# 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 1vjkA 98 1.61e-06 d.15.3.1 108631 1xlqA 106 2.69e-04 1oqqA 106 2.98e-04 d.15.4.1 93422 1frrA 95 7.25e-04 1awd d.15.4.1 37674 1zud2 66 1.74e-03 1fm0D 81 2.57e-03 1fmaD d.15.3.1 37642 1uwmA 106 3.76e-03 2bwfA 77 1.55e-02 1l5pA 93 1.80e-02 d.15.4.1 73598 2bb6A 414 2.12e-02 1jl0A 334 5.07e-02 1jenA d.156.1.1 63155 1f1xA 322 9.04e-02 d.32.1.3,d.32.1.3 83208,83209 1frd 98 9.39e-02 1awd d.15.4.1 37648 2bpsA 81 9.85e-02 1f1uA 323 1.02e-01 d.32.1.3,d.32.1.3 83200,83201 1i7hA 111 1.09e-01 d.15.4.1 71122 2cu3A 64 1.11e-01 1rfkA 98 1.39e-01 1l7yA 94 1.56e-01 d.15.1.6 73676 1ogwA 76 1.57e-01 d.15.1.1 87001 2f4pA 147 1.77e-01 1awd 94 1.77e-01 1awd d.15.4.1 37673 1k07A 263 2.20e-01 d.157.1.1 77218 1doi 128 2.20e-01 1awd d.15.4.1 37676 1offA 97 2.24e-01 d.15.4.1 86947 1wm3A 72 2.62e-01 1siqA 392 2.89e-01 a.29.3.1,e.6.1.1 105585,105586 1wgrA 100 2.89e-01 1czpA 98 3.03e-01 1awd d.15.4.1 37645 1yj1A 76 3.16e-01 1r3eA 309 4.54e-01 b.122.1.1,d.265.1.2 96907,96908 1r5lA 262 4.76e-01 a.5.3.1,c.13.1.1 97099,97100 1t6aA 126 5.21e-01 d.129.8.1 106555 2al3A 90 5.88e-01 1dmhA 311 6.29e-01 1dmhA b.3.6.1 22633 2bt6A 108 7.03e-01 1pvmA 184 7.51e-01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1ib8A 164 7.74e-01 b.38.2.1,d.52.4.1 71168,71169 1ra6A 461 7.77e-01 e.8.1.4 104879 1euvB 86 7.90e-01 1a5r d.15.1.1 37598 2bkdN 134 8.75e-01 2fcr 173 9.39e-01 1rcf c.23.5.1 31151 1yqbA 100 9.51e-01 1a70 97 1.14e+00 1awd d.15.4.1 37678 2apoA 357 1.18e+00 2c5lC 117 1.24e+00 1so9A 164 1.27e+00 b.146.1.1 105842 1omzA 293 1.38e+00 c.68.1.15 87093 1krhA 338 1.48e+00 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 2fqmA 75 1.52e+00 1zu0A 529 1.66e+00 1o54A 277 1.68e+00 c.66.1.13 92482 1lm8B 118 1.79e+00 d.15.1.1 74033 2fcfA 103 1.81e+00 1wwtA 88 1.81e+00 2a4hA 126 2.06e+00 1gvp 87 2.08e+00 1gvp b.40.4.7 25369 1t5hX 504 2.11e+00 e.23.1.1 106449 1wjuA 100 2.13e+00 1gpr 162 2.20e+00 1gpr b.84.3.1 28267 1woqA 267 2.25e+00 c.55.1.10,c.55.1.10 109462,109463 2b0vA 153 2.28e+00 1c1yB 77 2.29e+00 1c1yB d.15.1.5 37618 2fexA 188 2.32e+00 1gcqC 70 2.44e+00 1gcpA b.34.2.1 60436 1tmxA 293 2.46e+00 2d42A 249 2.47e+00 2fnjB 118 2.48e+00 1cxyA 90 2.55e+00 1cyo d.120.1.1 41085 1zn8A 180 2.67e+00 2gaxA 135 2.87e+00 1ad2 228 2.97e+00 1ad2 e.24.1.1 43353 1vr6A 350 2.99e+00 1k8wA 327 3.01e+00 b.122.1.1,d.265.1.2 83094,90388 1pl8A 356 3.18e+00 b.35.1.2,c.2.1.1 94878,94879 1o50A 