# List of top-scoring protein chains for t04-100-30-alpha-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 2gvkA 317 9.30e-35 1omzA 293 4.86e-01 c.68.1.15 87093 1x1nA 524 7.83e-01 1o12A 376 8.67e-01 b.92.1.5,c.1.9.10 80758,80759 3gcb 470 1.37e+00 3gcb d.3.1.1 37032 1gcb 454 1.41e+00 3gcb d.3.1.1 37034 1o08A 221 1.57e+00 c.108.1.6 86525 1uf2A 1019 2.07e+00 e.28.1.2 99289 1vdwA 254 2.22e+00 e.7.1.1 100569 1xkrA 206 2.27e+00 1chmA 401 2.35e+00 1chmA c.55.2.1,d.127.1.1 33545,41142 1zdzA 302 2.73e+00 2cb2A 318 2.76e+00 1rlhA 173 2.77e+00 d.256.1.1 97646 1fm0E 150 4.07e+00 1fmaE d.41.5.1 38629 1t0tV 248 4.29e+00 d.58.4.10 106229 1tz0A 114 4.73e+00 d.58.4.5 107463 1czaN 917 5.06e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1r8gA 372 5.53e+00 d.128.1.3 104845 1bia 321 6.25e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1j58A 385 6.30e+00 b.82.1.2 71531 2g8lA 299 6.31e+00 1iirA 415 6.51e+00 1iirA c.87.1.5 62453 1kaeA 434 6.70e+00 c.82.1.2 72247 2cg4A 152 6.91e+00 1zxzA 197 7.32e+00 2bleA 367 7.54e+00 1bbpA 173 7.55e+00 1bbpA b.60.1.1 27147 1esc 306 7.90e+00 1esc c.23.10.1 31334 2aalA 131 8.04e+00 1nt4A 391 8.26e+00 c.60.1.2 92102 1jeoA 180 8.57e+00 c.80.1.3 66611 1c4kA 730 9.42e+00 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1txvB 440 9.51e+00 1ys4A 354 1.01e+01 1uxtA 501 1.05e+01 c.82.1.1 108125 1x7oA 287 1.05e+01 1p7tA 731 1.14e+01 c.1.13.1 94319 2bkyX 89 1.19e+01 1z6kA 293 1.22e+01 1foeA 377 1.28e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1zq1C 633 1.30e+01 1zjcA 418 1.31e+01 1ofdA 1520 1.33e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1zejA 293 1.34e+01 1tk9A 188 1.36e+01 c.80.1.3 107082 1mp9A 198 1.43e+01 d.129.1.1,d.129.1.1 91385,91386 1e8cA 498 1.50e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1ow1A 195 1.51e+01 b.131.1.3 93625 1aoeA 192 1.54e+01 1aoeA c.71.1.1 34923 1wi1A 126 1.56e+01 1j27A 102 1.57e+01 d.58.50.1 90778 1l1sA 113 1.58e+01 c.114.1.1 73484 1wu7A 434 1.62e+01 2bklA 695 1.63e+01 1zy1B 197 1.63e+01 2b25A 336 1.69e+01 1fo8A 343 1.72e+01 1foaA c.68.1.10 59927 1f0xA 571 1.80e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1g0hA 252 1.83e+01 1dk4A e.7.1.1 60171 1hf2A 210 1.83e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1u04A 771 1.84e+01 b.34.14.1,c.55.3.10 107539,107540 1souA 194 1.87e+01 c.124.1.6 105858 1bkpA 278 1.89e+01 1bkpA d.117.1.1 41029 1jyhA 157 1.95e+01 d.60.1.3 71956 1sgvA 316 1.95e+01 b.122.1.1,d.265.1.2 98858,98859 1rv9A 259 1.99e+01 d.194.1.2 105105 1grj 158 1.99e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1moq 368 2.03e+01 