# 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 2ae0X 345 2.97e-02 2gaeA 346 4.04e-02 1aohA 147 7.76e-01 1aohA b.2.2.2 22401 1b0pA 1231 8.75e-01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 2c3mA 1231 1.16e+00 1cqyA 99 1.21e+00 1b9zA b.3.1.1 22527 1kekA 1231 1.22e+00 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1y2tA 142 1.28e+00 1lzlA 323 1.56e+00 c.69.1.2 78306 2gokA 429 1.86e+00 1utiA 58 1.96e+00 b.34.2.1 99962 8dfr 189 2.21e+00 1aoeA c.71.1.1 34895 1ryp2 233 2.25e+00 1ryp2 1cr1A 296 2.89e+00 1cr1A c.37.1.11 32286 1vc3B 97 3.06e+00 1ahsA 126 3.10e+00 1ahsA b.19.1.1 23794 1oebA 62 3.51e+00 b.34.2.1 86909 2ghsA 326 3.57e+00 1cjbA 231 3.59e+00 1qk3A c.61.1.1 34079 1vjhA 122 3.81e+00 d.129.3.1 100811 1pb7A 292 3.85e+00 c.94.1.1 88025 1s5uA 138 3.97e+00 d.38.1.1 98573 1pqhA 143 4.08e+00 b.52.2.1 95017 1yueA 427 4.33e+00 1sq9A 397 5.43e+00 b.69.4.1 105889 1mjfA 281 5.59e+00 c.66.1.17 79198 1fsgA 233 5.63e+00 1qk3A c.61.1.1 34029 1aw8B 91 5.76e+00 1aw8B 1zd0A 150 5.82e+00 1zk7A 467 5.84e+00 1uj0A 62 6.35e+00 b.34.2.1 99449 1r8nA 185 6.54e+00 b.42.4.1 104851 1nmoA 247 6.55e+00 c.135.1.1 91980 1efdN 266 6.77e+00 1efdN c.92.2.1 35597 1l2tA 235 7.01e+00 c.37.1.12 73514 1dyoA 160 7.07e+00 1dyoA b.18.1.7 23771 1itcA 516 7.21e+00 b.3.1.1,c.1.8.1 83705,83706 1lyqA 104 7.55e+00 b.1.18.17 78302 1vemA 516 7.63e+00 2arcA 164 8.17e+00 2arcA b.82.4.1 28148 1sgjA 284 8.18e+00 c.1.12.5 105535 1pgl1 185 8.27e+00 1ti6B 274 8.33e+00 b.3.5.1,d.58.1.5 106976,106977 1q6oA 216 8.35e+00 c.1.2.3 95986 1v25A 541 8.41e+00 e.23.1.1 108275 1zh5A 195 8.85e+00 1qznA 173 9.16e+00 b.2.2.2 104669 2bnmA 198 9.18e+00 1vdmA 153 9.59e+00 1kmvA 186 9.84e+00 c.71.1.1 72757 2fg9A 178 9.88e+00 2cwzA 141 1.01e+01 1umuA 116 1.02e+01 1umuA b.87.1.1 28382 1dbiA 280 1.04e+01 1gci c.41.1.1 32543 1zzcA 198 1.05e+01 2fnjA 226 1.06e+01 1kbvA 327 1.07e+01 b.6.1.3,b.6.1.3 68395,68396 1t3oA 95 1.09e+01 1gw0A 559 1.11e+01 b.6.1.3,b.6.1.3,b.6.1.3 70623,70624,70625 1qhqA 140 1.15e+01 1qhqA b.6.1.1 63326 2fdbM 164 1.16e+01 1bmv1 198 1.22e+01 1bmv1 2akaB 299 1.23e+01 1gcqA 61 1.24e+01 1ckaA b.34.2.1 60434 1rwsA 77 1.27e+01 d.15.3.2 97991 1fyeA 229 1.27e+01 1fyeA c.23.16.4 31477 1q5fA 156 1.28e+01 d.24.1.1 104536 1kv8A 216 1.30e+01 c.1.2.3 73054 1w94A 156 1.30e+01 1hdfA 102 1.33e+01 1ag4 b.11.1.1 23627 1m98A 317 1.44e+01 a.175.1.1,d.17.4.6 78866,78867 1dzfA 215 1.48e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1ixh 321 1.49e+01 1ixh c.94.1.1 35761 2c3gA 98 1.52e+01 1mrg 263 1.53e+01 1mrj d.165.1.1 42183 2shpA 525 1.59e+01 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 