157 3.35e+00 d.37.1.1,d.37.1.1 92478,92479 2gk3A 256 3.40e+00 1t0qC 86 3.46e+00 d.15.12.1 106222 1pg4A 652 3.54e+00 e.23.1.1 88067 2as0A 396 3.85e+00 1ryaA 160 3.90e+00 d.113.1.5 105122 1vybA 238 4.14e+00 d.151.1.1 108897 1z2mA 155 4.25e+00 1ghhA 81 4.29e+00 1ghhA d.57.1.1 38940 1oruA 195 4.54e+00 b.58.1.2 93464 1wwkA 307 4.57e+00 1agjA 242 4.57e+00 1agjA b.47.1.1 25827 1snzA 344 5.35e+00 b.30.5.4 98930 1wmzA 140 5.38e+00 d.169.1.1 109422 1ykdA 398 5.52e+00 1wruA 379 5.56e+00 1dg6A 191 5.67e+00 1d4vB b.22.1.1 23883 1l2hA 153 5.68e+00 b.42.1.2 77655 1owfB 94 5.73e+00 a.55.1.1 87488 1cnzA 363 5.79e+00 1cnzA c.77.1.1 35061 1wmmA 145 5.99e+00 2azeB 106 6.05e+00 1b7yB 785 6.10e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1wzlA 585 6.41e+00 1k3sA 113 6.60e+00 d.198.1.1 68120 1uqtA 482 6.65e+00 c.87.1.6 99794 1i0rA 169 6.96e+00 1i0rA b.45.1.2 61489 1oboA 169 7.11e+00 c.23.5.1 86776 1ypyA 184 7.20e+00 2g1lA 104 7.53e+00 1zvtA 256 7.83e+00 2evbA 74 8.04e+00 2fi1A 190 8.40e+00 1xdyA 298 8.54e+00 1ooyA 481 8.55e+00 c.124.1.3,c.124.1.2 93388,93389 1q2lA 939 8.77e+00 1kqfC 217 9.03e+00 f.21.1.1 72874 2au3A 407 9.03e+00 1htrP 43 9.09e+00 1htrP b.50.1.2 26852 1ey4A 149 9.09e+00 1snc b.40.1.1 24815 2pia 321 9.20e+00 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1vknA 351 9.22e+00 c.2.1.3,d.81.1.1 108676,108677 1fi2A 201 9.67e+00 1fi2A b.82.1.2 59845 2bh8A 101 9.71e+00 1kk1A 410 9.90e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1qh5A 260 1.03e+01 1qh5A d.157.1.2 42057 1mdl 359 1.03e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 2fmpA 335 1.04e+01 1txqA 93 1.07e+01 1lfdA 87 1.08e+01 1lfdA d.15.1.5 37622 1yfbA 59 1.09e+01 1msk 331 1.10e+01 1msk d.173.1.1 42495 2sns 149 1.12e+01 1snc b.40.1.1 24860 1eo6A 117 1.12e+01 1eo6A d.15.1.3 37609 2et1A 201 1.19e+01 1tygB 87 1.22e+01 d.15.3.2 107455 1ylxA 103 1.23e+01 2fp4B 395 1.24e+01 1ip9A 85 1.27e+01 1ip9A d.15.2.2 62638 1xc3A 302 1.27e+01 1ag9A 175 1.27e+01 1rcf c.23.5.1 31178 2cb4A 291 1.27e+01 1l7aA 318 1.29e+01 c.69.1.25 77772 1xe1A 116 1.29e+01 b.43.3.1 109571 1z06A 189 1.29e+01 1gttA 429 1.30e+01 d.177.1.1,d.177.1.1 70529,70530 2h2bA 107 1.32e+01 1zy4A 303 1.32e+01 1wkaA 147 1.32e+01 2amdA 311 1.34e+01 1qxoA 388 1.34e+01 d.258.1.1 96539 2fueA 262 1.38e+01 1jb3A 131 1.41e+01 1jc7A b.40.3.2 62833 2cr5A 109 1.43e+01 1gnuA 117 1.47e+01 d.15.1.3 65403 1sgvA 316 1.52e+01 b.122.1.1,d.265.1.2 98858,98859 1k94A 165 1.54e+01 