# List of top-scoring protein chains for t04-100-30-bys-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 2fneA 117 7.12e-19 1tp5A 119 3.60e-17 1be9A 119 5.11e-17 1pdr b.36.1.1 24774 2fe5A 94 5.98e-17 2fcfA 103 2.03e-16 1qavA 90 4.67e-16 1qauA b.36.1.1 24777 1g9oA 91 8.58e-16 1pdr b.36.1.1 60400 2h2bA 107 2.71e-15 1n7eA 97 3.80e-15 b.36.1.1 91691 1n7fA 97 8.50e-15 b.36.1.1 91692 1l6oA 95 1.12e-14 b.36.1.1 84534 2f0aA 98 1.50e-14 1ihjA 98 1.93e-14 1pdr b.36.1.1 62382 1q3oA 109 2.97e-14 b.36.1.1 95700 1mfgA 95 7.78e-14 b.36.1.1 79043 1nf3C 128 9.69e-14 b.36.1.1 85596 1wf7A 103 2.15e-13 1qauA 112 2.67e-13 1qauA b.36.1.1 24779 2h3lA 103 3.15e-13 1v5lA 103 7.78e-13 b.36.1.1 108378 1kwaA 88 8.37e-13 1kwaA b.36.1.1 24772 1nteA 82 1.25e-12 b.36.1.1 86163 1r6jA 82 1.37e-12 b.36.1.1 97151 2f5yA 91 1.81e-12 1fc6A 388 4.80e-09 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 3.44e-06 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 1.44e-04 1sotA 320 6.78e-03 b.36.1.4,b.47.1.1 105852,105853 1y8tA 324 7.55e-03 1qb7A 236 7.06e-02 1qb7A c.61.1.1 34087 1zn8A 180 9.07e-02 1r13A 148 2.59e-01 d.169.1.1,h.1.1.1 96782,96783 1koe 172 3.54e-01 1koe d.169.1.5 42448 1mkmA 249 6.99e-01 a.4.5.33,d.110.2.2 79242,79243 1lw6I 64 8.66e-01 d.40.1.1 74294 2d4pA 141 9.73e-01 1to2I 64 1.14e+00 1t6t1 118 1.33e+00 1zsyA 357 1.62e+00 1bu6O 501 1.75e+00 1glcG c.55.1.4,c.55.1.4 33499,33500 1cq3A 233 1.82e+00 1cq3A b.27.1.1 23923 1poiA 317 1.91e+00 1poiA c.124.1.2 34153 1uc2A 481 2.22e+00 d.261.1.1 99161 1iw7C 1119 2.44e+00 e.29.1.1 71474 1ypcI 64 2.74e+00 2sniI d.40.1.1 38570 1g38A 393 3.29e+00 2admA c.66.1.27 60235 1rutX 188 3.45e+00 1kw4A 89 3.52e+00 a.60.1.2 73077 1kk1A 410 3.56e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1i4jA 110 3.60e+00 d.55.1.1 76734 1x3mA 415 4.08e+00 2fvgA 340 4.21e+00 1eaxA 241 4.28e+00 b.47.1.2 64889 1fr3A 67 5.21e+00 1fr3A b.40.6.1 25436 1vraB 215 5.30e+00 1uh5A 329 5.36e+00 c.2.1.2 107840 1vpqA 273 6.07e+00 3aprE 325 6.09e+00 2er7E b.50.1.2 26820 1o6dA 163 6.12e+00 c.116.1.3 92567 1h3gA 601 6.21e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1x6vA 630 6.33e+00 1w99A 558 6.55e+00 1yb2A 275 6.64e+00 2apr 325 7.03e+00 2er7E b.50.1.2 26819 1ti6A 875 7.58e+00 b.52.2.2,c.81.1.1 106974,106975 1w94A 156 8.22e+00 1hnjA 317 8.44e+00 1hn9A c.95.1.2,c.95.1.2 35969,35970 2fuqA 747 9.32e+00 2ckiA 262 9.34e+00 1zm8A 259 9.38e+00 2bsyA 278 9.46e+00 1q52A 314 9.51e+00 c.14.1.3 95846 1od5A 492 9.67e+00 b.82.1.2,b.82.1.2 86832,86833 1ojhA 65 9.86e+00 a.214.1.1 103976 1g57A 217 9.89e+00 1g57A d.115.1.2 60253 1y7lA 316 9.90e+00 1ypvA 313 1.00e+01 1vkmA 297 1.02e+01 c.138.1.1 108670 2cc0A 195 1.03e+01 1o88A 353 1.03e+01 b.80.1.1 81178 1yezA 68 1.04e+01 