# List of top-scoring protein chains for t06-100-30-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 2.30e-02 2gaeA 346 3.10e-02 1aohA 147 6.06e-01 1aohA b.2.2.2 22401 2c3mA 1231 8.84e-01 1cqyA 99 9.47e-01 1b9zA b.3.1.1 22527 1y2tA 142 1.00e+00 1lzlA 323 1.21e+00 c.69.1.2 78306 2gokA 429 1.45e+00 1utiA 58 1.51e+00 b.34.2.1 99962 1ryp2 233 1.80e+00 1ryp2 8dfr 189 1.88e+00 1aoeA c.71.1.1 34895 1cr1A 296 2.18e+00 1cr1A c.37.1.11 32286 1ahsA 126 2.36e+00 1ahsA b.19.1.1 23794 1vc3B 97 2.36e+00 2ghsA 326 2.65e+00 1vjhA 122 2.87e+00 d.129.3.1 100811 1pb7A 292 2.98e+00 c.94.1.1 88025 1s5uA 138 3.11e+00 d.38.1.1 98573 1pqhA 143 3.14e+00 b.52.2.1 95017 1yueA 427 3.20e+00 1fsgA 233 4.03e+00 1qk3A c.61.1.1 34029 1sq9A 397 4.10e+00 b.69.4.1 105889 1zk7A 467 4.40e+00 1mjfA 281 4.44e+00 c.66.1.17 79198 1zd0A 150 4.46e+00 1r8nA 185 4.76e+00 b.42.4.1 104851 1uj0A 62 4.99e+00 b.34.2.1 99449 1nmoA 247 5.12e+00 c.135.1.1 91980 1efdN 266 5.19e+00 1efdN c.92.2.1 35597 1l2tA 235 5.30e+00 c.37.1.12 73514 1lyqA 104 5.32e+00 b.1.18.17 78302 1dyoA 160 5.44e+00 1dyoA b.18.1.7 23771 1vemA 516 5.92e+00 2arcA 164 6.05e+00 2arcA b.82.4.1 28148 1pgl1 185 6.30e+00 1q6oA 216 6.66e+00 c.1.2.3 95986 1sgjA 284 6.71e+00 c.1.12.5 105535 2bnmA 198 6.71e+00 1v25A 541 6.71e+00 e.23.1.1 108275 1zh5A 195 6.74e+00 1ti6B 274 6.76e+00 b.3.5.1,d.58.1.5 106976,106977 1qznA 173 6.98e+00 b.2.2.2 104669 1vdmA 153 7.26e+00 1kbvA 327 7.81e+00 b.6.1.3,b.6.1.3 68395,68396 1dbiA 280 7.83e+00 1gci c.41.1.1 32543 2cwzA 141 7.98e+00 1kmvA 186 8.12e+00 c.71.1.1 72757 2fnjA 226 8.38e+00 2fdbM 164 8.38e+00 2fg9A 178 8.56e+00 2akaB 299 8.90e+00 1qhqA 140 9.07e+00 1qhqA b.6.1.1 63326 1gcqA 61 9.41e+00 1ckaA b.34.2.1 60434 1q5fA 156 9.63e+00 d.24.1.1 104536 1fyeA 229 9.78e+00 1fyeA c.23.16.4 31477 1w94A 156 1.01e+01 1dzfA 215 1.07e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1ixh 321 1.08e+01 1ixh c.94.1.1 35761 1m98A 317 1.10e+01 a.175.1.1,d.17.4.6 78866,78867 2c3gA 98 1.14e+01 1mrg 263 1.16e+01 1mrj d.165.1.1 42183 1guqA 348 1.24e+01 1guqA d.13.1.2,d.13.1.2 37522,37523 1v04A 355 1.24e+01 b.68.6.2 100240 1rocA 155 1.26e+01 b.1.22.1 97673 1wdeA 294 1.26e+01 2cyeA 133 1.26e+01 1jk4A 89 1.27e+01 b.9.1.1 77130 1ftrA 296 1.27e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1qgdA 662 1.31e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1o54A 277 1.32e+01 c.66.1.13 92482 3cox 507 1.35e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1mj5A 302 1.37e+01 c.69.1.8 91285 2booA 247 1.41e+01 2bopA 85 1.42e+01 2bopA d.58.8.1 39217 1v5vA 401 1.44e+01 1ckmA 330 1.46e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1sqrA 95 1.52e+01 1wucA 250 1.52e+01 1nulA 152 1.54e+01 1nulA c.61.1.1 34011 1vqvA 306 1.54e+01 1id2A 106 1.54e+01 1aac b.6.1.1 62288 1at3A 247 1.55e+01 1at3A b.57.1.1 27021 2a25A 193 1.59e+01 1yf2A 425 1.63e+01 1b9mA 265 