# 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 1dyqA 234 2.16e-01 3seb b.40.2.2,d.15.6.1 59140,59141 1pnsC 206 5.91e-01 i.1.1.1 88170 1zynA 202 5.98e-01 2rslA 140 6.01e-01 2rslA c.53.1.1 33345 2ewrA 170 7.75e-01 1fjgC 239 7.85e-01 1fjfC d.52.3.1,d.53.1.1 38831,38839 2fclA 169 8.52e-01 1sqsA 242 1.19e+00 c.23.5.5 98968 1repC 251 1.21e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1m93A 55 1.37e+00 e.1.1.1 91235 1hyuA 521 1.48e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1qhlA 227 2.29e+00 1qhlA c.37.1.12 32382 1ycyA 71 3.01e+00 2bg5A 324 3.17e+00 1a0rP 245 3.30e+00 1b9yC c.47.1.6 33054 1ydmA 187 3.84e+00 1ex0A 731 4.02e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1regX 122 4.03e+00 1regX d.58.27.1 39406 1evuA 731 4.23e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 2g9iA 249 4.30e+00 1y96B 85 4.34e+00 2pil 159 4.97e+00 2pil d.24.1.1 38376 1zpvA 91 4.98e+00 1iz5A 249 5.13e+00 d.131.1.2,d.131.1.2 83834,83835 1od8A 313 5.15e+00 c.1.8.3 86838 1v0lA 313 5.19e+00 c.1.8.3 108207 2afbA 351 5.22e+00 1e0wA 313 5.25e+00 1taxA c.1.8.3 59150 1d2oA 187 5.39e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1c7qA 445 5.45e+00 2pgi c.80.1.2 35307 2cxcA 144 5.72e+00 2b7eA 59 5.98e+00 1c52 131 6.13e+00 1c52 a.3.1.1 15810 1kqpA 271 6.16e+00 c.26.2.1 72883 1hdoA 206 6.48e+00 1he2A c.2.1.2 60965 1ih8A 271 6.51e+00 2nsyA c.26.2.1 62377 1s55A 156 6.58e+00 1iqaA 160 6.72e+00 b.22.1.1 71274 1d2rA 326 7.36e+00 1d2rB c.26.1.1 31572 1lwjA 441 7.67e+00 b.71.1.1,c.1.8.1 74303,74304 1e0tA 470 7.96e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2b33A 140 8.22e+00 2flsA 132 8.36e+00 1b25A 619 8.86e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 1a53 247 8.92e+00 1a53 c.1.2.4 28564 1exg 110 9.00e+00 1exg b.2.2.1 22387 1t8qA 336 9.11e+00 c.1.18.3 106669 1igs 248 9.29e+00 1a53 c.1.2.4 28565 1sek 378 1.00e+01 1sek e.1.1.1 42675 1vkuA 100 1.01e+01 a.28.1.1 108690 2gmqA 118 1.02e+01 1zruA 264 1.06e+01 1o1zA 234 1.06e+01 c.1.18.3 86555 2bsdA 264 1.08e+01 1pbgA 468 1.11e+01 1e70M c.1.8.4 28946 1o6dA 163 1.11e+01 c.116.1.3 92567 2fgtA 417 1.15e+01 1m4jA 142 1.18e+01 d.109.1.2 78602 1j5vA 351 1.19e+01 c.72.1.1 71585 1h72C 296 1.23e+01 d.14.1.5,d.58.26.1 60712,60713 1r5jA 337 1.23e+01 c.77.1.5 97097 1m07A 111 1.27e+01 d.5.1.1 78328 1qavA 90 1.28e+01 1qauA b.36.1.1 24777 1n8kA 374 1.32e+01 b.35.1.2,c.2.1.1 80298,80299 1hetA 374 1.33e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1i6lA 328 1.35e+01 c.26.1.1 66041 1bn8A 420 1.35e+01 1pcl b.80.1.1 28022 1a99A 344 1.38e+01 1pot c.94.1.1 35812 1o0yA 260 1.46e+01 c.1.10.1 80756 1tf1A 198 1.46e+01 d.110.2.2 106826 1b56 135 1.47e+01 1hmt b.60.1.2 27183 1t0hA 132 1.51e+01 b.34.2.1 106207 1bia 321 1.53e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1xwvA 129 1.54e+01 1t0aA 159 1.59e+01 1s0pA 176 1.67e+01 a.192.1.1 98300 2ohxA 374 