a.39.1.8 68333 2bs3C 256 1.55e+01 2fzsA 193 1.56e+01 1ws8A 109 1.57e+01 1yg6A 193 1.58e+01 1vlaA 150 1.59e+01 d.227.1.2 108735 1otgA 125 1.62e+01 1otgA d.80.1.2 39831 1f06A 320 1.66e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1sv6A 269 1.67e+01 d.177.1.1 106043 1knmA 130 1.67e+01 b.42.2.1 72781 1vr9A 213 1.70e+01 1wb4A 297 1.71e+01 1onrA 316 1.74e+01 1onrA c.1.10.1 29169 2cwpA 112 1.75e+01 2dafA 118 1.75e+01 1gsmA 210 1.80e+01 b.1.1.4,b.1.1.4 65535,65536 1v4aA 440 1.83e+01 a.24.16.4,d.218.1.9 108350,108351 1by2 119 1.86e+01 1by2 d.170.1.1 42452 1q1oA 98 1.87e+01 d.15.2.2 95596 1x8qA 184 1.87e+01 1m93B 245 1.89e+01 1vlbA 907 1.89e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1uhgA 385 1.90e+01 e.1.1.1 88491 2btzA 394 1.92e+01 1wg8A 285 1.97e+01 1ogdA 131 1.99e+01 c.133.1.1 92893 1lbvA 252 1.99e+01 e.7.1.1 73813 1vp4A 425 2.01e+01 1tg7A 971 2.01e+01 1xkpA 246 2.02e+01 1yb5A 351 2.05e+01 2b3nA 159 2.07e+01 2cfeA 162 2.09e+01 2dbyA 368 2.11e+01 1ojqA 212 2.14e+01 d.166.1.1 93146 1vq2A 193 2.14e+01 1ejbA 168 2.16e+01 1rvv1 c.16.1.1 59417 1xjjA 644 2.17e+01 2apxA 112 2.18e+01 2h1tA 188 2.21e+01 1vgjA 184 2.22e+01 2g8lA 299 2.25e+01 1g5cA 170 2.25e+01 1g5cA c.53.2.1 60264 1nlnA 204 2.26e+01 d.3.1.7 91962 1wstA 417 2.27e+01 1pgs 314 2.29e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 2h3bA 494 2.35e+01 1d1qA 161 2.40e+01 1dg9A c.44.1.1 32642 2gcuA 245 2.40e+01 1xgsA 295 2.40e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1zx8A 136 2.40e+01 1yn9A 169 2.44e+01 2fb6A 117 2.45e+01 1sfe 180 2.47e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1xt8A 292 2.48e+01 1dl5A 317 2.50e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1ukkA 142 2.50e+01 d.227.1.1 99491 1ecrA 309 2.51e+01 1ecrA e.2.1.1 42678 1rktA 205 2.51e+01 a.4.1.9,a.121.1.1 97623,97624 1aohA 147 2.53e+01 1aohA b.2.2.2 22401 2fclA 169 2.53e+01 1vcdA 126 2.53e+01 1b9mA 265 2.55e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1o5xA 248 2.63e+01 c.1.1.1 92528 1dkzA 219 2.63e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1j98A 157 2.66e+01 1j98A d.185.1.2 62755 1u3wA 374 2.67e+01 2f96A 224 2.71e+01 1yqtA 538 2.73e+01 1zavA 180 2.80e+01 2a5zA 262 2.80e+01 1yb2A 275 2.80e+01 1p4oA 322 2.85e+01 d.144.1.7 87775 1inlA 296 2.85e+01 c.66.1.17 66220 2btiA 63 2.93e+01 1bdb 277 2.96e+01 1bdb c.2.1.2 29874 1avbA 226 2.96e+01 1led b.29.1.1 24158 1p0fA 373 2.98e+01 b.35.1.2,c.2.1.1 87642,87643 1qrvA 