1.63e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 2cxcA 144 1.63e+01 1w3iA 293 1.64e+01 c.1.10.1 109152 1uheA 97 1.64e+01 1t0yA 122 1.64e+01 d.15.1.1 99066 1g291 372 1.67e+01 1g291 1z7gA 217 1.67e+01 1b8aA 438 1.79e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1who 96 1.82e+01 1who b.7.3.1 23215 1wmhA 89 1.83e+01 1i0lA 221 1.84e+01 c.61.1.1 71096 2cx1A 187 1.84e+01 1zsyA 357 1.85e+01 1n67A 359 1.89e+01 b.2.3.4,b.2.3.4 85354,85355 1wi1A 126 1.89e+01 1ok8A 394 1.90e+01 b.1.18.4,f.10.1.1 93236,93237 1ixlA 131 1.90e+01 d.38.1.5 90717 1n9lA 109 1.90e+01 d.110.3.6 85468 1uu1A 335 2.07e+01 c.67.1.1 99993 1kzfA 230 2.14e+01 d.108.1.3 73354 2a50A 73 2.25e+01 1q1rA 431 2.25e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 2gw6A 123 2.27e+01 1hmt 132 2.27e+01 1hmt b.60.1.2 27169 1ro7A 259 2.35e+01 c.130.1.1 97667 1vpmA 169 2.40e+01 1q3lA 69 2.40e+01 1vr8A 142 2.40e+01 1x7dA 350 2.43e+01 1b9hA 388 2.43e+01 1b9hA c.67.1.4 34488 1wwrA 171 2.49e+01 1rjdA 334 2.51e+01 c.66.1.37 97558 1yzsA 121 2.55e+01 1fqtA 112 2.59e+01 1fqtA b.33.1.1 24441 1v3yA 192 2.62e+01 2afwA 329 2.63e+01 1d2fA 390 2.68e+01 1d2fA c.67.1.3 34411 1bdmA 327 2.69e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1r1mA 164 2.71e+01 d.79.7.1 96820 1i9zA 347 2.76e+01 1i9yA d.151.1.2 62102 1tp5A 119 2.78e+01 1quqA 129 2.80e+01 1quqA b.40.4.3 25303 2dpmA 284 2.81e+01 2dpmA c.66.1.28 34246 1fc6A 388 2.85e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1cfzA 162 2.87e+01 1cfzA c.56.1.1 33754 1tqyB 415 2.89e+01 c.95.1.1,c.95.1.1 107247,107248 1rypJ 204 2.89e+01 d.153.1.4 41878 1m2tA 254 2.90e+01 d.165.1.1 84761 1l3iA 192 2.97e+01 c.66.1.22 77676 2ew2A 316 2.97e+01 1xw3A 110 2.99e+01 1o12A 376 3.00e+01 b.92.1.5,c.1.9.10 80758,80759 2d1pC 95 3.02e+01 1b0uA 262 3.02e+01 1b0uA c.37.1.12 32370 1xuvA 178 3.04e+01 2ch4A 320 3.05e+01 1xpkC 388 3.06e+01 2awfA 172 3.12e+01 1uirA 314 3.15e+01 c.66.1.17 99429 1xm8A 254 3.16e+01 1tt8A 164 3.16e+01 1xrsA 516 3.18e+01 1kkhA 317 3.21e+01 d.14.1.5,d.58.26.3 72645,72646 1oe1A 336 3.24e+01 b.6.1.3,b.6.1.3 86891,86892 1rypL 212 3.25e+01 d.153.1.4 41880 1x8vA 455 3.26e+01 1ex0A 731 3.30e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1ihgA 370 3.38e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1g2rA 100 3.39e+01 1g2rA d.192.1.1 60231 1xpmA 396 3.43e+01 1x3lA 440 3.43e+01 1uq5A 263 3.45e+01 d.165.1.1 99778 1cz4A 185 3.52e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1uk8A 282 3.53e+01 c.69.1.10 107907 1wmhB 86 3.57e+01 1dkqA 410 3.67e+01 1dklA c.60.1.2 33998 1qy5A 269 3.69e+01 d.122.1.1 96573 1n40A 396 3.77e+01 a.104.1.1 79977 1mrj 247 3.78e+01 1mrj d.165.1.1 42177 1dgwA 178 3.81e+01 1dgwA b.82.1.2 28090 3pcgM 238 3.86e+01 3pchM b.3.6.1 22742 1fjgK 129 3.88e+01 1fjfK c.55.4.1 33733 1riiA 265 3.89e+01 1gen 218 3.92e+01 1gen b.66.1.1 27536 1bvoA 175 3.98e+01 1a3qA b.2.5.3 22457 1zn8A 180 4.00e+01 1h4rA 314 