1.69e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1qlmA 316 1.73e+01 1qlmA d.147.1.1 41765 2aefA 234 1.82e+01 1u3wA 374 1.85e+01 1vqoL 165 1.85e+01 1nijA 318 1.85e+01 c.37.1.10,d.237.1.1 85741,85742 1xcbA 211 1.93e+01 a.4.5.38,c.2.1.12 109552,109553 2cygA 312 1.96e+01 2gfgA 193 1.97e+01 1qzgA 187 2.01e+01 b.40.4.3 96643 1xhfA 123 2.02e+01 1idk 359 2.02e+01 1qcxA b.80.1.2 28025 1wwhA 119 2.05e+01 1vcvA 226 2.06e+01 1ej0A 180 2.09e+01 1ej0A c.66.1.2 34179 1wu3I 161 2.10e+01 1gyxA 76 2.10e+01 d.80.1.1 76387 1i8fA 81 2.11e+01 1i8fA b.38.1.1 61959 1qy1A 174 2.13e+01 b.60.1.1 96568 1s9rA 410 2.15e+01 d.126.1.4 98758 1ois 223 2.17e+01 1a36A e.15.1.1 43267 1s50A 259 2.19e+01 2etxA 209 2.20e+01 1dkuA 317 2.24e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1wrjA 156 2.25e+01 2asbA 251 2.27e+01 1fh9A 312 2.32e+01 1taxA c.1.8.3 28913 2fbyA 205 2.34e+01 1ydyA 356 2.35e+01 1fhdA 312 2.39e+01 1taxA c.1.8.3 28915 1zthA 258 2.39e+01 1fwkA 296 2.42e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 2his 312 2.44e+01 1taxA c.1.8.3 28918 2bwfA 77 2.46e+01 1ma3A 253 2.48e+01 c.31.1.5 78883 5nul 138 2.48e+01 5nul c.23.5.1 31191 1plq 258 2.49e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1p3dA 475 2.51e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2amhA 207 2.52e+01 1vjpA 394 2.55e+01 c.2.1.3,d.81.1.3 100828,100829 1ml9A 302 2.56e+01 b.85.7.1 79282 1f0cA 305 2.62e+01 1c8oA e.1.1.1 42676 1tt8A 164 2.72e+01 1fw9A 164 2.73e+01 1fw9A d.190.1.1 60059 1oj4A 283 2.74e+01 d.14.1.5,d.58.26.5 93083,93084 1jj2K 164 2.84e+01 1ffkJ c.12.1.1 63096 2bo4A 397 2.86e+01 2adoA 196 2.87e+01 1nf3C 128 2.88e+01 b.36.1.1 85596 1xkrA 206 2.88e+01 2gw6A 123 2.88e+01 1svpA 161 2.90e+01 1svpA b.47.1.3 26384 1vjjA 692 2.92e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1juvA 193 2.95e+01 c.71.1.1 90912 4uagA 437 2.98e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1h8vA 218 3.02e+01 2nlrA b.29.1.11 60795 1cfr 285 3.04e+01 1cfr c.52.1.7 33312 1zndA 174 3.05e+01 1q8hA 49 3.05e+01 g.32.1.1 96207 1i06A 180 3.08e+01 1mup b.60.1.1 27131 1vddA 228 3.09e+01 e.49.1.1 108519 1oa2A 218 3.13e+01 b.29.1.11 86721 1u2xA 474 3.21e+01 c.72.1.3 107622 1mup 166 3.23e+01 1mup b.60.1.1 27133 1u1hA 765 3.26e+01 c.1.22.2,c.1.22.2 107580,107581 1hqz1 141 3.27e+01 1ygs 234 3.29e+01 1ygs b.26.1.1 23907 1jv4A 162 3.29e+01 b.60.1.1 67343 1tlk 154 3.33e+01 1tlk b.1.1.4 21707 1u1jA 765 3.33e+01 c.1.22.2,c.1.22.2 107590,107591 1ztxL 212 3.37e+01 1zp4A 304 3.39e+01 1s72L 165 3.42e+01 c.12.1.1 105331 1shsA 147 3.44e+01 1shsA b.15.1.1 23675 1aq0A 306 3.46e+01 1aq0A c.1.8.3 28842 1z5sD 83 3.56e+01 1nu4A 97 3.56e+01 d.58.7.1 80731 1qi9A 556 3.57e+01 1qhbA a.111.1.2 19053 1ukuA 102 3.59e+01 d.58.5.2 99533 1qopB 396 3.61e+01 2tysB c.79.1.1 35270 1vr7A 142 3.71e+01 1o58A 303 3.72e+01 c.79.1.1 92491 1gewA 356 3.77e+01 1gewA c.67.1.1 60470 1nf2A 268 3.88e+01 c.108.1.10 91849 