1moq c.80.1.1 35302 2gfhA 260 2.06e+01 1jmsA 381 2.06e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1wxxA 382 2.07e+01 1nnhA 294 2.07e+01 d.104.1.1 92005 1jayA 212 2.08e+01 c.2.1.6 66478 1fw9A 164 2.10e+01 1fw9A d.190.1.1 60059 1tt8A 164 2.12e+01 1hlrA 907 2.22e+01 1vlbA 907 2.23e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1wruA 379 2.23e+01 2bjqA 345 2.24e+01 1o20A 427 2.25e+01 c.82.1.1 86556 1cs8A 316 2.29e+01 1cs8A d.3.1.1 37065 1ni4B 341 2.30e+01 c.36.1.7,c.48.1.2 85729,85730 1v9mA 323 2.32e+01 f.40.1.1 100543 2gnpA 266 2.40e+01 1v1rB 342 2.48e+01 c.36.1.7,c.48.1.2 108273,108274 1x7yB 342 2.54e+01 1uc2A 481 2.56e+01 d.261.1.1 99161 1kz7A 353 2.58e+01 a.87.1.1,b.55.1.1 73333,73334 1z7gA 217 2.60e+01 1ewqA 765 2.60e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1ri7A 171 2.65e+01 a.4.5.32,d.58.4.2 97504,97505 1yirA 408 2.71e+01 1cjxA 357 2.77e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 2bzpA 226 2.80e+01 2b8nA 429 2.90e+01 1udvA 89 2.91e+01 d.68.6.1 99224 1ugpA 203 2.91e+01 d.149.1.1 107831 1q9jA 422 2.92e+01 c.43.1.2,c.43.1.2 104590,104591 1s6yA 450 2.96e+01 c.2.1.5,d.162.1.2 105314,105315 2bfdB 345 2.97e+01 1rypD 241 3.01e+01 1rypD d.153.1.4 41935 2ffjA 300 3.01e+01 1ki1B 352 3.06e+01 a.87.1.1,b.55.1.1 72497,72498 1nw3A 416 3.14e+01 c.66.1.31 86288 1sc6A 404 3.16e+01 1j08A 226 3.18e+01 c.47.1.2,c.47.1.2 83855,83856 1q2lA 939 3.20e+01 1zvdA 380 3.21e+01 1t1dA 100 3.24e+01 1t1dA d.42.1.2 38637 1t8hA 277 3.39e+01 d.194.1.2 106664 3pmgA 561 3.41e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1olsB 342 3.47e+01 c.36.1.7,c.48.1.2 93332,93333 1nqkA 381 3.48e+01 c.1.16.4 92050 2chnA 716 3.52e+01 1gnxA 479 3.68e+01 c.1.8.4 76241 1qqgA 264 3.68e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1hp5A 512 3.74e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1o0uA 429 3.75e+01 c.118.1.1 80743 1d2mA 665 3.76e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1v7oA 165 3.76e+01 d.67.1.2 100480 1ireA 204 3.78e+01 d.149.1.1 76769 1vkwA 218 3.78e+01 d.90.1.2 108695 2fug7 129 3.80e+01 1y8aA 332 3.92e+01 2bgiA 272 3.92e+01 1ha3A 405 3.94e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1k4zA 159 3.96e+01 b.80.5.1 72070 2gaxA 135 3.99e+01 1d8cA 723 3.99e+01 1d8cA c.1.13.1 29325 1ipaA 274 4.02e+01 c.116.1.1,d.79.3.3 71254,71255 1qwrA 319 4.08e+01 b.82.1.3 96491 1ss9A 311 4.15e+01 c.68.1.4 105978 1iq4A 179 4.15e+01 1iq4A d.77.1.1 62641 2f8mA 244 4.15e+01 1jg1A 235 4.17e+01 c.66.1.7 66661 1aszB 490 4.20e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1xygD 359 4.24e+01 1hc7A 477 