# List of top-scoring protein chains for t06-100-30-str2-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 1gmyA 261 1.21e-01 d.3.1.1 76236 1el5A 389 3.84e-01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1xngA 268 1.03e+00 1dgwA 178 1.13e+00 1dgwA b.82.1.2 28090 1wosA 364 1.28e+00 b.44.2.1,d.250.1.1 109468,109469 1p5dX 463 1.41e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1dq3A 454 1.49e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 2cokA 113 1.83e+00 1v8hA 107 1.83e+00 2gxfA 142 2.06e+00 1xfsA 178 2.66e+00 d.129.3.5 109589 1ut7A 171 3.24e+00 b.143.1.1 99906 1jmxB 349 3.51e+00 b.69.2.2 66906 1s3cA 141 3.61e+00 1qmeA 702 3.61e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 2d13A 227 3.75e+00 2aioA 269 3.82e+00 1rsy 152 4.00e+00 1rsy b.7.1.2 23192 2a7mA 250 4.49e+00 1k07A 263 4.55e+00 d.157.1.1 77218 1upiA 225 4.62e+00 b.82.1.1 99757 1tif 78 4.63e+00 1tif d.15.8.1 37836 2blnA 305 4.96e+00 1lkdA 297 5.23e+00 d.32.1.3,d.32.1.3 78059,78060 1yu0A 381 5.28e+00 1gpmA 525 5.69e+00 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1tzyD 103 5.73e+00 a.22.1.1 107533 1iloA 77 5.78e+00 c.47.1.1 66205 1lgpA 116 5.92e+00 b.26.1.2 73890 1mvfA 135 6.15e+00 b.1.1.1 85141 1f89A 291 6.53e+00 d.160.1.1 64988 1nezG 128 7.34e+00 b.1.1.1 85592 1bb8 71 8.01e+00 2bb8 d.10.1.1 37478 1r26A 125 8.43e+00 c.47.1.1 96847 1mhnA 59 8.87e+00 b.34.9.1 84964 1h8eA 510 9.10e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1l5wA 796 9.17e+00 c.87.1.4 73605 1snnA 227 9.29e+00 d.115.1.2 105821 1io1A 398 9.32e+00 1io1A e.32.1.1 62611 2ck3A 510 9.66e+00 2gfaA 119 9.69e+00 1wy2A 351 9.89e+00 2g76A 335 9.97e+00 2fk9A 157 1.01e+01 1ofdA 1520 1.02e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1hfuA 503 1.05e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 2bu3A 254 1.12e+01 1xfpA 142 1.13e+01 b.1.1.1 109587 1k3iA 656 1.14e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1v6tA 255 1.16e+01 1x99A 145 1.16e+01 1wdtA 665 1.16e+01 1rzfL 213 1.19e+01 b.1.1.1,b.1.1.2 98152,98153 1lucB 324 1.36e+01 1lucA c.1.16.1 29548 1zvhA 134 1.49e+01 1dxrH 258 1.49e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1qw1A 121 1.53e+01 2ew2A 316 1.53e+01 1qwdA 177 1.54e+01 b.60.1.1 96471 1xer 103 1.56e+01 1xer d.58.1.3 38990 2g6fX 59 1.56e+01 2f9lA 199 1.56e+01 1tuhA 156 1.59e+01 d.17.4.11 107345 2f5tX 233 1.63e+01 1g1cA 99 1.64e+01 b.1.1.4 65078 1wsrA 375 1.67e+01 1xh3A 276 1.75e+01 1pguA 615 1.78e+01 b.69.4.1,b.69.4.1 88069,88070 1xzoA 174 1.79e+01 1chmA 401 1.86e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1vckA 115 1.92e+01 1cb8A 678 1.93e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1un3A 