73 2.98e+01 1cktA a.21.1.1 16425 2fm8A 135 3.05e+01 1yumA 242 3.05e+01 2av4A 162 3.05e+01 1iueA 98 3.06e+01 d.15.4.1 90697 2fug1 438 3.07e+01 3il8 72 3.08e+01 1tvxA d.9.1.1 37356 1kmvA 186 3.10e+01 c.71.1.1 72757 2azwA 148 3.11e+01 1egpA 45 3.11e+01 1egpA d.40.1.1 38561 1zbxB 141 3.12e+01 2aioA 269 3.14e+01 1yopA 83 3.15e+01 1xm3A 264 3.16e+01 1r31A 428 3.19e+01 d.58.20.1,d.179.1.1 96897,96898 1aym3 238 3.20e+01 1aym3 1h4xA 117 3.22e+01 1auz c.13.2.1 60626 1nytA 271 3.23e+01 c.2.1.7,c.58.1.5 86417,86418 1bqsA 209 3.26e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1ekeA 230 3.27e+01 1ekeA c.55.3.1 33572 1z6bA 154 3.27e+01 2b3gA 123 3.30e+01 2bf9A 36 3.31e+01 3prn 289 3.39e+01 3prn f.4.3.1 43761 1pz7A 204 3.51e+01 b.29.1.4 95405 2a6sA 84 3.51e+01 1m6iA 493 3.53e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1f8vA 355 3.53e+01 2bbvA b.121.4.4 23329 1fmtA 314 3.55e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1m4jA 142 3.55e+01 d.109.1.2 78602 1twfK 120 3.55e+01 1w61A 414 3.55e+01 1xdzA 240 3.60e+01 1oxxK 353 3.61e+01 b.40.6.3,c.37.1.12 93715,93716 1v9sA 208 3.62e+01 1yymG 313 3.62e+01 1x99A 145 3.66e+01 1v58A 241 3.67e+01 c.47.1.9,d.17.3.1 108371,108372 1uuqA 440 3.69e+01 c.1.8.3 100015 8dfr 189 3.72e+01 1aoeA c.71.1.1 34895 1fxlA 167 3.74e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 2fr2A 172 3.76e+01 1pi1A 185 3.77e+01 a.29.7.1 94699 2go7A 207 3.79e+01 1oi2A 366 3.80e+01 c.119.1.2 103802 1q6zA 528 3.81e+01 1iyjB 817 3.82e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 76948,76949,76950,76951,76952 1czfA 362 3.84e+01 1czfA b.80.1.3 28031 1sc3A 178 3.86e+01 c.17.1.1 105416 2fomB 185 3.94e+01 1g8kA 825 3.94e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1pcxA 810 3.97e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 2g5cA 281 3.99e+01 1nszA 347 4.02e+01 b.30.5.4 80724 1r53A 382 4.02e+01 d.258.1.1 97063 1s2oA 244 4.04e+01 1vd5A 377 4.07e+01 a.102.1.7 108518 2a38A 194 4.07e+01 1xuvA 178 4.09e+01 1pk1B 89 4.12e+01 1k2eA 156 4.16e+01 d.113.1.1 72010 2fazA 78 4.21e+01 1m6yA 301 4.21e+01 a.60.13.1,c.66.1.23 78716,78717 1y7mA 164 4.24e+01 2hlcA 230 4.24e+01 5ptp b.47.1.2 26074 1jvwA 167 4.25e+01 d.26.1.1 71907 1cznA 169 4.40e+01 1rcf c.23.5.1 31181 1ja1A 622 4.44e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1stfI 98 4.47e+01 1stfI d.17.1.2 38006 1mqiA 263 4.51e+01 c.94.1.1 91398 1uj8A 77 4.51e+01 1qqp3 220 4.52e+01 1qqp3 1ui5A 215 