1z85A 234 1.07e+01 2f51A 118 1.10e+01 2g8yA 385 1.11e+01 1hvyA 288 1.15e+01 1bkpA d.117.1.1 41049 1h1dA 221 1.21e+01 c.66.1.1 83452 1rlyA 60 1.27e+01 g.41.3.1 104988 1dl6A 58 1.27e+01 1dl6A g.41.3.1 45207 1ad3A 452 1.28e+01 1ad3A c.82.1.1 35335 1vdmA 153 1.33e+01 1vid 221 1.38e+01 1vid c.66.1.1 34178 2h03A 291 1.41e+01 2fa1A 160 1.44e+01 1fm0E 150 1.45e+01 1fmaE d.41.5.1 38629 2g76A 335 1.45e+01 1air 353 1.50e+01 1air b.80.1.1 28018 1j08A 226 1.52e+01 c.47.1.2,c.47.1.2 83855,83856 1x1oA 286 1.52e+01 1yvcA 70 1.53e+01 1yjmA 110 1.55e+01 1f28A 297 1.56e+01 1bkpA d.117.1.1 59608 1db3A 372 1.56e+01 1db3A c.2.1.2 29813 1ifyA 49 1.63e+01 a.5.2.1 71207 1sfjA 238 1.64e+01 1vz6A 393 1.66e+01 d.154.1.2 108949 1z96A 40 1.70e+01 2hc1A 291 1.70e+01 1eceA 358 1.76e+01 1eceA c.1.8.3 28813 2c9wA 169 1.77e+01 1gjjA 168 1.84e+01 a.140.1.1,a.140.1.1 83291,83292 1xfoA 357 1.86e+01 1yg9A 330 1.87e+01 1vqvA 306 1.88e+01 1nmeA 146 1.91e+01 c.17.1.1 85874 2bw3A 534 1.96e+01 1lghB 45 1.98e+01 1lghB f.3.1.1 43734 1earA 147 2.05e+01 b.107.1.1,d.58.38.1 64875,64876 1fxlA 167 2.07e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1qzzA 374 2.11e+01 a.4.5.29,c.66.1.12 96719,96720 1zh5A 195 2.11e+01 2fxqA 264 2.11e+01 1xkzA 255 2.15e+01 2a6cA 83 2.16e+01 1r6wA 322 2.23e+01 c.1.11.2,d.54.1.1 97165,97166 1zckA 154 2.25e+01 1wkvA 389 2.30e+01 1lba 146 2.33e+01 1lba d.118.1.1 41062 1jmuB 666 2.34e+01 1a8l 226 2.36e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1ji0A 240 2.37e+01 c.37.1.12 71665 1y0yA 353 2.37e+01 1jnyA 435 2.37e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1v93A 296 2.39e+01 c.1.23.1 100532 2d9iA 96 2.39e+01 1ujxA 119 2.40e+01 b.26.1.2 99473 1js8A 394 2.42e+01 a.86.1.1,b.112.1.1 67219,67220 1wxxA 382 2.42e+01 1zo2A 129 2.56e+01 1ym5A 300 2.58e+01 2d1pC 95 2.59e+01 1sknP 92 2.60e+01 1sknP a.37.1.1 17127 1xv5A 401 2.63e+01 1a8vA 121 2.63e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 2ghpA 292 2.64e+01 1xtlA 175 2.72e+01 2g8mA 264 2.73e+01 1rrmA 386 2.77e+01 e.22.1.2 105081 2bhoA 130 2.77e+01 1wkyA 464 2.78e+01 1d7oA 297 2.81e+01 1enp c.2.1.2 29907 1jndA 420 2.81e+01 c.1.8.5,d.26.3.1 71757,71758 1ebfA 358 2.82e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1h2vC 771 2.86e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1rxdA 159 2.88e+01 1bxeA 113 2.88e+01 1bxeA d.55.1.1 38898 1i8dA 213 2.88e+01 b.43.4.3,b.43.4.3 61953,61954 1z1dA 103 2.89e+01 1iznB 277 2.89e+01 e.43.1.2 83848 1sflA 238 2.90e+01 1cliA 345 2.93e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1v7lA 163 2.97e+01 2ptd 298 2.98e+01 2plc c.1.18.2 29605 1xdnA 277 3.01e+01 2a6zA 222 3.01e+01 1uheA 97 3.06e+01 2ahqA 76 3.11e+01 2ampA 304 3.12e+01 1fxrA 64 3.16e+01 1fxd