4.00e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1kolA 398 4.01e+01 b.35.1.2,c.2.1.1 77474,77475 1z9zA 60 4.01e+01 1dxrH 258 4.02e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1z5hA 780 4.06e+01 1dekA 241 4.07e+01 1dekA c.37.1.1 31842 1ylxA 103 4.09e+01 1uvjA 664 4.11e+01 e.8.1.6 100045 1imjA 210 4.14e+01 c.69.1.23 71246 1q5dA 419 4.14e+01 a.104.1.1 95891 2d4rA 147 4.14e+01 1dkmA 410 4.16e+01 1dklA c.60.1.2 34000 1utyA 187 4.18e+01 b.147.1.1 108036 2d28C 149 4.20e+01 2fa1A 160 4.23e+01 1vlyA 338 4.24e+01 b.44.2.1,d.250.1.1 108871,108872 1knmA 130 4.26e+01 b.42.2.1 72781 1g2qA 187 4.26e+01 c.61.1.1 65117 1uuzA 137 4.28e+01 d.233.1.1 100024 1tc1A 220 4.28e+01 1tc1A c.61.1.1 34083 1ptf 88 4.29e+01 1ptf d.94.1.1 40549 1m5q1 130 4.32e+01 1v2bA 177 4.36e+01 d.107.1.2 108279 1pdo 135 4.40e+01 1pdo c.54.1.1 33376 1k7cA 233 4.44e+01 c.23.10.4 68267 2napA 723 4.47e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1j98A 157 4.50e+01 1j98A d.185.1.2 62755 1g8aA 227 4.52e+01 c.66.1.3 90506 1t2wA 145 4.60e+01 b.100.1.1 106289 1bn7A 294 4.61e+01 1bn6A c.69.1.8 34677 2pth 193 4.61e+01 2pth c.56.3.1 33793 1bb8 71 4.62e+01 2bb8 d.10.1.1 37478 1gntA 553 4.69e+01 e.26.1.1 70290 1c96A 753 4.76e+01 1amj c.8.2.1,c.83.1.1 30727,35403 2bm8A 236 4.77e+01 2b4aA 138 4.77e+01 2aukA 190 4.77e+01 1zx0A 236 4.82e+01 1quqB 121 4.82e+01 1quqB b.40.4.3 25305 2bkyA 97 4.93e+01 1byfA 125 5.00e+01 1byfA d.169.1.1 42419 2czlA 272 5.02e+01 1qexA 288 5.05e+01 1qexA b.32.1.1 24425 1z6fA 363 5.07e+01 2bt9A 90 5.12e+01 1uz5A 402 5.17e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1vclA 432 5.17e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1a8d 452 5.24e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 2frgP 106 5.30e+01 2gnpA 266 5.30e+01 1ru3A 732 5.32e+01 e.26.1.3 97835 1xipA 388 5.37e+01 1r61A 207 5.38e+01 c.8.8.1 97138 1g79A 218 5.52e+01 1ci0A b.45.1.1 25752 1vh5A 148 5.54e+01 d.38.1.5 100642 1my7A 114 5.57e+01 b.1.18.1 79675 1zkpA 268 5.58e+01 1ufkA 254 5.64e+01 c.66.1.39 99340 1oxxK 353 5.64e+01 b.40.6.3,c.37.1.12 93715,93716 1dl5A 317 5.65e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1yemA 179 5.67e+01 1tu1A 148 5.73e+01 d.107.1.3 107316 2ftrA 108 5.77e+01 1atg 231 5.84e+01 1atg c.94.1.1 35834 1jhfA 202 5.86e+01 a.4.5.2,b.87.1.1 63057,63058 1z2mA 155 5.93e+01 1zoiA 276 5.95e+01 1u9yA 284 5.95e+01 2bwkA 121 5.97e+01 1lnsA 763 6.02e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1ukgA 252 6.02e+01 b.29.1.1 99489 1vk6A 269 6.02e+01 d.113.1.4,d.113.1.4 100851,100852 1dceA 567 6.02e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1dnlA 199 6.06e+01 1ci0A b.45.1.1 25753 1np6A 174 6.08e+01 c.37.1.10 85954 1x31C 206 6.12e+01 1jdpA 441 6.13e+01 c.93.1.1 62906 1rtqA 299 6.13e+01 c.56.5.4 97819 1rdo1 113 6.13e+01 1rtm1 1o69A 394 6.14e+01 c.67.1.4 92560 1idk 359 6.14e+01 1qcxA b.80.1.2 28025 1rzfL 213 6.16e+01 