# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1y96B 85 1.33e-01 1wmhB 86 1.25e+00 1urnA 97 1.85e+00 1urnA d.58.7.1 39153 1hyuA 521 2.12e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1oiaA 95 2.16e+00 d.58.7.1 87051 1fr3A 67 2.69e+00 1fr3A b.40.6.1 25436 1u24A 337 2.78e+00 2cunA 410 3.03e+00 1xewY 172 3.72e+00 2etxA 209 4.79e+00 1repC 251 4.96e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1xn5A 146 5.46e+00 1hqz1 141 6.17e+00 1vp2A 208 6.26e+00 1o0pA 104 6.35e+00 d.58.7.1 86535 1tlk 154 7.13e+00 1tlk b.1.1.4 21707 1pnsC 206 7.60e+00 i.1.1.1 88170 1iw7C 1119 7.62e+00 e.29.1.1 71474 2adoA 196 7.66e+00 1d4tA 104 7.95e+00 1d4tA d.93.1.1 40537 1gutA 68 8.10e+00 b.40.6.1 65576 1nu4A 97 8.15e+00 d.58.7.1 80731 1oeyJ 107 8.20e+00 d.15.2.2 92804 2d9rA 104 8.24e+00 8rucI 123 8.29e+00 1rboC d.73.1.1 39629 2frnA 278 8.51e+00 1fhgA 154 9.00e+00 1tlk b.1.1.4 21706 1s12A 94 9.55e+00 2gmqA 118 9.96e+00 1h2cA 140 1.08e+01 b.31.1.1 83462 1dyqA 234 1.12e+01 3seb b.40.2.2,d.15.6.1 59140,59141 1vhxA 150 1.13e+01 c.55.3.8 100712 1xtoA 311 1.15e+01 2amyA 246 1.23e+01 1e3aB 560 1.24e+01 1ajqB 1w2iA 91 1.25e+01 d.58.10.1 109127 1nrlA 316 1.25e+01 a.123.1.1 92091 2c1lA 358 1.26e+01 1qwlA 505 1.33e+01 e.5.1.1 96483 1kjwA 295 1.38e+01 b.34.2.1,c.37.1.1 68643,68644 1vr7A 142 1.39e+01 2ewrA 170 1.42e+01 1t0hA 132 1.43e+01 b.34.2.1 106207 2bkfA 87 1.46e+01 1gk9B 557 1.48e+01 1div 149 1.51e+01 1div d.99.1.1,d.100.1.1 40692,40693 1rfeA 162 1.52e+01 1fjgC 239 1.55e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1uurA 473 1.58e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1wkqA 164 1.61e+01 c.97.1.2 109393 2b25A 336 1.64e+01 1fw9A 164 1.68e+01 1fw9A d.190.1.1 60059 2fclA 169 1.70e+01 1aho 64 1.70e+01 1aho g.3.7.1 44127 1yukB 120 1.71e+01 1x74A 360 1.78e+01 1ycyA 71 1.84e+01 1zpvA 91 1.86e+01 1ylqA 96 1.89e+01 1f7sA 139 1.90e+01 1cof d.109.1.2 40857 1qopB 396 1.96e+01 2tysB c.79.1.1 35270 2ak5A 64 1.96e+01 1yg6A 193 1.97e+01 1s4nA 348 1.97e+01 c.68.1.16 98501 1tiyA 164 1.98e+01 c.97.1.2 107012 2fhzB 108 2.02e+01 1zynA 202 2.08e+01 1nteA 82 2.09e+01 b.36.1.1 86163 1tt8A 164 2.15e+01 1wyxA 69 2.17e+01 1r6jA 82 2.20e+01 b.36.1.1 97151 1luzA 88 2.28e+01 b.40.4.5 74271 1c9oA 66 2.33e+01 1mjc b.40.4.5 25325 2dfkA 402 2.35e+01 1hh2P 344 2.45e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1ip9A 85 2.47e+01 1ip9A d.15.2.2 62638 2d00A 109 2.49e+01 1vbvA 105 2.49e+01 2bpa1 426 2.52e+01 2bpa1 1toaA 313 2.52e+01 1toaA c.92.2.2 35598 2g6fX 59 2.54e+01 1tluA 130 2.63e+01 d.156.1.2 107139 2g64A 140 2.64e+01 1vr4A 103 2.65e+01 2ewcA 126 2.68e+01 1quqB 121 2.70e+01 1quqB b.40.4.3 25305 1m5q1 130 2.71e+01 2gw6A 123 2.73e+01 1ml8A 134 2.75e+01 d.227.1.2 85013 1di2A 69 2.79e+01 1di2A d.50.1.1 38780 1ft5A 211 2.79e+01 1bvb a.138.1.3 19681 1oj4A 283 2.85e+01 d.14.1.5,d.58.26.5 93083,93084 1wmhA 89 2.89e+01 1z6gA 218 2.95e+01 1vkuA 100 3.03e+01 a.28.1.1 108690 1wrjA 156 