d.58.1.4 38993 2frgP 106 3.17e+01 1mvwB 145 3.18e+01 i.15.1.1 79524 1se8A 301 3.18e+01 b.40.4.3 105448 1avaC 181 3.19e+01 1avaC b.42.4.1 25604 1a62 130 3.22e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1h6kA 757 3.27e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1xa1A 255 3.30e+01 e.3.1.1 109529 1shxA 138 3.31e+01 1v0eA 666 3.32e+01 1vheA 373 3.36e+01 b.49.3.1,c.56.5.4 100669,100670 1txvA 452 3.41e+01 1w2iA 91 3.43e+01 d.58.10.1 109127 1bouA 139 3.54e+01 1bouA a.88.1.1 18521 1dljA 402 3.57e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1wj7A 104 3.61e+01 1zq9A 285 3.62e+01 1n0qA 93 3.63e+01 k.37.1.1 79754 1zuoA 186 3.64e+01 1id2A 106 3.68e+01 1aac b.6.1.1 62288 2cw9A 194 3.68e+01 1b25A 619 3.69e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1bx4A 345 3.73e+01 1bx4A c.72.1.1 34935 1w5tA 412 3.73e+01 1at0 145 3.75e+01 1at0 b.86.1.1 28374 1ci9A 392 3.76e+01 e.3.1.1 64767 1ex7A 186 3.77e+01 1gky c.37.1.1 59537 1dzfA 215 3.77e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1rxwA 336 3.77e+01 a.60.7.1,c.120.1.2 98059,98060 1ltlA 279 3.78e+01 b.40.4.11 84701 2gaeA 346 3.79e+01 1iscA 192 3.79e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1x92A 199 3.82e+01 2g8oA 264 3.84e+01 1fcjA 322 3.86e+01 1oasA c.79.1.1 35289 1eyqA 222 3.88e+01 1eypA d.36.1.1 38534 1dkuA 317 3.89e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1ml9A 302 3.89e+01 b.85.7.1 79282 2gwnA 452 3.90e+01 1qhxA 178 3.98e+01 1qhsA c.37.1.3 31936 1t3qB 788 4.08e+01 d.41.1.1,d.133.1.1 106369,106370 1f5nA 592 4.14e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 2bkfA 87 4.14e+01 1sw5A 275 4.14e+01 c.94.1.1 106069 2abwA 227 4.14e+01 2c6cA 707 4.14e+01 1gky 187 4.16e+01 1gky c.37.1.1 31839 2a6tA 271 4.27e+01 1mpp 361 4.34e+01 2rmpA b.50.1.2 26856 1d8cA 723 4.34e+01 1d8cA c.1.13.1 29325 1q2yA 140 4.35e+01 d.108.1.1 95655 2agcA 162 4.39e+01 1k1vA 41 4.39e+01 a.37.1.1 71999 1dcjA 81 4.41e+01 1dcjA d.68.3.3 59115 2as0A 396 4.42e+01 1es9A 232 4.43e+01 1wab c.23.10.3 31340 1zkkA 167 4.45e+01 2f9hA 129 4.47e+01 1i2kA 269 4.48e+01 e.17.1.1 90661 1m9xC 146 4.48e+01 a.73.1.1 84907 2bsjA 133 4.54e+01 1yloA 348 4.56e+01 1fhuA 320 4.57e+01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1m45A 148 4.59e+01 a.39.1.5 78598 1csh 435 4.61e+01 1csh a.103.1.1 18880 1o5oA 221 4.63e+01 c.61.1.1 92509 1vcoA 550 4.68e+01 c.23.16.1,c.37.1.10 108508,108509 2b18A 164 4.71e+01 1nwbA 124 4.72e+01 b.124.1.1 86296 2cxaA 256 4.72e+01 1pk1B 89 4.72e+01 1m6yA 301 4.77e+01 a.60.13.1,c.66.1.23 78716,78717 2cwaA 263 4.80e+01 1enp 312 4.84e+01 1enp c.2.1.2 29906 1sw5B 275 4.91e+01 c.94.1.1 106070 1wab 232 4.92e+01 1wab c.23.10.3 31341 1f8fA 371 4.95e+01 b.35.1.2,c.2.1.1 83246,83247 