1wdeA 294 1.61e+01 1g7oA 215 1.64e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 1rocA 155 1.65e+01 b.1.22.1 97673 1v04A 355 1.67e+01 b.68.6.2 100240 1jk4A 89 1.67e+01 b.9.1.1 77130 1ftrA 296 1.69e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1qgdA 662 1.70e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1guqA 348 1.76e+01 1guqA d.13.1.2,d.13.1.2 37522,37523 1o54A 277 1.77e+01 c.66.1.13 92482 2cyeA 133 1.79e+01 3cox 507 1.81e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 2bopA 85 1.83e+01 2bopA d.58.8.1 39217 1mj5A 302 1.84e+01 c.69.1.8 91285 1v5vA 401 1.86e+01 2booA 247 1.88e+01 1wucA 250 1.95e+01 1npoA 95 1.95e+01 1npoA b.9.1.1 23270 1id2A 106 1.96e+01 1aac b.6.1.1 62288 1ckmA 330 1.96e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1vqvA 306 1.99e+01 1sqrA 95 2.05e+01 1at3A 247 2.06e+01 1at3A b.57.1.1 27021 2a25A 193 2.09e+01 1w3iA 293 2.09e+01 c.1.10.1 109152 1u13A 455 2.10e+01 a.104.1.1 107578 1t0yA 122 2.11e+01 d.15.1.1 99066 2cxcA 144 2.12e+01 1g291 372 2.12e+01 1g291 1b9mA 265 2.14e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1nulA 152 2.15e+01 1nulA c.61.1.1 34011 1n2fA 142 2.19e+01 d.227.1.1 79853 1z7gA 217 2.20e+01 1yf2A 425 2.21e+01 1ov3A 138 2.24e+01 b.34.2.1,b.34.2.1 87451,87452 1uheA 97 2.26e+01 1zs7A 190 2.29e+01 2cx1A 187 2.33e+01 1b8aA 438 2.34e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1e9xA 455 2.38e+01 1ea1A a.104.1.1 18969 1ycyA 71 2.39e+01 1cv2A 296 2.40e+01 1bn6A c.69.1.8 34680 1wmhA 89 2.40e+01 1pda 315 2.43e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1zsyA 357 2.43e+01 1n9lA 109 2.45e+01 d.110.3.6 85468 1ixlA 131 2.48e+01 d.38.1.5 90717 2pil 159 2.50e+01 2pil d.24.1.1 38376 1uu1A 335 2.50e+01 c.67.1.1 99993 1wi1A 126 2.55e+01 1who 96 2.55e+01 1who b.7.3.1 23215 1i0lA 221 2.57e+01 c.61.1.1 71096 8acn 754 2.59e+01 1amj c.8.2.1,c.83.1.1 30724,35400 1n67A 359 2.61e+01 b.2.3.4,b.2.3.4 85354,85355 1ok8A 394 2.66e+01 b.1.18.4,f.10.1.1 93236,93237 1kzfA 230 2.82e+01 d.108.1.3 73354 1b9hA 388 2.88e+01 1b9hA c.67.1.4 34488 1xw4X 110 2.92e+01 1vr8A 142 2.93e+01 2gw6A 123 2.94e+01 1hmt 132 2.95e+01 1hmt b.60.1.2 27169 1g6oA 330 3.00e+01 1g6oA c.37.1.11 32430 2a50A 73 3.03e+01 1ro7A 259 3.07e+01 c.130.1.1 97667 1q1rA 431 3.09e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1q3lA 69 3.14e+01 1v1pA 211 3.14e+01 b.40.2.2,d.15.6.1 108268,108269 1vpmA 169 3.16e+01 1r1mA 164 3.23e+01 d.79.7.1 96820 1tp5A 119 3.24e+01 1p3wA 404 3.24e+01 c.67.1.3 87752 1y4oA 104 3.30e+01 1rjdA 334 3.34e+01 c.66.1.37 97558 1nj4A 363 3.34e+01 b.105.1.1,e.3.1.1 80545,80546 