1epwA 1290 3.90e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1wlyA 333 3.92e+01 2aq4A 434 3.95e+01 1xdpA 687 3.95e+01 1hm9A 468 3.97e+01 b.81.1.4,c.68.1.5 65866,65867 1vi7A 217 3.98e+01 d.14.1.11,d.58.11.2 100740,100741 1qorA 327 3.98e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1rwzA 245 3.99e+01 d.131.1.2,d.131.1.2 98005,98006 1qhtA 775 4.00e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1bdfA 235 4.02e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1nq6A 302 4.06e+01 c.1.8.3 92046 1xn5A 146 4.06e+01 1jy5A 212 4.08e+01 d.124.1.1 71940 2fh7A 595 4.08e+01 1gxqA 106 4.15e+01 a.4.6.1 70721 1r9gA 216 4.20e+01 c.23.16.1 97258 1h6lA 353 4.21e+01 b.68.3.1 60687 1quqB 121 4.26e+01 1quqB b.40.4.3 25305 1urnA 97 4.28e+01 1urnA d.58.7.1 39153 2fcjA 119 4.31e+01 1i05A 180 4.34e+01 1mup b.60.1.1 27130 1kshA 186 4.40e+01 c.37.1.8 72914 1ri7A 171 4.41e+01 a.4.5.32,d.58.4.2 97504,97505 1fg7A 356 4.45e+01 1gewA c.67.1.1 59819 1htjF 210 4.45e+01 1htjF a.91.1.1 61254 1yiyA 429 4.50e+01 1g7nA 131 4.52e+01 b.60.1.2 83274 1vbuA 328 4.56e+01 1cojA 212 4.58e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1mkp 144 4.60e+01 1vhrA c.45.1.1 32654 2b2aA 199 4.64e+01 1k0rA 366 4.69e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1cf7B 95 4.70e+01 1cf7B a.4.5.17 16152 1z90A 469 4.72e+01 1sr4B 261 4.75e+01 d.151.1.1 105949 1b43A 340 4.76e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 2amyA 246 4.80e+01 1e9rA 437 4.85e+01 c.37.1.11 64827 1i8dA 213 4.88e+01 b.43.4.3,b.43.4.3 61953,61954 1u55A 188 5.03e+01 d.278.1.1 107677 1pyfA 312 5.04e+01 c.1.7.1 95334 1kq1A 77 5.08e+01 b.38.1.2 72848 1je0A 236 5.11e+01 c.56.2.1 66581 1xklA 273 5.12e+01 1ns5A 155 5.14e+01 c.116.1.3 80705 1luzA 88 5.14e+01 b.40.4.5 74271 1ur1A 378 5.15e+01 c.1.8.3 99804 1x8dA 104 5.18e+01 1xtoA 311 5.20e+01 1n8jA 186 5.21e+01 c.47.1.10 85401 1tygB 87 5.23e+01 d.15.3.2 107455 1b0uA 262 5.31e+01 1b0uA c.37.1.12 32370 1xyiA 66 5.31e+01 2alzA 390 5.31e+01 1uc7A 125 5.33e+01 c.47.1.1 99163 1ft5A 211 5.38e+01 1bvb a.138.1.3 19681 1lid 131 5.39e+01 1hmt b.60.1.2 27184 1udc 338 5.42e+01 1xel c.2.1.2 29785 4pfk 319 5.42e+01 3pfk c.89.1.1 35582 1rwrA 301 5.46e+01 b.80.1.11 97990 2f6hX 419 5.53e+01 1wohA 305 5.54e+01 c.42.1.1 109446 2cq2A 114 5.57e+01 1u6bA 98 5.65e+01 d.58.7.1 107703 1xel 338 5.65e+01 1xel c.2.1.2 29786 1vm6A 228 5.68e+01 c.2.1.3,d.81.1.3 108876,108877 1t3nA 388 5.69e+01 d.240.1.1,e.8.1.7 106363,106364 1larA 575 5.69e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1yb2A 275 5.81e+01 1fzqA 181 5.86e+01 1hurA c.37.1.8 32060 2g5dA 422 5.88e+01 1gntA 553 5.88e+01 e.26.1.1 70290 1b5tA 275 5.95e+01 1b5tA c.1.23.1 29676 1zetA 388 5.97e+01 1yoaA 159 5.98e+01 1fhgA 154 5.99e+01 1tlk b.1.1.4 21706 1e2uA 553 5.99e+01 1e1dA e.26.1.1 43362 2tpt 440 5.99e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1l1sA 113 5.99e+01 c.114.1.1 