3.06e+01 2aj6A 159 3.06e+01 1segA 64 3.09e+01 g.3.7.1 105453 1x8dA 104 3.11e+01 1ma3A 253 3.13e+01 c.31.1.5 78883 1pz1A 333 3.14e+01 c.1.7.1 95390 1z52A 470 3.16e+01 1omzA 293 3.24e+01 c.68.1.15 87093 1pbjA 125 3.35e+01 d.37.1.1,d.37.1.1 94414,94415 1whbA 157 3.46e+01 1uwdA 103 3.46e+01 1wz7A 111 3.48e+01 1smxA 96 3.50e+01 b.40.4.5 105772 1wh0A 134 3.53e+01 2a4dA 160 3.58e+01 1b66A 140 3.60e+01 1b66A d.96.1.2 40657 1tr0A 108 3.61e+01 d.58.4.4 107261 1yv4A 104 3.64e+01 2a6aA 218 3.74e+01 1jx2B 315 3.74e+01 c.37.1.8 67404 1zc1A 208 3.78e+01 1kzlA 208 3.79e+01 b.43.4.3,b.43.4.3 77635,77636 1sqsA 242 3.84e+01 c.23.5.5 98968 1wspA 84 3.88e+01 1preA 470 3.91e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1r1qA 100 4.01e+01 d.93.1.1 104763 1i8fA 81 4.02e+01 1i8fA b.38.1.1 61959 1wojA 214 4.02e+01 2cu6A 103 4.03e+01 1u6bA 98 4.03e+01 d.58.7.1 107703 2fueA 262 4.03e+01 2g3aA 152 4.04e+01 2cu1A 103 4.08e+01 1h54A 754 4.14e+01 a.102.1.4,b.30.5.3 60634,60635 1ny4A 82 4.18e+01 b.40.4.5 92316 1d1gA 168 4.20e+01 1d1gA c.71.1.1 34889 1uheA 97 4.25e+01 1lq9A 112 4.29e+01 d.58.4.3 78129 1xsqA 168 4.30e+01 1m07A 111 4.33e+01 d.5.1.1 78328 1eziA 228 4.34e+01 1eyrA c.68.1.13 34512 1yqcA 170 4.35e+01 1j7dA 145 4.41e+01 1jatB d.20.1.1 62680 1b33N 67 4.43e+01 1b33N d.30.1.1 38459 1nwaA 203 4.45e+01 d.58.28.1 86295 1d2sA 170 4.45e+01 1d2sA b.29.1.4 24221 1kv0A 66 4.46e+01 g.3.7.1 91040 1id0A 152 4.50e+01 d.122.1.3 66111 1xsrA 168 4.50e+01 1rwsA 77 4.59e+01 d.15.3.2 97991 1mo9A 523 4.61e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1no5A 114 4.64e+01 d.218.1.5 92014 1c52 131 4.75e+01 1c52 a.3.1.1 15810 2c7hA 86 4.82e+01 1bia 321 4.82e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1nt2A 210 4.83e+01 c.66.1.3 86149 2fiuA 99 4.83e+01 2aw42 46 4.84e+01 1go3E 187 4.85e+01 b.40.4.5,d.230.1.1 83054,83055 1lqtA 456 4.85e+01 c.3.1.1,c.4.1.1 74198,74199 1f06A 320 4.90e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1sn4A 64 4.90e+01 1aho g.3.7.1 44136 1zud1 251 4.97e+01 2g6tA 306 5.01e+01 1m93A 55 5.10e+01 e.1.1.1 91235 1y14B 171 5.17e+01 1v9jA 113 5.25e+01 d.52.6.1 100542 1kgdA 180 5.25e+01 c.37.1.1 68582 1zvpA 133 5.32e+01 2gi9A 56 5.34e+01 1hfoA 113 5.36e+01 d.80.1.3 61006 1kz7A 353 5.51e+01 a.87.1.1,b.55.1.1 73333,73334 1nwwA 149 5.56e+01 d.17.4.8 86306 1ztcA 221 5.57e+01 1omrA 201 5.58e+01 a.39.1.5 93349 1upiA 225 5.60e+01 b.82.1.1 99757 1a0rP 245 5.64e+01 1b9yC c.47.1.6 33054 1l3iA 192 5.68e+01 c.66.1.22 77676 1qysA 106 5.72e+01 k.41.1.1 96603 1cf7B 95 5.77e+01 1cf7B a.4.5.17 16152 1vrtA 560 5.80e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1mwwA 128 5.84e+01 d.80.1.4 91483 1tig 94 5.86e+01 1tig d.68.1.1 39566 1fvgA 199 5.89e+01 1fvaA d.58.28.1 39408 1rec 201 5.96e+01 1rec a.39.1.5 17326 1jenB 67 5.97e+01 1jenB d.156.1.1 42029 1e25A 282 6.04e+01 1e25A e.3.1.1 42731 2fmr 65 6.07e+01 2fmr d.51.1.1 38808 1w2lA 99 6.08e+01 1qb2A 109 6.12e+01 1qb2A a.36.1.1 