1vd2A 89 3.36e+01 d.15.2.2 108517 1bmdA 327 3.41e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1wwrA 171 3.43e+01 1xseA 295 3.43e+01 1d2fA 390 3.47e+01 1d2fA c.67.1.3 34411 1v3yA 192 3.47e+01 1bzyA 217 3.47e+01 1qk3A c.61.1.1 34071 1nzoA 363 3.48e+01 b.105.1.1,e.3.1.1 92383,92384 1w3fA 315 3.50e+01 1fqtA 112 3.50e+01 1fqtA b.33.1.1 24441 1h9sA 140 3.50e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2afwA 329 3.51e+01 1bdmA 327 3.54e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 2dpmA 284 3.57e+01 2dpmA c.66.1.28 34246 1tqyB 415 3.58e+01 c.95.1.1,c.95.1.1 107247,107248 1x7dA 350 3.62e+01 1l3iA 192 3.66e+01 c.66.1.22 77676 1i9zA 347 3.67e+01 1i9yA d.151.1.2 62102 1quqA 129 3.71e+01 1quqA b.40.4.3 25303 1fc6A 388 3.72e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 2ew2A 316 3.83e+01 1rl2A 137 3.84e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 2d1pC 95 3.86e+01 1cfzA 162 3.89e+01 1cfzA c.56.1.1 33754 1rypJ 204 3.89e+01 d.153.1.4 41878 1b0uA 262 3.90e+01 1b0uA c.37.1.12 32370 1yzsA 121 3.99e+01 1m2tA 254 4.00e+01 d.165.1.1 84761 1xuvA 178 4.06e+01 2ch4A 320 4.08e+01 1uirA 314 4.09e+01 c.66.1.17 99429 1x3lA 440 4.11e+01 1o12A 376 4.14e+01 b.92.1.5,c.1.9.10 80758,80759 1tt8A 164 4.15e+01 1fw9A 164 4.15e+01 1fw9A d.190.1.1 60059 1g2rA 100 4.20e+01 1g2rA d.192.1.1 60231 1xrsA 516 4.21e+01 1kkhA 317 4.24e+01 d.14.1.5,d.58.26.3 72645,72646 2awfA 172 4.27e+01 1xpkC 388 4.30e+01 1oe1A 336 4.34e+01 b.6.1.3,b.6.1.3 86891,86892 1be9A 119 4.34e+01 1pdr b.36.1.1 24774 1xm8A 254 4.35e+01 1rypL 212 4.40e+01 d.153.1.4 41880 1x8vA 455 4.41e+01 1ex0A 731 4.50e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1nfjA 89 4.53e+01 d.68.6.1 91866 1uq5A 263 4.58e+01 d.165.1.1 99778 1ihgA 370 4.60e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1cz4A 185 4.63e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1wmhB 86 4.66e+01 1xw3A 110 4.69e+01 1uk8A 282 4.70e+01 c.69.1.10 107907 1iupA 282 4.70e+01 c.69.1.10 76815 1xpmA 396 4.79e+01 1dkqA 410 4.80e+01 1dklA c.60.1.2 33998 1ef1A 294 4.84e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1mrj 247 4.88e+01 1mrj d.165.1.1 42177 3pcgM 238 4.92e+01 3pchM b.3.6.1 22742 1n40A 396 5.01e+01 a.104.1.1 79977 1fjgK 129 5.05e+01 1fjfK c.55.4.1 33733 1kolA 398 5.05e+01 b.35.1.2,c.2.1.1 77474,77475 1g9mG 321 5.11e+01 1gc1G d.172.1.1 42492 1gen 218 5.13e+01 1gen b.66.1.1 27536 1sz6A 249 5.13e+01 1oxsC 353 5.13e+01 b.40.6.3,c.37.1.12 87519,87520 1bvoA 175 5.15e+01 1a3qA b.2.5.3 22457 1wlpB 138 5.16e+01 1riiA 265 5.18e+01 1dxrH 258 5.21e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1ktjA 