 149 5.05e-15 2geyA 158 4.00e-13 1ocvA 125 2.81e-12 d.17.4.3 86810 1ohpA 125 3.09e-12 d.17.4.3 118702 1buqA 125 5.87e-12 1opy d.17.4.3 38111 1nwwA 149 7.63e-12 d.17.4.8 86306 1oh0A 131 2.63e-11 d.17.4.3 87004 1opy 131 2.83e-11 1opy 1ea2A 131 3.27e-11 d.17.4.3 64860 1dmmA 131 5.85e-11 1opy d.17.4.3 38114 1tuhA 156 7.95e-11 d.17.4.11 107345 2a15A 139 9.56e-08 d.17.4.3 125973 2gxfA 142 1.15e-07 3b7cA 122 7.92e-07 1s5aA 150 2.13e-06 d.17.4.10 98525 1sjwA 144 2.37e-06 d.17.4.9 98899 2imjA 166 2.01e-05 3cu3A 172 6.95e-05 1hkxA 147 3.37e-04 d.17.4.7 83567 2ux0A 143 5.87e-04 1m98A 317 8.14e-04 a.175.1.1,d.17.4.6 78866,78867 1tp6A 128 1.17e-03 d.17.4.12 107184 3cnxA 170 7.37e-02 2nlvA 112 7.43e-02 d.326.1.1 138362 2r4iA 123 7.74e-02 2chcA 170 7.79e-02 2rgqA 144 7.84e-02 2owpA 129 8.37e-02 3blzA 128 1.24e-01 2fxtA 192 3.87e-01 2retB 175 4.70e-01 1m1hA 248 5.02e-01 b.114.1.1,d.58.42.1 78415,78416 2rfrA 155 6.32e-01 3bb9A 148 7.39e-01 1x2gA 337 9.84e-01 1xu1A 138 1.34e+00 b.22.1.1 116033 1n3bA 216 1.37e+00 c.37.1.1 79959 2gojA 197 1.66e+00 1z4eA 153 1.80e+00 d.108.1.1 124431 2hjeA 221 1.87e+00 1lcyA 325 2.08e+00 b.36.1.4,b.47.1.1 73834,73835 1vhtA 218 2.24e+00 c.37.1.1 100700 2o3bB 136 2.49e+00 d.221.1.1 138902 1knyA 253 2.67e+00 1knyA a.24.16.1,d.218.1.1 75896,75897 1zhhB 242 2.76e+00 1zd7A 159 2.87e+00 1a9xA 1058 2.96e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1wmmA 145 3.19e+00 b.122.1.8 121049 1htwA 158 3.19e+00 c.37.1.18 71083 1zeeA 403 3.23e+00 a.266.1.2 124981 1c3oA 1073 3.41e+00 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 2nwbA 400 3.51e+00 1v6fA 151 3.71e+00 d.109.1.2 108395 1ixlA 131 4.08e+00 d.38.1.5 90717 2v9kA 530 4.09e+00 2hd9A 145 4.13e+00 1cs0A 1073 4.69e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1on3A 523 5.12e+00 c.14.1.4,c.14.1.4 87107,87108 2retA 103 5.19e+00 1h70A 255 5.25e+00 1h70A d.126.1.3 60711 1qo8A 566 5.53e+00 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19696,30433,42316 1ym5A 300 5.70e+00 2cb4A 291 5.91e+00 1iscA 192 6.08e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1v7rA 186 6.12e+00 c.51.4.1 100482 1wy7A 207 6.36e+00 c.66.1.32 121433 2cw8A 537 6.48e+00 2nybA 192 6.69e+00 a.2.11.1,d.44.1.1 138804,138805 1shkA 173 6.77e+00 1shkA c.37.1.2 31932 1dcqA 278 7.09e+00 1dcqA d.211.1.1,g.45.1.1 19178,45326 2r78A 117 7.44e+00 1e6cA 173 