# List of top-scoring protein chains for t04-100-30-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 1xx4A 261 3.49e-02 1z47A 355 3.72e-02 1l2tA 235 8.91e-02 c.37.1.12 73514 1fobA 334 2.00e-01 c.1.8.3 83255 1sg4A 260 2.78e-01 1c9kA 180 2.88e-01 1c9kB c.37.1.11 32363 1jf8A 131 4.10e-01 c.44.1.1 66621 1yvkA 163 5.17e-01 2b99A 156 5.21e-01 1yuwA 554 1.31e+00 1vplA 256 1.34e+00 2reb 352 1.37e+00 2reb c.37.1.11,d.48.1.1 32282,38767 1gvoA 364 1.42e+00 c.1.4.1 76357 2gqrA 237 1.48e+00 1b0uA 262 1.54e+00 1b0uA c.37.1.12 32370 1nekA 588 1.73e+00 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1u94A 356 1.80e+00 c.37.1.11,d.48.1.1 107743,107744 1vypX 364 1.81e+00 c.1.4.1 108905 1t6kA 278 2.01e+00 1h61A 364 2.13e+00 1oyc c.1.4.1 60657 1vyrA 364 2.13e+00 c.1.4.1 108906 2abbA 364 2.29e+00 1srrA 124 2.69e+00 1dz3A c.23.1.1 31110 1f28A 297 2.72e+00 1bkpA d.117.1.1 59608 1a04A 215 2.79e+00 1a04A a.4.6.2,c.23.1.1 16234,31089 1mb3A 124 2.87e+00 c.23.1.1 78907 1u1wA 298 2.95e+00 1y9kA 157 2.98e+00 1c44A 123 3.10e+00 1qndA d.106.1.1 40795 1e19A 314 3.14e+00 1b7bA c.73.1.1 34967 1lt8A 406 3.17e+00 c.1.26.1 78186 1v33A 366 3.28e+00 d.264.1.1 100278 1m3uA 264 3.71e+00 c.1.12.8 84784 2f9zC 159 3.80e+00 2anuA 255 3.81e+00 1u0sY 118 4.02e+00 c.23.1.1 107566 1z2lA 423 4.31e+00 1tmy 120 4.39e+00 1dbwA c.23.1.1 31083 1xubA 298 4.46e+00 1bupA 386 4.56e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1kay 381 4.63e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1kutA 230 5.29e+00 d.143.1.1 73017 1w44A 331 5.49e+00 1g291 372 5.57e+00 1g291 1hkkA 364 5.86e+00 c.1.8.5,d.26.3.1 90634,90635 2bvpA 276 5.99e+00 1wb0A 445 6.11e+00 2gtrA 261 6.13e+00 1e6uA 321 6.43e+00 1bsvA c.2.1.2 29805 1gheA 177 6.84e+00 d.108.1.1 76222 1e9lA 377 6.99e+00 1e9lA c.1.8.5,d.26.3.1 59395,59396 1iy8A 267 7.35e+00 c.2.1.2 83774 1cr1A 296 7.57e+00 1cr1A c.37.1.11 32286 2c31A 568 7.90e+00 1i39A 225 7.92e+00 1ekeA c.55.3.1 61585 2czdA 208 8.13e+00 1vl8A 267 8.15e+00 c.2.1.2 108733 1e7rA 321 8.20e+00 1bsvA c.2.1.2 29808 1cnzA 363 8.47e+00 1cnzA c.77.1.1 35061 1vf8A 377 8.55e+00 1ofuA 320 9.33e+00 c.32.1.1,d.79.2.1 86972,86973 2b0vA 153 1.01e+01 1z41A 338 1.03e+01 1zanL 214 1.04e+01 1yavA 159 1.06e+01 1yqvL 211 1.06e+01 1ospL 214 1.09e+01 32c2A b.1.1.1,b.1.1.2 20116,21146 1ctn 540 1.10e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 2a1xA 308 1.14e+01 1fbnA 230 1.16e+01 1fbnA c.66.1.3 34181 1k77A 260 1.19e+01 c.1.15.5 72096 1o0iA 138 1.20e+01 d.38.1.5 86532 1g8sA 230 1.21e+01 c.66.1.3 90507 1n0wA 243 1.23e+01 c.37.1.11 79772 1p5jA 372 1.27e+01 