b.1.1.1,b.1.1.2 98152,98153 1o5uA 101 6.16e+01 b.82.1.8 92518 1yymG 313 6.21e+01 1ohpA 125 6.22e+01 1fl0A 171 6.28e+01 1eujA b.40.4.4 25315 1xtmA 175 6.30e+01 1wi5A 119 6.31e+01 1nlqA 108 6.34e+01 b.121.3.1 85853 1dfmA 223 6.37e+01 1d2iA c.52.1.5 33295 1qtoA 122 6.38e+01 1bylA d.32.1.2 38494 1vqoT 120 6.41e+01 1zo2A 129 6.43e+01 1whi 122 6.44e+01 1whi b.39.1.1 24810 1dkuA 317 6.45e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1izoA 417 6.47e+01 a.104.1.1 83851 1yqfA 203 6.47e+01 1rhfA 182 6.47e+01 b.1.1.1,b.1.1.4 97469,97470 1ylnA 252 6.49e+01 2a9dA 372 6.52e+01 2fywA 267 6.62e+01 1ko3A 230 6.63e+01 d.157.1.1 90974 1a34A 159 6.63e+01 1a34A b.121.7.1 23286 2cohA 202 6.67e+01 1ytqA 204 6.68e+01 2bw4A 340 6.68e+01 2cw9A 194 6.76e+01 1n62B 809 6.76e+01 d.41.1.1,d.133.1.1 80092,80093 1ejeA 192 6.80e+01 1ejeA b.45.1.2 25757 1aoeA 192 6.80e+01 1aoeA c.71.1.1 34923 1h6hA 143 6.83e+01 d.189.1.1 65681 1x3mA 415 6.89e+01 1y5eA 169 6.95e+01 1v70A 105 6.97e+01 1z2wA 192 6.97e+01 1ct9A 553 6.98e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1l1oC 181 6.99e+01 b.40.4.3 73480 1ii5A 233 6.99e+01 c.94.1.1 62412 1arb 268 7.03e+01 1arb b.47.1.1 25766 1bcpD 110 7.06e+01 1bcpD b.40.2.1 25132 1vhh 162 7.10e+01 1vhh d.65.1.2 39550 1ryp1 222 7.13e+01 1ryp1 1ukcA 522 7.16e+01 c.69.1.17 107911 2apjA 260 7.16e+01 2c3nA 247 7.17e+01 1vchA 175 7.25e+01 1pguA 615 7.29e+01 b.69.4.1,b.69.4.1 88069,88070 2cxxA 190 7.30e+01 1qj4A 257 7.34e+01 1qj4A c.69.1.20 34796 1iq8A 582 7.39e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1deuA 277 7.47e+01 1theB d.3.1.1 37085 1zlmA 58 7.57e+01 1gvhA 396 7.69e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1ok7A 366 7.72e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1ocxA 182 7.75e+01 b.81.1.3 86814 1pgl2 370 7.76e+01 2bdrA 175 7.77e+01 1pm3A 78 7.84e+01 b.41.1.2 94889 1vkyA 347 7.93e+01 e.53.1.1 108696 1tif 78 7.97e+01 1tif d.15.8.1 37836 1nnwA 252 8.04e+01 d.159.1.5 80674 1z57A 339 8.04e+01 1ex2A 189 8.06e+01 1ex2A c.51.4.2 33225 1oacA 727 8.06e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1rgyA 360 8.10e+01 e.3.1.1 97456 1sn4A 64 8.13e+01 1aho g.3.7.1 44136 1pn0A 665 8.21e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1m6iA 493 8.24e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1dbfA 127 8.36e+01 2chsA d.79.1.2 39761 1gouA 116 8.40e+01 d.1.1.2 65429 1n7fA 97 8.43e+01 b.36.1.1 91692 1un7A 400 8.44e+01 b.92.1.5,c.1.9.10 99657,99658 1yphE 97 8.44e+01 1gqzA 274 8.44e+01 d.21.1.1,d.21.1.1 83311,83312 1v0jA 399 8.44e+01 2dri 271 8.46e+01 2dri c.93.1.1 35637 1jmcA 246 8.46e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1vkdA 338 8.48e+01 b.67.2.4 108644 1kutA 230 8.53e+01 d.143.1.1 73017 1m3sA 186 8.55e+01 c.80.1.3 78573 1eu8A 409 8.65e+01 1eu8A c.94.1.1 59502 2c0rA 362 8.66e+01 1xu9A 286 8.76e+01 2eu9A 355 8.95e+01 1ks9A 291 8.96e+01 a.100.1.7,c.2.1.6 68857,68858