7.50e+00 1shkA c.37.1.2 59296 2eq6A 464 7.51e+00 2h4aA 325 8.14e+00 3ckmA 327 8.37e+00 1jj2L 194 8.65e+00 1ffkI d.12.1.2 63097 1a2vA 655 8.78e+00 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 2z0jA 237 9.07e+00 2f86B 143 9.47e+00 1vbkA 307 9.54e+00 c.26.2.6,d.308.1.1 119957,119958 2awpA 198 9.97e+00 2oqeA 660 1.00e+01 b.30.2.1,d.17.2.1,d.17.2.1 139222,139223,139224 1pz4A 116 1.02e+01 d.106.1.1 95400 1wurA 220 1.04e+01 d.96.1.1 121309 1ebdA 455 1.04e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 2ckwA 515 1.05e+01 2a2jA 246 1.07e+01 b.45.1.1 126033 1vplA 256 1.07e+01 c.37.1.12 113966 1gk8I 140 1.10e+01 d.73.1.1 65242 1h6qA 168 1.11e+01 1h6qA b.88.1.2 60692 1w1wA 430 1.17e+01 c.37.1.12 114080 2ifuA 307 1.20e+01 1txoA 237 1.22e+01 d.219.1.1 112781 1whzA 70 1.33e+01 d.50.3.2 114656 1ucdA 190 1.34e+01 d.124.1.1 107767 2ywrA 216 1.35e+01 1q7lA 198 1.36e+01 c.56.5.4 96044 1q60A 99 1.46e+01 d.288.1.1 111654 1ir21 140 1.48e+01 1w6nA 134 1.48e+01 b.29.1.3 114275 1kk1A 410 1.55e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2nwvA 114 1.57e+01 d.326.1.1 138720 2q3xA 171 1.58e+01 2ek8A 421 1.59e+01 2bi0A 337 1.61e+01 d.38.1.4,d.38.1.4 128565,128566 1xg1A 67 1.62e+01 a.4.1.4 121973 2i9sA 97 1.63e+01 3bs4A 260 1.63e+01 1u04A 771 1.63e+01 b.34.14.1,c.55.3.10 107539,107540 2ghsA 326 1.66e+01 b.68.6.1 135209 1pguA 615 1.76e+01 b.69.4.1,b.69.4.1 88069,88070 2awfA 172 1.77e+01 d.20.1.1 127432 2ozgA 396 1.78e+01 2e55A 208 1.80e+01 1wmhB 86 1.80e+01 d.15.2.2 114745 1avmA 201 1.81e+01 1avmA a.2.11.1,d.44.1.1 15782,38745 2cw3A 280 1.85e+01 1vqoM 195 1.86e+01 d.12.1.2 120374 1bsmA 201 1.89e+01 1avmA a.2.11.1,d.44.1.1 15780,38743 2nv4A 147 1.89e+01 1x3sA 195 1.90e+01 c.37.1.8 121670 3c5cA 187 1.98e+01 1k8kG 151 1.99e+01 a.118.13.1 68313 1jb0D 138 2.01e+01 1jb0D d.187.1.1 62823 2pzeA 229 2.03e+01 2o28A 184 2.05e+01 2r85A 334 2.05e+01 2h36X 112 2.06e+01 1xrtA 467 2.07e+01 b.92.1.3,c.1.9.6 122258,122259 2fp3A 316 2.12e+01 2ifsA 169 2.13e+01 2bo9A 308 2.14e+01 c.56.5.1 128897 1elwA 118 2.14e+01 1a17 a.118.8.1 19207 1f3uB 171 2.19e+01 1f3uB b.65.1.1 27525 2jaeA 489 2.25e+01 1iv3A 152 2.31e+01 d.79.5.1 76828 1hg5A 289 2.37e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 1ufaA 520 2.37e+01 a.8.3.3,c.6.2.4 99329,99330 2fgsA 179 2.52e+01 1qp8A 303 2.57e+01 1qp8A c.2.1.4,c.23.12.1 30092,31352 1e85A 127 