73484 2fn0A 437 6.02e+01 1m12A 84 6.04e+01 a.64.1.1 84745 1h09A 338 6.04e+01 b.109.1.1,c.1.8.8 83420,83421 1whvA 100 6.10e+01 1vknA 351 6.11e+01 c.2.1.3,d.81.1.1 108676,108677 1in0A 163 6.14e+01 d.58.49.1,d.58.49.1 83694,83695 2c3zA 222 6.16e+01 2polA 366 6.25e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1f9vA 347 6.26e+01 1bg2 c.37.1.9 59745 1ve0A 134 6.27e+01 1umuA 116 6.31e+01 1umuA b.87.1.1 28382 2as9A 210 6.37e+01 1u7eB 154 6.39e+01 1xvqA 175 6.39e+01 1i1rB 181 6.53e+01 1i1rB a.26.1.1 61548 1g291 372 6.55e+01 1g291 1o69A 394 6.56e+01 c.67.1.4 92560 1v30A 124 6.60e+01 1nteA 82 6.60e+01 b.36.1.1 86163 1vbvA 105 6.66e+01 1gs5A 258 6.68e+01 c.73.1.2 70395 2fkcA 247 6.72e+01 1r6xA 395 6.75e+01 b.122.1.3,c.26.1.5 97167,97168 1tluA 130 6.76e+01 d.156.1.2 107139 1ob8A 135 6.77e+01 1txvB 440 6.77e+01 1xfcA 384 6.84e+01 1zhvA 134 6.84e+01 2ftzA 284 6.88e+01 1wfeA 86 6.88e+01 1bby 69 6.92e+01 2bby a.4.5.15 16149 1pbjA 125 6.93e+01 d.37.1.1,d.37.1.1 94414,94415 2a41C 32 6.98e+01 1ktjA 129 6.98e+01 b.1.18.7 72974 2aioA 269 7.14e+01 1y43B 173 7.17e+01 1tiqA 180 7.19e+01 d.108.1.1 107010 1bg6 359 7.19e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1njhA 119 7.20e+01 b.128.1.1 85787 1jp4A 308 7.20e+01 1jp4A e.7.1.1 63223 2trcP 217 7.22e+01 1b9yC c.47.1.6 33051 2adcA 229 7.32e+01 1duvG 333 7.33e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1cq3A 233 7.36e+01 1cq3A b.27.1.1 23923 1no5A 114 7.40e+01 d.218.1.5 92014 1g97A 459 7.41e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1smlA 269 7.50e+01 1smlA d.157.1.1 42053 1ynmA 247 7.56e+01 1yizA 429 7.60e+01 1r6jA 82 7.70e+01 b.36.1.1 97151 1ze3C 205 7.71e+01 1ljoA 77 7.74e+01 b.38.1.1 73941 2dfkA 402 7.75e+01 1iwmA 186 7.76e+01 b.125.1.2 83758 2f42A 179 7.83e+01 1ghhA 81 7.90e+01 1ghhA d.57.1.1 38940 1eceA 358 7.90e+01 1eceA c.1.8.3 28813 1y96A 86 7.95e+01 1h6zA 913 8.04e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1wgbA 159 8.16e+01 1cxc 124 8.18e+01 1ycc a.3.1.1 15890 1khbA 625 8.20e+01 c.91.1.1,c.109.1.1 68606,68607 1uxzA 131 8.22e+01 b.18.1.10 100170 1fnuA 221 8.22e+01 3seb b.40.2.2,d.15.6.1 25212,37801 1a8q 274 8.24e+01 1brt c.69.1.12 34702 1zpsA 138 8.25e+01 2ptd 298 8.29e+01 2plc c.1.18.2 29605 1ee6A 197 8.30e+01 1ee6A b.80.1.1 28024 1k38A 254 8.41e+01 e.3.1.1 84303 1ok7A 366 8.43e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1ijgA 309 8.48e+01 1fouA e.27.1.1 62493 1ta8A 332 8.50e+01 1s14A 194 8.54e+01 d.122.1.2 98329 1uc2A 481 8.55e+01 d.261.1.1 99161 1jx7A 117 8.55e+01 c.114.1.1 77195 1z7aA 308 8.58e+01 2b4rO 345 8.60e+01 1c7gA 456 8.61e+01 c.67.1.2 90415 1azsA 220 8.75e+01 1azsA d.58.29.1 39416 1du9A 28 8.76e+01 g.3.7.2 44148 1q3lA 69 8.77e+01 1josA 128 8.78e+01 d.52.7.1 84191 2hvm 273 8.78e+01 1cnv c.1.8.5 28985 1qg8A 255 8.91e+01 1qg8A c.68.1.1 34505 1v5tA 90 8.93e+01 d.15.1.1 108385 2gh1A 301 8.93e+01 2gk3A 256 8.97e+01