c.79.1.1 104067 1erzA 303 1.28e+01 1erzA d.160.1.2 59498 1uf5A 303 1.28e+01 d.160.1.2 107808 2fbjL 213 1.30e+01 8fabA b.1.1.1,b.1.1.2 19850,20954 2axyA 73 1.30e+01 2adgA 214 1.32e+01 2ajuL 216 1.36e+01 1iktA 120 1.36e+01 d.106.1.1 66188 1ztxL 212 1.37e+01 1fzqA 181 1.37e+01 1hurA c.37.1.8 32060 1forL 210 1.37e+01 8fabA b.1.1.1,b.1.1.2 19988,21044 1vpqA 273 1.41e+01 1vjoA 393 1.42e+01 c.67.1.3 100827 2bbsA 290 1.45e+01 1siiA 646 1.45e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1rjoA 646 1.46e+01 1y1oA 203 1.47e+01 1szoA 257 1.50e+01 c.14.1.3 106164 1s7jA 262 1.50e+01 d.21.1.2 98647 1g6hA 257 1.52e+01 1gajA c.37.1.12 60318 1i6wA 181 1.55e+01 1i6wA c.69.1.18 61859 1ispA 181 1.56e+01 c.69.1.18 76778 1rthA 560 1.60e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1q9rA 219 1.61e+01 b.1.1.1,b.1.1.2 96305,96306 1g71A 347 1.63e+01 1g71A d.264.1.1 43268 1phk 298 1.66e+01 1cdkA d.144.1.7 41635 2f5gA 133 1.68e+01 1nffA 260 1.72e+01 c.2.1.2 80457 1xmiA 291 1.73e+01 1pwxA 254 1.74e+01 c.2.1.2 95262 1i60A 278 1.75e+01 c.1.15.4 71118 1mlbA 214 1.79e+01 8fabA b.1.1.1,b.1.1.2 20050,21092 2aabL 218 1.86e+01 1vfvA 366 1.90e+01 c.37.1.9 108592 1w2xA 758 1.90e+01 c.14.1.4,c.14.1.4 109134,109135 1rurL 217 1.92e+01 b.1.1.1,b.1.1.2 97881,97882 1t71A 281 1.93e+01 1mexL 213 1.96e+01 b.1.1.1,b.1.1.2 91259,91260 1uyrA 737 1.96e+01 c.14.1.4,c.14.1.4 100188,100189 1zmtA 254 1.99e+01 1wy5A 317 2.01e+01 1jbkA 195 2.02e+01 c.37.1.20 71631 1vetA 124 2.04e+01 d.110.7.1 108553 1t8tA 271 2.05e+01 c.37.1.5 106685 1xp8A 366 2.07e+01 2fexA 188 2.09e+01 1px5A 349 2.10e+01 a.160.1.2,d.218.1.6 95277,95278 2fyxA 143 2.10e+01 1seqL 213 2.11e+01 1j8mF 297 2.13e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1uh5A 329 2.18e+01 c.2.1.2 107840 1ryiA 382 2.18e+01 1repC 251 2.19e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1g0cA 364 2.24e+01 7a3hA c.1.8.3 60165 1edqA 540 2.27e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1mvoA 136 2.27e+01 c.23.1.1 79513 1mjuL 219 2.28e+01 b.1.1.1,b.1.1.2 91304,91305 1vm7A 311 2.32e+01 c.72.1.1 108884 1jmvA 141 2.33e+01 c.26.2.4 66897 1lnsA 763 2.33e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1zuhA 168 2.34e+01 1j8yF 297 2.35e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1w78A 422 2.36e+01 1e6oL 212 2.36e+01 32c2A b.1.1.1,b.1.1.2 20494,21452 1gmlA 178 2.42e+01 c.8.5.2 70273 1me8A 503 2.44e+01 c.1.5.1 79028 2azpA 318 2.44e+01 1ek0A 170 2.45e+01 1ctqA c.37.1.8 32076 1o8uA 257 2.46e+01 c.14.1.3 81194 1r0wA 286 2.48e+01 c.37.1.12 96754 2ae2A 260 2.50e+01 1bdb c.2.1.2 