2.57e+01 1bbhA a.24.3.2 16549 3cg5A 265 2.58e+01 2gdnA 267 2.64e+01 2vptA 215 2.70e+01 1j57A 143 2.79e+01 d.221.1.1 77079 1x8gA 227 2.80e+01 d.157.1.1 114960 3c9uA 342 2.80e+01 1j4aA 333 2.80e+01 c.2.1.4,c.23.12.1 71502,71503 1tfuA 157 2.84e+01 c.26.1.3 106859 1bo1A 416 2.91e+01 1bo1A d.143.1.2 41591 1x8hA 228 2.99e+01 d.157.1.1 114961 1wleA 501 3.05e+01 1xl4A 301 3.06e+01 b.1.18.16,f.14.1.1 115430,115431 1mwsA 646 3.06e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1no1A 126 3.07e+01 a.179.1.1 85913 1ra6A 461 3.13e+01 e.8.1.4 104879 2a13A 166 3.14e+01 b.60.1.8 125971 2b9uA 176 3.15e+01 2zaiA 497 3.24e+01 2r55A 231 3.25e+01 2p8tA 200 3.28e+01 1i7kA 179 3.31e+01 1u9aA d.20.1.1 61889 2q4nA 166 3.34e+01 b.60.1.8 139871 1korA 400 3.38e+01 c.26.2.1,d.210.1.1 72824,72825 2f7vA 369 3.47e+01 2egjA 128 3.53e+01 1r71A 178 3.53e+01 a.4.14.1 104823 1jb2A 127 3.54e+01 d.17.4.2 71624 1j3aA 142 3.56e+01 c.21.1.1 77070 2ywwA 149 3.57e+01 2c1cA 312 3.59e+01 c.56.5.1 129630 1rypC 244 3.64e+01 1rypC d.153.1.4 41934 1p3wA 404 3.64e+01 c.67.1.3 87752 1sjyA 159 3.65e+01 d.113.1.1 98900 1w0uA 55 3.66e+01 a.4.1.4 114072 2uy1A 493 3.66e+01 2novA 496 3.67e+01 1t7vA 278 3.68e+01 b.1.1.2,d.19.1.1 112302,112303 1r2qA 170 3.77e+01 c.37.1.8 96874 1u5xA 140 3.77e+01 b.22.1.1 113055 1bavA 309 3.81e+01 1aye c.56.5.1 33806 2jbwA 386 3.84e+01 1si6X 282 3.88e+01 d.151.1.2 118968 1e4eA 343 3.89e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1t6jA 714 3.89e+01 a.127.1.2 112259 1ysrA 150 3.94e+01 d.122.1.3 123981 1gv3A 248 3.96e+01 a.2.11.1,d.44.1.1 70585,70586 2e58A 308 3.99e+01 1kr4A 125 4.01e+01 d.58.5.2 72889 1idsA 207 4.01e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1fl9A 161 4.05e+01 c.37.1.18 70137 2cw6A 298 4.08e+01 1c8uA 285 4.10e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1t0bA 252 4.10e+01 c.23.16.6 106199 2gu3A 136 4.12e+01 1zd9A 188 4.13e+01 c.37.1.8 124938 1oapA 109 4.19e+01 d.79.7.1 92706 1m1zA 513 4.20e+01 c.26.2.1,d.153.1.1 78457,78458 2cm1A 260 4.27e+01 2z8rA 591 4.30e+01 2yvtA 260 4.32e+01 1e3sA 261 4.40e+01 1e6wA c.2.1.2 59201 2qdsA 227 4.40e+01 1p97A 114 4.42e+01 d.110.3.7 94382 2ew1A 201 4.43e+01 c.37.1.8 132446 1y0hA 105 4.44e+01 d.58.4.11 116303 1bxeA 113 4.45e+01 1bxeA d.55.1.1 38898 2q8oA 136 4.52e+01 2gekA 406 4.58e+01 2imqX 282 4.62e+01 2j6bA 109 4.70e+01 d.321.1.1 138078 