4.29e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 2bmfA 451 4.30e+01 1koqA 253 4.31e+01 2cba b.74.1.1 27964 1qhfA 240 4.32e+01 1qhfA c.60.1.1 33960 1r5zA 323 4.35e+01 f.40.1.1 97135 1hfuA 503 4.36e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1dbhA 354 4.36e+01 1awe a.87.1.1,b.55.1.1 18514,26967 6mhtA 327 4.42e+01 6mhtA c.66.1.26 34226 1a68 95 4.45e+01 1t1dA d.42.1.2 38639 1q0pA 223 4.48e+01 c.62.1.1 95507 2c7pA 327 4.50e+01 1c0pA 363 4.50e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1jpzA 473 4.55e+01 a.104.1.1 67069 1q47A 495 4.63e+01 b.69.12.1 104532 7aatA 401 4.65e+01 1ajsA c.67.1.1 34250 1b4bA 71 4.70e+01 1b4aA d.74.2.1 39718 1sq5A 308 4.75e+01 c.37.1.6 105882 1wbpA 397 4.75e+01 1iatA 557 4.77e+01 1dqrA c.80.1.2 62123 1yueA 427 4.79e+01 2fjlA 150 4.80e+01 1vrmA 325 4.84e+01 1fj2A 232 4.87e+01 1auoA c.69.1.14 34720 2gn4A 344 4.89e+01 2b20A 403 4.90e+01 1ga8A 311 4.91e+01 1ga8A c.68.1.4 34516 1mml 265 4.96e+01 1mml e.8.1.2 43015 1jfrA 262 4.96e+01 1jfrA c.69.1.16 34724 1vprA 374 4.97e+01 1dxeA 256 4.99e+01 1dxeA c.1.12.5 29310 1y8qB 640 5.05e+01 1p9aG 290 5.16e+01 c.10.2.7 87990 1ovlA 271 5.19e+01 a.123.1.1 87455 1nriA 306 5.21e+01 c.80.1.3 86123 2c30A 321 5.22e+01 1eulA 994 5.26e+01 1eulA 1v4pA 157 5.29e+01 1f45B 197 5.30e+01 1f45B a.26.1.1 59642 1a65A 504 5.30e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1wosA 364 5.31e+01 b.44.2.1,d.250.1.1 109468,109469 1rm8A 169 5.35e+01 d.92.1.11 97660 1a6jA 163 5.36e+01 1a6jA d.112.1.1 40915 2b8lA 405 5.38e+01 1vimA 200 5.41e+01 c.80.1.3 100758 1xrsA 516 5.46e+01 1udxA 416 5.48e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1u8xX 472 5.48e+01 c.2.1.5,d.162.1.2 107741,107742 1ht6A 405 5.51e+01 b.71.1.1,c.1.8.1 83629,83630 1vr8A 142 5.64e+01 2ftrA 108 5.67e+01 2f8lA 344 5.69e+01 1jakA 512 5.75e+01 c.1.8.6,d.92.2.1 66472,66473 1n7vA 555 5.77e+01 b.126.1.1 85377 1dtwB 342 5.77e+01 1qs0B c.36.1.7,c.48.1.2 31828,33102 1rwtA 232 5.86e+01 f.43.1.1 97992 1dciA 275 5.92e+01 1dciA c.14.1.3 30918 1sfe 180 5.97e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1aqcA 172 6.01e+01 1x11A b.55.1.2 26983 1ezfA 340 6.12e+01 1ezfA a.128.1.2 19440 1o0xA 262 6.13e+01 d.127.1.1 80755 1i58A 189 6.15e+01 1b3qA d.122.1.3 61773 1n83A 270 6.30e+01 a.123.1.1 80276 1dsxA 87 6.31e+01 1t1dA d.42.1.2 38644 1xrhA 351 6.37e+01 2c7hA 86 6.40e+01 1twuA 139 6.41e+01 d.32.1.8 107413 2a1iA 146 6.42e+01 1oaoC 729 6.49e+01 e.26.1.3 86746 2avuE 192 6.51e+01 1c4oA 664 6.53e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1kmvA 186 6.56e+01 c.71.1.1 72757 1v5vA 401 6.63e+01 1ek1A 554 