29945 1wt4A 73 2.55e+01 1ncwL 219 2.56e+01 b.1.1.1,b.1.1.2 85557,85558 1zmoA 244 2.60e+01 1lwjA 441 2.60e+01 b.71.1.1,c.1.8.1 74303,74304 1vh5A 148 2.65e+01 d.38.1.5 100642 1ei6A 406 2.71e+01 c.76.1.4 90443 1e55A 512 2.72e+01 1e70M c.1.8.4 28934 1xb4A 202 2.73e+01 1ltzA 297 2.74e+01 d.178.1.1 74254 1iqyA 638 2.74e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 2ct8A 497 2.75e+01 2av4A 162 2.76e+01 1h49A 512 2.82e+01 c.1.8.4 83477 1m7gA 211 2.89e+01 c.37.1.4 78724 1avk 638 2.96e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1z5yE 149 2.97e+01 1eiwA 111 2.98e+01 1eiwA c.23.3.1 31130 1ekeA 230 2.98e+01 1ekeA c.55.3.1 33572 7odcA 424 3.06e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 2fukA 220 3.09e+01 1n13B 113 3.10e+01 2cvhA 220 3.14e+01 1q74A 303 3.23e+01 c.134.1.1 96019 1ebfA 358 3.23e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 2bo4A 397 3.24e+01 1xwiA 322 3.24e+01 1w6gA 646 3.24e+01 1rvgA 305 3.38e+01 c.1.10.2 97920 1s8nA 205 3.43e+01 c.23.1.1 105374 1nu7D 282 3.48e+01 a.8.6.1,a.8.6.1 92191,92192 1vdmA 153 3.58e+01 2dri 271 3.58e+01 2dri c.93.1.1 35637 1tetL 216 3.59e+01 32c2A b.1.1.1,b.1.1.2 19902,20996 1h3fA 432 3.63e+01 c.26.1.1,d.66.1.4 76631,76632 1ji0A 240 3.63e+01 c.37.1.12 71665 2bl5A 140 3.66e+01 1ps9A 671 3.68e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1svdA 473 3.70e+01 2ethA 154 3.73e+01 1ui8A 638 3.74e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1rl2A 137 3.77e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1zhvA 134 3.78e+01 1ubeA 349 3.79e+01 c.37.1.11,d.48.1.1 88412,88413 1gefA 123 3.79e+01 1gefA c.52.1.18 60465 1eq2A 310 3.85e+01 1eq2A c.2.1.2 29814 2fl4A 149 3.86e+01 2ftxB 64 3.87e+01 2gr8A 99 3.88e+01 1gvnB 287 3.90e+01 c.37.1.21 76354 1bg4 302 4.03e+01 1taxA c.1.8.3 28806 1xgyL 216 4.04e+01 7a3hA 303 4.04e+01 7a3hA c.1.8.3 28817 1g7sA 594 4.07e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1z7bA 358 4.09e+01 2cqnA 77 4.11e+01 1mi8A 158 4.11e+01 b.86.1.2 91279 1xq6A 253 4.14e+01 1dbiA 280 4.17e+01 1gci c.41.1.1 32543 1v5wA 343 4.21e+01 c.37.1.11 108387 1s2dA 167 4.26e+01 c.23.14.1 98377 1ne9A 335 4.27e+01 d.108.1.4,d.108.1.4 91839,91840 1har 216 4.30e+01 1rthA e.8.1.2 43025 1a0cA 438 4.32e+01 1a0cA c.1.15.3 29529 2amyA 246 4.33e+01 1u2eA 289 4.40e+01 1nif 340 4.40e+01 1nif b.6.1.3,b.6.1.3 23048,23049 1nu0A 138 4.41e+01 c.55.3.8 92165 1ig3A 263 4.43e+01 1ig3A b.82.6.1,c.100.1.1 62358,62359 1ma3A 253 4.44e+01 c.31.1.5 78883 1skoA 143 4.48e+01 d.110.7.1 105676 1i6iA 366 4.50e+01 1bg2 c.37.1.9 61844 1vrtA 560 