123 1.93e+01 d.5.1.1 99646 1dp4A 435 1.95e+01 1dp4A c.93.1.1 35710 1nr0A 611 1.99e+01 b.69.4.1,b.69.4.1 86078,86079 1svpA 161 2.02e+01 1svpA b.47.1.3 26384 1odkA 235 2.05e+01 c.56.2.1 86863 2g6bA 180 2.07e+01 1ejxC 567 2.07e+01 b.92.1.1,c.1.9.2 83184,83185 2axcA 264 2.16e+01 1zvyA 136 2.23e+01 2fomB 185 2.23e+01 1lvwA 295 2.24e+01 c.68.1.6 84723 1mbmA 198 2.27e+01 b.47.1.3 78916 1jalA 363 2.27e+01 c.37.1.8,d.15.10.2 84138,84139 1s68A 249 2.32e+01 d.142.2.4 98591 1kkeA 210 2.34e+01 b.21.1.2,b.83.1.2 68669,68670 2absA 383 2.35e+01 1x1rA 178 2.39e+01 1w85I 49 2.40e+01 1ekgA 127 2.44e+01 1dlxA d.82.2.1 40021 1bxoA 323 2.44e+01 2er7E b.50.1.2 26805 1i9gA 280 2.46e+01 c.66.1.13 62090 1jm1A 204 2.48e+01 b.33.1.1 71745 1jssA 224 2.53e+01 d.129.3.2 71844 1i4uA 181 2.56e+01 b.60.1.1 61732 1vrmA 325 2.56e+01 1ra0A 430 2.57e+01 1wy5A 317 2.62e+01 1knmA 130 2.69e+01 b.42.2.1 72781 1qy6A 274 2.76e+01 b.47.1.1 96574 1ek0A 170 2.76e+01 1ctqA c.37.1.8 32076 1vqoT 120 2.78e+01 1u0qA 125 2.82e+01 1viaA 175 2.84e+01 c.37.1.2 100754 2a2pA 129 2.86e+01 1t7lA 766 2.89e+01 1iq4A 179 2.92e+01 1iq4A d.77.1.1 62641 1tt8A 164 2.92e+01 1w4vA 119 2.95e+01 1obdA 306 2.95e+01 d.143.1.1 86767 2g5dA 422 2.97e+01 1o6sB 105 3.00e+01 b.1.6.1 81096 1tjyA 316 3.03e+01 c.93.1.1 107062 1mqkH 127 3.06e+01 b.1.1.1 85053 1u4gA 301 3.07e+01 d.92.1.2 107670 1cojA 212 3.07e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1zvnA 99 3.08e+01 1j83A 180 3.10e+01 b.18.1.12 66430 2bkdN 134 3.11e+01 2fhxA 246 3.13e+01 1c7qA 445 3.15e+01 2pgi c.80.1.2 35307 1dyoA 160 3.17e+01 1dyoA b.18.1.7 23771 1m98A 317 3.17e+01 a.175.1.1,d.17.4.6 78866,78867 1f1xA 322 3.19e+01 d.32.1.3,d.32.1.3 83208,83209 1o4wA 147 3.22e+01 c.120.1.1 86629 2a5jA 191 3.23e+01 1yhtA 367 3.23e+01 1os8A 223 3.25e+01 b.47.1.1 93481 1wlgA 299 3.27e+01 1k3yA 221 3.29e+01 a.45.1.1,c.47.1.5 77245,77246 1v30A 124 3.32e+01 1dg6A 191 3.34e+01 1d4vB b.22.1.1 23883 1qr0A 228 3.37e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1jbeA 128 3.39e+01 3chy c.23.1.1 62845 1xcbA 211 3.41e+01 a.4.5.38,c.2.1.12 109552,109553 1hyxH 224 3.43e+01 1igtB b.1.1.1,b.1.1.2 20167,21191 1yoxA 250 3.45e+01 1i4fA 275 3.50e+01 1agdA b.1.1.2,d.19.1.1 61687,61688 1rq6A 62 3.52e+01 1y96A 86 3.56e+01 1rgxA 114 3.58e+01 g.77.1.1 104932 1j8mF 297 3.60e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1dqiA 124 3.61e+01 1do6A b.1.13.1 22357 1v76A 96 3.62e+01 1nnxA 109 3.64e+01 b.40.10.1 92013 1sglA 209 3.69e+01 d.124.1.1 105536 1kt6A 183 3.72e+01 b.60.1.1 84466 2c0zA 216 3.72e+01 1uwcA 261 3.72e+01 c.69.1.17 100101 1qsmA 152 3.73e+01 1qsmA d.108.1.1 40808 1gycA 499 