1vqqA 646 4.71e+01 d.17.4.5,d.175.1.1,e.3.1.1 114009,114010,114011 1sltA 134 4.72e+01 1c1lA b.29.1.3 24186 1vh5A 148 4.74e+01 d.38.1.5 100642 2gtiA 370 4.76e+01 c.66.1.48,d.294.1.2 135652,135653 1iktA 120 4.79e+01 d.106.1.1 66188 2c2hA 192 4.80e+01 c.37.1.8 129668 2pi1A 334 4.83e+01 2geeA 203 4.87e+01 1gnxA 479 4.91e+01 c.1.8.4 76241 2qwc 388 4.92e+01 2qwc 1f8eA 388 4.92e+01 2qwc b.68.1.1 59694 1vqvA 306 4.96e+01 d.79.4.1,d.139.1.1 114024,114025 1fsz 372 4.97e+01 1fsz 1b78A 193 4.97e+01 1b78A c.51.4.1 33221 1q1uA 144 4.99e+01 b.42.1.1 95608 1pz1A 333 4.99e+01 c.1.7.1 95390 1rtqA 299 5.00e+01 c.56.5.4 97819 1shdA 107 5.02e+01 1fmk d.93.1.1 40440 1ayzA 169 5.04e+01 1u9aA d.20.1.1 38326 3b2nA 133 5.07e+01 1jqgA 433 5.07e+01 c.56.5.1,d.58.3.1 71791,71792 1ejbA 168 5.08e+01 1rvv1 c.16.1.1 59417 1d7yA 408 5.10e+01 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 2avkA 136 5.14e+01 1yrvA 169 5.15e+01 d.20.1.1 123941 2c3vA 102 5.16e+01 3c5oA 157 5.17e+01 2icrA 237 5.23e+01 1b06A 210 5.28e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1vkkA 154 5.29e+01 d.109.1.2 108669 1kanA 253 5.37e+01 1knyA a.24.16.1,d.218.1.1 75878,75879 2e57A 637 5.45e+01 1m2oA 768 5.46e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1uzxA 169 5.46e+01 d.20.1.2 100238 2zgwA 235 5.54e+01 1o7jA 327 5.56e+01 c.88.1.1 81140 1rq2A 382 5.71e+01 c.32.1.1,d.79.2.1 105048,105049 1xbtA 193 5.72e+01 c.37.1.24,g.39.1.14 115080,115081 1l7aA 318 5.79e+01 c.69.1.25 77772 2al6A 375 5.81e+01 a.11.2.1,b.55.1.5,d.15.1.4 126966,126967,126968 2jwyA 168 5.82e+01 2oemA 413 5.83e+01 1a9cA 221 5.83e+01 1a8rA d.96.1.1 40602 1gzwA 134 5.86e+01 b.29.1.3 90535 2gqwA 408 5.88e+01 2pt7A 330 5.92e+01 1lf6A 684 5.94e+01 a.102.1.5,b.30.5.5 77918,77919 1n9lA 109 6.01e+01 d.110.3.6 85468 1z6kA 293 6.05e+01 2v9dA 343 6.05e+01 2oq8A 160 6.08e+01 1u14A 172 6.11e+01 c.51.4.3 107579 1uj8A 77 6.11e+01 a.159.5.1 119683 1jkxA 212 6.17e+01 c.65.1.1 66813 1hg3A 225 6.21e+01 1hg3A c.1.1.1 61025 1g6oA 330 6.22e+01 1g6oA c.37.1.11 32430 1p7gA 222 6.27e+01 a.2.11.1,d.44.1.1 94223,94224 2atvA 196 6.27e+01 c.37.1.8 127308 1hf8A 289 6.30e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 2b78A 385 6.30e+01 b.122.1.9,c.66.1.51 128025,128026 4kbpA 432 6.37e+01 4kbpA b.1.12.1,d.159.1.1 22345,42064 2h5eA 529 6.38e+01 1ebmA 317 6.43e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 