4.51e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1ekqA 272 4.53e+01 1c3qA c.72.1.2 34941 1shsA 147 4.54e+01 1shsA b.15.1.1 23675 1u9jA 358 4.54e+01 1jx7A 117 4.59e+01 c.114.1.1 77195 1h54A 754 4.65e+01 a.102.1.4,b.30.5.3 60634,60635 1jx2B 315 4.71e+01 c.37.1.8 67404 1ih8A 271 4.73e+01 2nsyA c.26.2.1 62377 1t6cA 315 4.81e+01 c.55.1.8,c.55.1.8 106558,106559 1kafA 108 4.81e+01 d.199.1.1 68372 1xttA 216 4.82e+01 1gvfA 286 4.83e+01 c.1.10.2 70599 1v7lA 163 4.88e+01 1kqpA 271 4.89e+01 c.26.2.1 72883 2b6eA 146 5.01e+01 1ng4A 390 5.02e+01 c.3.1.2,d.16.1.3 85666,85667 1j5sA 463 5.12e+01 c.1.9.8 71580 1vp8A 201 5.13e+01 1nzjA 298 5.17e+01 c.26.1.1 92377 1f9aA 168 5.18e+01 1f9aA c.26.1.3 31602 1ezm 301 5.20e+01 1hyt d.92.1.2 58980 1qqqA 264 5.21e+01 1bkpA d.117.1.1 40931 1dysA 348 5.22e+01 1bvwA c.6.1.1 30669 1qv9A 283 5.23e+01 c.127.1.1 96356 1tfr 305 5.30e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1yu6A 275 5.33e+01 2h1nA 567 5.39e+01 2acaA 189 5.45e+01 1gcoA 261 5.45e+01 1ybvA c.2.1.2 29884 1geeA 261 5.58e+01 c.2.1.2 90509 1ilr1 152 5.60e+01 1irp 1dkiA 371 5.60e+01 1dkiA d.3.1.1 37090 1hzdA 272 5.63e+01 c.14.1.3 65969 1qhtA 775 5.66e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1gvnA 90 5.70e+01 a.8.2.1 76353 2au3A 407 5.81e+01 1g5aA 628 5.84e+01 b.71.1.1,c.1.8.1 65152,65153 1t9bA 677 5.86e+01 1n2eA 300 5.91e+01 c.26.1.4 85268 1auk 489 5.94e+01 1auk c.76.1.2 35030 2bllA 345 5.98e+01 1a48 306 5.98e+01 1a48 d.143.1.1 41590 6mhtA 327 6.03e+01 6mhtA c.66.1.26 34226 1f5aA 513 6.03e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1v72A 356 6.04e+01 1svfB 38 6.12e+01 1svfB h.3.2.1 45764 1yh3A 256 6.16e+01 1j7nA 776 6.19e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1hh1A 143 6.19e+01 1gefA c.52.1.18 61036 1o66A 275 6.19e+01 c.1.12.8 92547 1orrA 347 6.22e+01 c.2.1.2 93460 1o70A 324 6.30e+01 b.118.1.1,b.118.1.1 81115,81116 1xk7A 408 6.30e+01 1cseE 274 6.31e+01 1gci c.41.1.1 32481 1xhlA 297 6.36e+01 c.2.1.2 109591 1m3qA 317 6.38e+01 a.96.1.3,d.129.1.2 91184,91185 1q45A 391 6.38e+01 c.1.4.1 95780 2ac2A 309 6.41e+01 1es9A 232 6.47e+01 1wab c.23.10.3 31340 1r0rE 274 6.48e+01 c.41.1.1 96735 1vp2A 208 6.53e+01 1wqaA 455 6.58e+01 2fbiA 142 6.63e+01 1hl9A 449 6.64e+01 b.71.1.3,c.1.8.11 90650,90651 2ac4A 309 6.69e+01 2fo1D 85 6.71e+01 2b61A 377 6.72e+01 1ayoA 130 6.72e+01 1ayoA b.2.4.1 22431 1yd9A 193 6.72e+01 1o69A 394 6.74e+01 c.67.1.4 92560 1vcdA 126 6.76e+01 1vk6A 269 6.87e+01 d.113.1.4,d.113.1.4 100851,100852 1wab 232 6.87e+01 1wab c.23.10.3 31341 1xa3A 437 6.89e+01 1ef8A 261 6.91e+01 1ef8A c.14.1.3 30921 