3.80e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1xe7A 203 3.85e+01 2gjgA 248 3.96e+01 1y2tA 142 4.00e+01 1nycA 111 4.03e+01 b.61.2.2 92336 1fmtA 314 4.11e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1lbvA 252 4.18e+01 e.7.1.1 73813 1nykA 165 4.22e+01 b.33.1.1 86408 1kuuA 202 4.25e+01 d.153.2.1 73019 1eylA 186 4.27e+01 1wba b.42.4.1 25593 1dbhA 354 4.29e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1ryiA 382 4.30e+01 1p9bA 442 4.30e+01 c.37.1.10 94385 1rkd 309 4.32e+01 1rkd c.72.1.1 34928 1ht6A 405 4.41e+01 b.71.1.1,c.1.8.1 83629,83630 1dy9A 187 4.42e+01 1jxpA b.47.1.3 26400 1uwvA 433 4.48e+01 b.40.4.12,c.66.1.40 100128,100129 1oh0A 131 4.49e+01 d.17.4.3 87004 1l5xA 280 4.52e+01 c.106.1.1 77718 1qtnA 164 4.52e+01 1pauA c.17.1.1 30999 2basA 431 4.57e+01 1r0pA 312 4.61e+01 d.144.1.7 96734 1gxuA 91 4.67e+01 d.58.10.1 76378 1p0zA 131 4.68e+01 d.110.6.1 93882 1k8kC 372 4.72e+01 b.69.4.1 68308 1uz8B 212 4.76e+01 b.1.1.1,b.1.1.2 108168,108169 1q44A 326 4.79e+01 c.37.1.5 95779 1kl9A 182 4.83e+01 b.40.4.5 72681 1rcwA 231 4.86e+01 a.132.1.4 97299 1j5xA 342 4.94e+01 c.80.1.1 71591 1khqA 212 4.94e+01 d.3.1.1 90964 1oaqH 121 5.00e+01 b.1.1.1 92707 1yhfA 115 5.03e+01 1d3cA 686 5.19e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1vfgA 390 5.21e+01 a.173.1.1,d.218.1.4 108570,108571 1cqqA 180 5.22e+01 1cqqA b.47.1.4 26422 1z5yE 149 5.25e+01 1wfxA 186 5.25e+01 1gvp 87 5.28e+01 1gvp b.40.4.7 25369 1kao 167 5.28e+01 1ctqA c.37.1.8 32014 1uv4A 293 5.30e+01 1f7dA 136 5.31e+01 1dun b.85.4.1 28353 1vsrA 136 5.43e+01 1vsrA c.52.1.15 33332 1f1uA 323 5.46e+01 d.32.1.3,d.32.1.3 83200,83201 1kmqA 184 5.50e+01 c.37.1.8 84412 1pmzA 86 5.52e+01 a.39.1.10 104195 1ryaA 160 5.55e+01 d.113.1.5 105122 1kw3B 292 5.57e+01 d.32.1.3,d.32.1.3 77549,77550 1g5cA 170 5.66e+01 1g5cA c.53.2.1 60264 1y8tA 324 5.69e+01 1wqsA 173 5.73e+01 1yb3A 175 5.78e+01 2bynA 227 5.80e+01 2gk3A 256 5.82e+01 1v5vA 401 5.84e+01 2aotA 292 5.86e+01 1vlmA 219 5.89e+01 c.66.1.41 108836 2fimA 276 5.97e+01 1wxrA 1048 5.99e+01 2bxxA 134 6.04e+01 1kk8B 139 6.04e+01 a.39.1.5 77430 1jl0A 334 6.06e+01 1jenA d.156.1.1 63155 1pyoA 167 6.08e+01 c.17.1.1 95370 1ayoA 130 6.09e+01 1ayoA b.2.4.1 22431 1kllA 130 6.13e+01 d.32.1.2 72720 1oaqL 120 6.14e+01 b.1.1.1 92708 1f1eA 154 6.15e+01 a.22.1.2 64927 1s21A 206 6.16e+01 d.166.1.4 105222 2gf9A 189 6.23e+01 1twfA 1733 6.24e+01 3pcgA 200 6.25e+01 3pchA b.3.6.1 22647 1oeyA 83 6.30e+01 d.15.2.2 92800 1h05A 146 6.36e+01 c.23.13.1 76433 1q1uA 144 6.36e+01 b.42.1.1 95608 1o7fA 469 6.37e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1bqcA 302 6.42e+01 1bqcA c.1.8.3 28831 1zxkA 98 6.42e+01 1x0vA 