1yt5A 258 6.44e+01 2v94A 107 6.44e+01 1xgkA 352 6.49e+01 c.2.1.2 115286 2gj3A 120 6.49e+01 2re9A 181 6.50e+01 4xiaA 393 6.51e+01 4xis c.1.15.3 29439 2ggtA 164 6.53e+01 c.47.1.10 135156 2gr8A 99 6.58e+01 d.24.1.4 135522 1iznA 286 6.60e+01 e.43.1.1 83847 2fclA 169 6.65e+01 d.218.1.11 133273 2ewrA 170 6.67e+01 d.218.1.11 132493 3bgaA 1010 6.69e+01 1lwyA 324 6.72e+01 a.96.1.3,d.129.1.2 78285,78286 1bxdA 161 6.77e+01 1bxdA d.122.1.3 41111 1qnxA 209 6.77e+01 1qnxA d.111.1.1 40914 1m3qA 317 6.78e+01 a.96.1.3,d.129.1.2 91184,91185 2b0rA 202 6.78e+01 2h6rA 219 6.80e+01 1m6jA 261 6.83e+01 c.1.1.1 78693 1ofzA 312 6.83e+01 b.68.8.1 86978 1uc2A 481 6.89e+01 d.261.1.1 99161 1on0A 158 6.91e+01 d.108.1.1 87095 1huqA 164 6.95e+01 1byuA c.37.1.8 32020 1bqg 451 7.04e+01 1bqg 1nfjA 89 7.09e+01 d.68.6.1 91866 1zs7A 190 7.10e+01 b.122.1.1,d.17.6.4 125593,125594 1k6xA 352 7.10e+01 c.2.1.2 68238 1b9hA 388 7.13e+01 1b9hA c.67.1.4 34488 2yweA 600 7.14e+01 2d0oA 610 7.14e+01 c.8.6.1,c.55.1.6,c.55.1.6 131075,131076,131077 3cswA 285 7.15e+01 1ko9A 345 7.16e+01 a.96.1.3,d.129.1.2 68717,68718 1uf3A 228 7.17e+01 d.159.1.6 99317 1wt7A 41 7.18e+01 g.3.7.2 114873 1b5qA 472 7.19e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1xg4A 295 7.22e+01 3cpkA 150 7.23e+01 1r6jA 82 7.24e+01 b.36.1.1 97151 2fjuB 799 7.26e+01 2ffjA 300 7.30e+01 e.50.1.1 133387 3cgxA 242 7.31e+01 1usuA 260 7.34e+01 d.14.1.8 99885 2aehA 369 7.36e+01 a.11.2.1,b.55.1.5,d.15.1.4 126625,126626,126627 1f0kA 364 7.37e+01 1f0kA c.87.1.2 35465 1knxA 312 7.41e+01 c.98.2.1,c.91.1.2 77459,77460 1utyA 187 7.42e+01 b.147.1.1 108036 2nx2A 181 7.46e+01 1n8mA 38 7.47e+01 g.3.7.2 91705 2ccmA 191 7.48e+01 1iow 306 7.49e+01 1iow 1iowA 306 7.49e+01 c.30.1.2,d.142.1.1 31713,41481 1chuA 540 7.52e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 2cbzA 237 7.56e+01 2j73A 103 7.58e+01 2hqsC 118 7.65e+01 d.79.7.1 136666 2culA 232 7.66e+01 c.3.1.7 130813 1oj5A 132 7.70e+01 d.110.3.8 93087 2hvwA 184 7.76e+01 2afwA 329 7.78e+01 c.56.5.8 126707 2jmbA 79 7.81e+01 1bia 321 7.83e+01 1bia 1biaA 321 7.83e+01 a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1qtnA 164 7.83e+01 1pauA c.17.1.1 30999 2z67A 456 7.85e+01 1ufhA 180 7.88e+01 d.108.1.1 88485 2vo1A 295 7.88e+01 1lgyA 269 7.92e+01 3tgl c.69.1.17 34758 2cjaA 522 7.95e+01 2giaA 195 7.98e+01 d.18.1.4 135221