1thm 279 6.92e+01 1gci c.41.1.1 32544 1ebmA 317 6.92e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 2d48A 129 6.94e+01 1q7zA 566 6.99e+01 c.1.21.2,c.1.26.1 96090,96091 1yvrA 538 7.01e+01 1fiy 883 7.03e+01 1fiy c.1.12.3 29307 2g5dA 422 7.06e+01 1fmcA 255 7.10e+01 1cydA c.2.1.2 29856 1obdA 306 7.10e+01 d.143.1.1 86767 1hziA 129 7.14e+01 1rcb a.26.1.2 61449 1gklA 297 7.24e+01 c.69.1.2 65250 1ursA 402 7.31e+01 c.94.1.1 99833 1meoA 209 7.33e+01 c.65.1.1 79035 1rcb 129 7.34e+01 1rcb a.26.1.2 16854 1itxA 419 7.38e+01 c.1.8.5,d.26.3.1 71425,71426 1ciy 590 7.38e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 2h88A 621 7.39e+01 2ai4A 119 7.39e+01 1qsgA 265 7.49e+01 1eny c.2.1.2 29935 2cbzA 237 7.50e+01 1iae 200 7.51e+01 1iae d.92.1.8 40311 1ta3B 303 7.52e+01 c.1.8.3 106732 1dozA 309 7.54e+01 1ak1 c.92.1.1 35592 1g0hA 252 7.54e+01 1dk4A e.7.1.1 60171 2fikA 287 7.58e+01 1eqjA 511 7.60e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1pda 315 7.65e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1s5lZ 62 7.69e+01 2g8mA 264 7.70e+01 2c7pA 327 7.73e+01 2his 312 7.78e+01 1taxA c.1.8.3 28918 2cnqA 306 7.79e+01 2g8oA 264 7.81e+01 1iab 200 7.85e+01 1iae d.92.1.8 40312 1cunA 213 7.88e+01 1cunA a.7.1.1,a.7.1.1 16313,16314 1nni1 174 7.91e+01 1w8iA 156 8.01e+01 2fbwA 621 8.05e+01 2h4vA 320 8.07e+01 1pg4A 652 8.08e+01 e.23.1.1 88067 1evfA 264 8.09e+01 1bkpA d.117.1.1 40932 1pwhA 327 8.11e+01 c.79.1.1 95224 2aefA 234 8.11e+01 1hp1A 516 8.13e+01 d.114.1.1,d.159.1.2 70976,70977 1amf 233 8.13e+01 1wod c.94.1.1 35833 1lehA 364 8.13e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1wod 233 8.16e+01 1wod c.94.1.1 35832 2af4C 333 8.18e+01 1kv8A 216 8.22e+01 c.1.2.3 73054 2gzxA 265 8.25e+01 1j31A 262 8.29e+01 d.160.1.2 90808 1wywA 230 8.36e+01 2ffjA 300 8.39e+01 1e5dA 402 8.39e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1w36C 1122 8.40e+01 1fts 295 8.44e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1zp4A 304 8.45e+01 1vc3B 97 8.46e+01 1odzA 386 8.47e+01 c.1.8.3 86889 1w1oA 534 8.61e+01 d.58.32.4,d.145.1.1 109071,109072 1zkpA 268 8.61e+01 1qsmA 152 8.62e+01 1qsmA d.108.1.1 40808 1mzjA 339 8.75e+01 c.95.1.2,c.95.1.2 79700,79701 1v5eA 590 8.78e+01 1b5tA 275 8.79e+01 1b5tA c.1.23.1 29676 1yvoA 172 8.80e+01 2ajrA 331 8.82e+01 1vk9A 151 8.84e+01 c.139.1.1 108640 1gtmA 419 8.84e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1ur3M 319 8.88e+01 c.1.7.1 99806 1u5tC 202 8.88e+01 a.4.5.54,a.4.5.54 107688,107689 1n7kA 234 8.91e+01 c.1.10.1 85374 2gkeA 274 8.94e+01 1m8jA 181 8.96e+01 c.26.1.3 84875