6.63e+01 1cr6B c.69.1.11,c.108.1.2 34685,43335 1xfuA 747 6.63e+01 1ntyA 311 6.66e+01 a.87.1.1,b.55.1.1 103873,103874 1t5jA 313 6.67e+01 a.209.1.1 99125 1esmA 316 6.69e+01 1esmA c.37.1.6 31953 1k1xA 659 6.81e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1d4xG 126 6.81e+01 1d0nA d.109.1.1 59109 1vggA 161 6.83e+01 1dz3A 130 6.93e+01 1dz3A c.23.1.1 31105 1jjyA 636 6.93e+01 1jjyA 1ud9A 245 6.98e+01 d.131.1.2,d.131.1.2 107768,107769 1as4B 37 6.99e+01 1as4B 2cxhA 217 6.99e+01 2fflA 756 7.00e+01 1ru3A 732 7.01e+01 e.26.1.3 97835 2ax3A 502 7.03e+01 1pch 88 7.04e+01 1ptf d.94.1.1 40564 1mwwA 128 7.10e+01 d.80.1.4 91483 1ufkA 254 7.18e+01 c.66.1.39 99340 2bbsA 290 7.18e+01 1dqsA 393 7.22e+01 1dqsA e.22.1.1 43347 2auaA 224 7.24e+01 2aotA 292 7.25e+01 2cxnA 557 7.33e+01 1e9rA 437 7.35e+01 c.37.1.11 64827 2bkkA 264 7.37e+01 2fnjB 118 7.37e+01 1j97A 211 7.41e+01 1f5sA c.108.1.4 62753 1yr2A 741 7.42e+01 1w6tA 444 7.45e+01 1w5fA 353 7.48e+01 2bhwA 232 7.52e+01 2az4A 429 7.52e+01 1csh 435 7.53e+01 1csh a.103.1.1 18880 1eonA 245 7.53e+01 1rvaA c.52.1.2 33238 1g6hA 257 7.55e+01 1gajA c.37.1.12 60318 1iyxA 432 7.56e+01 c.1.11.1,d.54.1.1 83815,83816 1qd1A 325 7.58e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 2cwlA 302 7.59e+01 2b67A 204 7.61e+01 1o97D 320 7.63e+01 c.26.2.3,c.31.1.2 81233,81234 2ga9D 469 7.63e+01 2f1kA 279 7.63e+01 1g2oA 268 7.68e+01 1b8oA c.56.2.1 60228 1q4rA 112 7.70e+01 d.58.4.4 95823 1sheA 103 7.72e+01 d.274.1.1 105551 1zh5A 195 7.77e+01 1wpoA 256 7.79e+01 1lay b.57.1.1 27012 2ajfA 597 7.84e+01 1jj2H 167 7.85e+01 1ffkF d.41.4.1 63093 1l7mA 211 7.85e+01 c.108.1.4 73664 1gg1A 350 7.94e+01 1qr7A c.1.10.4 29187 1wviA 257 7.96e+01 1vybA 238 8.00e+01 d.151.1.1 108897 1id1A 153 8.03e+01 1id1A c.2.1.9 62286 2bibA 547 8.04e+01 1xkpC 143 8.05e+01 1d3yA 301 8.07e+01 1d3yA e.12.1.1 43252 2d0oA 610 8.08e+01 2g2dA 193 8.12e+01 1ve6A 582 8.15e+01 1wloA 136 8.23e+01 2a5dA 175 8.23e+01 1u53A 196 8.24e+01 1k8kD 300 8.26e+01 d.198.2.1,d.198.2.1 68309,68310 1vpkA 378 8.27e+01 2fmr 65 8.47e+01 2fmr d.51.1.1 38808 1lfwA 470 8.49e+01 c.56.5.4,d.58.19.1 77942,77943 1uzeA 589 8.51e+01 d.92.1.5 108174 2a74A 643 8.53e+01 1hy7A 173 8.55e+01 d.92.1.11 65957 1smlA 269 8.57e+01 1smlA d.157.1.1 42053 1kwgA 645 8.69e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1mb4A 370 8.76e+01 c.2.1.3,d.81.1.1 78908,78909 1ftrA 296 8.80e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 2c6qA 351 8.81e+01 1x1gA 129 8.83e+01 1o5zA 442 8.93e+01 c.59.1.2,c.72.2.2 92530,92531 1wiwA 290 8.94e+01 1sg6A 393 8.94e+01 e.22.1.1 105522 1wphA 201 8.95e+01