129 5.22e+01 b.1.18.7 72974 1zn8A 180 5.25e+01 1dgwA 178 5.29e+01 1dgwA b.82.1.2 28090 1ylxA 103 5.30e+01 1g2qA 187 5.32e+01 c.61.1.1 65117 1z5hA 780 5.34e+01 1evuA 731 5.35e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1knmA 130 5.35e+01 b.42.2.1 72781 1qy5A 269 5.35e+01 d.122.1.1 96573 1h4rA 314 5.36e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1uvjA 664 5.37e+01 e.8.1.6 100045 1pdo 135 5.38e+01 1pdo c.54.1.1 33376 1z9zA 60 5.38e+01 1hhsA 664 5.40e+01 1hi0P e.8.1.6 61045 1imjA 210 5.48e+01 c.69.1.23 71246 1dkmA 410 5.48e+01 1dklA c.60.1.2 34000 1dekA 241 5.48e+01 1dekA c.37.1.1 31842 1ptf 88 5.49e+01 1ptf d.94.1.1 40549 1miwA 404 5.49e+01 a.173.1.1,d.218.1.4 79162,79163 1jpc 109 5.54e+01 1b2pA b.78.1.1 27986 1e2uA 553 5.54e+01 1e1dA e.26.1.1 43362 2d28C 149 5.60e+01 1vlyA 338 5.66e+01 b.44.2.1,d.250.1.1 108871,108872 1ift 263 5.66e+01 1mrj d.165.1.1 42211 1utyA 187 5.66e+01 b.147.1.1 108036 1lokA 291 5.67e+01 c.56.5.4 78122 1m5q1 130 5.70e+01 1bmv2 374 5.71e+01 1bmv2 1iz0A 302 5.71e+01 b.35.1.2,c.2.1.1 83821,83822 1g8aA 227 5.72e+01 c.66.1.3 90506 1uuzA 137 5.72e+01 d.233.1.1 100024 2fa1A 160 5.74e+01 2d4rA 147 5.78e+01 1j98A 157 5.87e+01 1j98A d.185.1.2 62755 1q5dA 419 5.88e+01 a.104.1.1 95891 1tc1A 220 5.89e+01 1tc1A c.61.1.1 34083 1e3jA 352 5.94e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1tvzA 388 5.95e+01 c.95.1.2,c.95.1.2 107367,107368 1t9mA 214 5.95e+01 1zx0A 236 5.99e+01 2bm8A 236 6.02e+01 1v2bA 177 6.02e+01 d.107.1.2 108279 1h5zA 455 6.03e+01 a.104.1.1 90622 2pth 193 6.04e+01 2pth c.56.3.1 33793 1bn7A 294 6.07e+01 1bn6A c.69.1.8 34677 1bb8 71 6.17e+01 2bb8 d.10.1.1 37478 1c96A 753 6.17e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1k7cA 233 6.19e+01 c.23.10.4 68267 1aonO 97 6.23e+01 b.35.1.1 24642 1t2wA 145 6.26e+01 b.100.1.1 106289 2bb2 181 6.36e+01 2bb2 b.11.1.1,b.11.1.1 23604,23605 2aukA 190 6.40e+01 1xbrA 184 6.40e+01 1xbrA b.2.5.4 22458 2napA 723 6.47e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1qexA 288 6.47e+01 1qexA b.32.1.1 24425 2czlA 272 6.59e+01 1quqB 121 6.61e+01 1quqB b.40.4.3 25305 1gntA 553 6.64e+01 e.26.1.1 70290 1tc6A 236 6.66e+01 d.122.1.1 106756 1z6fA 363 6.69e+01 1byfA 125 6.74e+01 1byfA d.169.1.1 42419 1y7tA 327 6.75e+01 1vh5A 148 6.76e+01 d.38.1.5 100642 2b4aA 138 6.79e+01 1g79A 218 6.81e+01 1ci0A b.45.1.1 25752 2bkyA 97 6.81e+01 1vclA 432 6.82e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1yasA 257 6.82e+01 1qj4A c.69.1.20 34801 1uz5A 402 6.84e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1ru3A 732 6.84e+01 e.26.1.3 97835 