17125 1dwkA 156 6.17e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 2gfgA 193 6.17e+01 1nhyA 219 6.17e+01 a.45.1.1,c.47.1.5 80520,80521 1uylA 236 6.27e+01 d.122.1.1 108147 1dkgA 197 6.30e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 2f06A 144 6.31e+01 1icxA 155 6.38e+01 d.129.3.1 71191 1gy6A 127 6.41e+01 d.17.4.2 70736 1pp0A 199 6.41e+01 d.103.1.1 104211 2gaiA 633 6.43e+01 2f9dA 125 6.48e+01 1pqzA 238 6.54e+01 b.1.1.2,d.19.1.1 104297,104298 1kl9A 182 6.57e+01 b.40.4.5 72681 1ifqA 138 6.61e+01 1ifqA d.110.4.1 62350 1tq8A 163 6.67e+01 c.26.2.4 107204 1k0fA 277 6.72e+01 c.92.2.2 71974 1njhA 119 6.76e+01 b.128.1.1 85787 1wr8A 231 6.90e+01 1yfbA 59 6.91e+01 1juvA 193 7.07e+01 c.71.1.1 90912 1k0hA 117 7.09e+01 b.106.1.2 71975 1jh3A 107 7.09e+01 d.66.1.4 71661 1ten 90 7.13e+01 1ten b.1.2.1 21990 1uzcA 71 7.13e+01 a.159.2.1 100222 1yqfA 203 7.17e+01 1j8bA 112 7.20e+01 d.222.1.1 77101 1tikA 213 7.21e+01 c.23.5.3 107003 1vdxA 184 7.28e+01 2gh1A 301 7.30e+01 1pvdA 537 7.34e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1djtA 64 7.34e+01 1aho g.3.7.1 44132 2myr 501 7.34e+01 1dptA 117 7.35e+01 1dptA d.80.1.3 39862 1ujrA 110 7.36e+01 1rmwA 212 7.37e+01 1kw4A 89 7.37e+01 a.60.1.2 73077 1wnyA 186 7.54e+01 1gouA 116 7.55e+01 d.1.1.2 65429 2bh4X 134 7.58e+01 1rp4A 389 7.58e+01 a.227.1.1 105027 1eejA 216 7.58e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1gkzA 388 7.59e+01 a.29.5.1,d.122.1.4 65268,65269 1v5tA 90 7.74e+01 d.15.1.1 108385 1nsf 273 7.75e+01 1d2nA c.37.1.20 32429 1vyiA 112 7.83e+01 1gg6B 131 7.86e+01 5ptp 1ri7A 171 7.88e+01 a.4.5.32,d.58.4.2 97504,97505 1ne5A 42 7.88e+01 g.3.7.2 85588 1f2tB 148 7.91e+01 1f2tB 1qdeA 224 7.91e+01 1qvaA c.37.1.19 32410 2eulA 156 7.92e+01 1b12A 248 7.93e+01 1b12A b.87.1.2 28388 1bn8A 420 7.94e+01 1pcl b.80.1.1 28022 1jogA 146 7.97e+01 a.24.16.2 77142 1n8nA 212 7.99e+01 c.108.1.12 91706 1vi7A 217 8.06e+01 d.14.1.11,d.58.11.2 100740,100741 1i7pA 274 8.10e+01 b.43.4.2,c.25.1.1 66048,66049 2b82A 211 8.12e+01 2mtaC 147 8.15e+01 2mtaC a.3.1.1 15908 1eg2A 319 8.17e+01 1eg2A c.66.1.11 34249 1vazA 88 8.18e+01 d.245.1.1 100554 1q68A 38 8.22e+01 j.48.1.1 95962 1u46A 291 8.23e+01 d.144.1.7 107656 2hrvA 142 8.28e+01 2hrvA b.47.1.4 26429 2bw2A 140 8.31e+01 1eijA 80 8.34e+01 1eijA a.5.6.1 16298 1s14A 194 8.38e+01 d.122.1.2 98329 1vmeA 410 8.45e+01 c.23.5.1,d.157.1.3 108893,108894 1xn7A 78 8.52e+01 1e4mM 501 8.52e+01 1e70M c.1.8.4 59226 2c6yA 111 8.58e+01 1zlhB 75 8.58e+01 1qhdA 398 8.61e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1xwvA 129 8.65e+01 1xkrA 206 8.69e+01 1whi 122 8.70e+01 1whi b.39.1.1 24810 1oa8A 133 8.70e+01 b.145.1.1 92698 1v8cA 168 8.72e+01 d.15.3.1,d.129.5.1 100495,100496 1fgyA 127 8.72e+01 1faoA b.55.1.1 26976 1gyxA 76 8.78e+01 d.80.1.1 76387 1si2A 149 8.96e+01 b.34.14.1 105569 1gpmA 525 8.98e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1ep0A 185 8.99e+01 1dzrA b.82.1.1 28080