4.54e+01 a.4.1.9,a.121.1.1 107856,107857 3grs 478 4.54e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1ku0A 388 4.54e+01 c.69.1.18 72994 1l2tA 235 4.57e+01 c.37.1.12 73514 1cseI 71 4.58e+01 1egpA d.40.1.1 38559 2b5wA 357 4.63e+01 1bbhA 131 4.64e+01 1bbhA a.24.3.2 16546 1j3mA 129 4.66e+01 d.129.7.1 103836 1meoA 209 4.74e+01 c.65.1.1 79035 1xqwA 293 4.77e+01 1wdvA 152 4.83e+01 1k8kC 372 4.85e+01 b.69.4.1 68308 2cunA 410 4.87e+01 1r89A 437 4.87e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1zn6A 227 4.90e+01 1iy8A 267 4.92e+01 c.2.1.2 83774 2fv1A 377 4.93e+01 2dkaA 544 4.94e+01 1p0kA 349 4.94e+01 c.1.4.1 87648 2gupA 292 4.99e+01 2gu3A 136 5.05e+01 1q4rA 112 5.06e+01 d.58.4.4 95823 2f02A 323 5.11e+01 1pbjA 125 5.11e+01 d.37.1.1,d.37.1.1 94414,94415 1bdo 80 5.13e+01 1bdo b.84.1.1 28214 1vqoT 120 5.16e+01 1spxA 278 5.17e+01 c.2.1.2 98958 1tvgA 153 5.18e+01 1p99A 295 5.22e+01 c.94.1.1 94384 1o17A 345 5.24e+01 a.46.2.1,c.27.1.1 80765,80766 1vqvA 306 5.27e+01 1x31D 99 5.30e+01 1uliA 460 5.33e+01 b.33.1.2,d.129.3.3 107921,107922 1s0yB 71 5.35e+01 d.80.1.1 98315 2cyjA 118 5.35e+01 1gskA 513 5.45e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1h8eA 510 5.50e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 2gsfA 373 5.52e+01 1h21A 247 5.52e+01 a.138.1.3 76510 1nw1A 429 5.55e+01 d.144.1.8 86286 1d02A 202 5.58e+01 1d02A c.52.1.8 33313 1nddA 76 5.60e+01 1ubi d.15.1.1 37599 1jbiA 100 5.60e+01 d.209.1.1 66481 1lurA 339 5.64e+01 b.30.5.4 84717 1yqgA 263 5.65e+01 1uasA 362 5.67e+01 b.71.1.1,c.1.8.1 88388,88389 1kdj 102 5.68e+01 1plc b.6.1.1 22864 1qfoA 119 5.74e+01 1qfoA b.1.1.1 19708 1f60B 94 5.78e+01 1b64 d.58.12.1 39307 1mtzA 293 5.93e+01 c.69.1.7 79467 1m1hA 248 5.96e+01 b.114.1.1,d.58.42.1 78415,78416 2gwgA 350 5.99e+01 1u94A 356 6.01e+01 c.37.1.11,d.48.1.1 107743,107744 1zrn 232 6.04e+01 1qq5A c.108.1.1 43323 1wvqA 167 6.05e+01 1whvA 100 6.12e+01 1wehA 171 6.15e+01 1v8fA 276 6.16e+01 c.26.1.4 100503 1vc3B 97 6.17e+01 1qmvA 197 6.19e+01 1qq2A c.47.1.10 33066 1jalA 363 6.20e+01 c.37.1.8,d.15.10.2 84138,84139 1uvqA 197 6.21e+01 b.1.1.2,d.19.1.1 100062,100063 1vkyA 347 6.21e+01 e.53.1.1 108696 1uheA 97 6.32e+01 2bmoB 194 6.45e+01 1h1yA 228 6.47e+01 c.1.2.2 76506 1drw 273 6.49e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1iq8A 582 6.51e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 2ai4A 119 6.55e+01 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