2gnpA 266 6.91e+01 1n3oA 252 7.06e+01 b.29.1.1 79967 1bwzA 274 7.09e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1amp 291 7.13e+01 1amp c.56.5.4 33837 1oxxK 353 7.13e+01 b.40.6.3,c.37.1.12 93715,93716 1xmrA 243 7.27e+01 2frgP 106 7.28e+01 1r61A 207 7.34e+01 c.8.8.1 97138 1dl5A 317 7.35e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1wdxA 69 7.38e+01 1dnlA 199 7.38e+01 1ci0A b.45.1.1 25753 2bt9A 90 7.41e+01 1c4xA 285 7.43e+01 1c4xA c.69.1.10 34684 1ufkA 254 7.49e+01 c.66.1.39 99340 1zkpA 268 7.51e+01 2ftrA 108 7.56e+01 1xipA 388 7.59e+01 1yemA 179 7.60e+01 1zoiA 276 7.65e+01 1z2mA 155 7.66e+01 1jhfA 202 7.74e+01 a.4.5.2,b.87.1.1 63057,63058 1u9yA 284 7.75e+01 1obr 326 7.75e+01 1aye c.56.5.2 33828 1atg 231 7.76e+01 1atg c.94.1.1 35834 1wi5A 119 7.79e+01 1a8d 452 7.83e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1ukgA 252 7.84e+01 b.29.1.1 99489 1dceA 567 7.84e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1np6A 174 7.85e+01 c.37.1.10 85954 1qciA 262 7.90e+01 1qi7A d.165.1.1 42201 1hh2P 344 7.92e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1uolA 219 7.94e+01 b.2.5.2 99695 1kcbA 340 7.94e+01 b.6.1.3,b.6.1.3 90951,90952 1yymG 313 7.96e+01 1rzfL 213 8.01e+01 b.1.1.1,b.1.1.2 98152,98153 1x31C 206 8.05e+01 1rtqA 299 8.05e+01 c.56.5.4 97819 1h0xA 100 8.06e+01 d.68.6.1 76451 1idk 359 8.17e+01 1qcxA b.80.1.2 28025 1o69A 394 8.20e+01 c.67.1.4 92560 1whi 122 8.23e+01 1whi b.39.1.1 24810 2bwkA 121 8.25e+01 1nfa 178 8.28e+01 1a02N b.2.5.3 22442 2fywA 267 8.29e+01 1xtmA 175 8.29e+01 1pwhA 327 8.30e+01 c.79.1.1 95224 1dfmA 223 8.33e+01 1d2iA c.52.1.5 33295 1ohpA 125 8.33e+01 1vk6A 269 8.34e+01 d.113.1.4,d.113.1.4 100851,100852 1lnsA 763 8.37e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1o5uA 101 8.37e+01 b.82.1.8 92518 1my7A 114 8.49e+01 b.1.18.1 79675 1tu1A 148 8.51e+01 d.107.1.3 107316 1rdo1 113 8.55e+01 1rtm1 1fl0A 171 8.56e+01 1eujA b.40.4.4 25315 1jv2A 957 8.58e+01 b.1.15.1,b.1.15.1,b.1.15.1,b.69.8.1 67334,67335,67336,67337 1zo2A 129 8.58e+01 1aoeA 192 8.60e+01 1aoeA c.71.1.1 34923 2cohA 202 8.61e+01 1ylnA 252 8.62e+01 2c3nA 247 8.64e+01 1ytqA 204 8.67e+01 1izoA 417 8.68e+01 a.104.1.1 83851 1dkuA 317 8.70e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1y5mA 276 8.73e+01 2bdrA 175 8.73e+01 1qtoA 122 8.74e+01 1bylA d.32.1.2 38494 1yqfA 203 8.74e+01 1y5eA 169 8.75e+01 1ko3A 230 8.77e+01 d.157.1.1 90974 1z2wA 192 8.78e+01 1nlqA 108 8.79e+01 b.121.3.1 85853 1h6hA 143 8.82e+01 d.189.1.1 65681 2a9dA 372 8.87e+01 1ukcA 522 8.88e+01 c.69.1.17 107911 1v70A 105 8.96e+01 2bw4A 340 8.98e+01 1x3mA 415 8.98e+01