354 6.44e+01 1jqlB 140 6.46e+01 c.37.1.20 63234 2a7yA 83 6.49e+01 1k5nA 276 6.50e+01 b.1.1.2,d.19.1.1 77266,77267 1qw9A 502 6.52e+01 b.71.1.2,c.1.8.3 96466,96467 1x6oA 174 6.56e+01 b.34.5.2,b.40.4.5 109493,109494 1tuaA 191 6.63e+01 d.51.1.1,d.51.1.1 107321,107322 1q7hA 153 6.63e+01 b.122.1.1,d.17.6.2 96042,96043 2ca6A 386 6.68e+01 1qhoA 686 6.72e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1vie 62 6.74e+01 1vie b.34.4.1 24592 1g6gA 127 6.74e+01 1g6gA b.26.1.2 23916 1m2tB 263 6.75e+01 b.42.2.1,b.42.2.1 84762,84763 2bw0A 329 6.81e+01 1ecsA 126 6.84e+01 1ecsA d.32.1.2 59407 1lcyA 325 6.88e+01 b.36.1.4,b.47.1.1 73834,73835 1nlnA 204 6.92e+01 d.3.1.7 91962 2f91B 35 6.94e+01 1rkqA 282 7.00e+01 c.108.1.10 97621 1a12A 413 7.01e+01 1a12A b.69.5.1 27663 1tp6A 128 7.06e+01 d.17.4.12 107184 1m4lA 307 7.07e+01 c.56.5.1 78604 2bdvA 231 7.10e+01 1k8kA 418 7.11e+01 c.55.1.1,c.55.1.1 68305,68306 2bo9A 308 7.13e+01 1lk2A 274 7.27e+01 b.1.1.2,d.19.1.1 91056,91057 1luzA 88 7.32e+01 b.40.4.5 74271 1khiA 176 7.33e+01 b.34.5.2,b.40.4.5 77408,77409 1f7sA 139 7.36e+01 1cof d.109.1.2 40857 1ul7A 102 7.37e+01 d.129.6.1 99540 2b4hA 254 7.38e+01 1o9wA 177 7.38e+01 b.2.3.5 86713 1f3lA 321 7.46e+01 1g6q2 c.66.1.6 59630 2fkbA 180 7.46e+01 1zy9A 564 7.50e+01 1gen 218 7.58e+01 1gen b.66.1.1 27536 1v10A 521 7.65e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1x0pA 143 7.73e+01 1wloA 136 7.78e+01 1ddgA 374 7.81e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1qg3A 195 7.81e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1tafB 70 7.85e+01 1tafB a.22.1.3 16482 1wu7A 434 7.92e+01 2bj0A 203 7.94e+01 1brt 277 7.98e+01 1brt c.69.1.12 34699 1vj7A 393 7.98e+01 a.211.1.1,d.218.1.8 100801,100802 1lfdA 87 8.04e+01 1lfdA d.15.1.5 37622 1srqA 341 8.08e+01 e.55.1.1 105967 1eny 268 8.08e+01 1eny c.2.1.2 29910 1f06A 320 8.13e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1vhoA 346 8.14e+01 b.49.3.1,c.56.5.4 100694,100695 1yhpA 212 8.15e+01 1o4sA 389 8.25e+01 c.67.1.1 86620 1l7mA 211 8.28e+01 c.108.1.4 73664 1xqaA 113 8.30e+01 1rz4A 226 8.30e+01 a.4.5.53,a.118.1.18 105131,105132 1ydxA 406 8.46e+01 1yc7A 124 8.47e+01 1wojA 214 8.48e+01 1v74B 87 8.54e+01 a.24.20.1 100443 1vhyA 257 8.55e+01 b.122.1.2,c.116.1.5 100714,100715 2aq8A 269 8.56e+01 1t2jA 116 8.60e+01 1dcfA 136 8.65e+01 1dcfA c.23.1.2 31124 1vhqA 232 8.67e+01 c.23.16.2 100696 1bbzA 58 8.67e+01 1bbzA b.34.2.1 24477 1s6lA 212 8.77e+01 1wdcB 156 8.86e+01 1wdcB a.39.1.5 17302 1mkfA 382 8.87e+01 b.116.1.1 79232 1aj2 282 8.92e+01 1aj2 c.1.21.1 29665 1rzhH 260 8.93e+01 b.41.1.1,f.23.10.1 98162,98163 1ogoX 574 8.93e+01 b.133.1.1,b.80.1.10 92925,92926