1egpA 45 4.95e+01 1egpA d.40.1.1 38561 2cyjA 118 5.03e+01 1gv3A 248 5.05e+01 a.2.11.1,d.44.1.1 70585,70586 1mvoA 136 5.06e+01 c.23.1.1 79513 1uzcA 71 5.11e+01 a.159.2.1 100222 1tr8A 102 5.14e+01 1ueoA 63 5.15e+01 j.107.1.1 99269 1z7wA 322 5.15e+01 1xe1A 116 5.15e+01 b.43.3.1 109571 1i9gA 280 5.15e+01 c.66.1.13 62090 2bneA 241 5.17e+01 1xodA 118 5.21e+01 2anuA 255 5.21e+01 2cu3A 64 5.26e+01 1evuA 731 5.31e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1x24A 180 5.32e+01 1m1hA 248 5.32e+01 b.114.1.1,d.58.42.1 78415,78416 2csbA 519 5.35e+01 1w30A 201 5.35e+01 1h05A 146 5.38e+01 c.23.13.1 76433 1s1iG 119 5.41e+01 i.1.1.1 105181 1y7rA 133 5.49e+01 1yb3A 175 5.50e+01 1jyhA 157 5.51e+01 d.60.1.3 71956 1vj0A 380 5.52e+01 b.35.1.2,c.2.1.1 100786,100787 1rypH 205 5.54e+01 d.153.1.4 41876 2affA 120 5.57e+01 1o63A 219 5.68e+01 c.94.1.1 92540 1flmA 122 5.69e+01 1axj b.45.1.1 25747 1ec7A 446 5.71e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1g4yR 148 5.74e+01 1cll a.39.1.5 60252 2ae0X 345 5.76e+01 1bqcA 302 5.77e+01 1bqcA c.1.8.3 28831 1l1dA 152 5.83e+01 b.88.1.3 73452 3tmkA 216 5.84e+01 3tmkA c.37.1.1 31920 1sdjA 310 5.86e+01 d.21.1.2,d.21.1.2 98807,98808 2brfA 110 5.86e+01 2gsaA 432 5.87e+01 2gsaA c.67.1.4 34446 1q7hA 153 5.87e+01 b.122.1.1,d.17.6.2 96042,96043 1ctf 74 5.88e+01 1ctf d.45.1.1 38759 1bkzA 135 5.92e+01 1a3k b.29.1.3 24202 1t6eX 381 5.99e+01 b.50.1.2 106564 1nulA 152 6.03e+01 1nulA c.61.1.1 34011 1yz7A 188 6.06e+01 1txvB 440 6.10e+01 1vs0A 310 6.16e+01 1sv6A 269 6.24e+01 d.177.1.1 106043 2coeA 120 6.28e+01 2a6hC 1119 6.28e+01 1wnfA 328 6.32e+01 1l3iA 192 6.33e+01 c.66.1.22 77676 1f60A 458 6.34e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1rl2A 137 6.40e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 2g0qA 173 6.40e+01 2bh8A 101 6.45e+01 1zmoA 244 6.50e+01 1sv0C 82 6.51e+01 a.60.1.1 106037 1g6hA 257 6.51e+01 1gajA c.37.1.12 60318 1oqvA 192 6.51e+01 d.24.1.2 87320 1rm6A 769 6.52e+01 2h3bA 494 6.55e+01 1kqwA 134 6.57e+01 b.60.1.2 72887 1oxsC 353 6.58e+01 b.40.6.3,c.37.1.12 87519,87520 1s29A 92 6.58e+01 a.4.5.46 98373 1erxA 184 6.61e+01 1np1A b.60.1.1 27164 2fojA 155 6.67e+01 1ir3A 306 6.67e+01 1fmk d.144.1.7 41702 1tygB 87 6.72e+01 d.15.3.2 107455 1fgkA 310 6.76e+01 1fgkA d.144.1.7 41693 2gfhA 260 7.00e+01 1phk 298 7.04e+01 1cdkA d.144.1.7 41635 1xewX 182 7.06e+01 1zmmA 33 7.08e+01 2b7uA 257 7.13e+01 1hq0A 295 7.17e+01 1hzgA d.194.1.1 61122 1vyqA 173 7.17e+01 2g6fX 59 7.18e+01 1srrA 124 7.18e+01 1dz3A c.23.1.1 31110 1s4iA 175 7.20e+01 1bxaA 105 7.27e+01 1aac b.6.1.1 22839 1ih8A 271 7.28e+01 2nsyA c.26.2.1 62377 1i45A 248 7.35e+01 1amk c.1.1.1 61665 1shwA 138 7.37e+01 b.6.1.5 105562 1et0A 269 7.37e+01 1et0A e.17.1.1 43289 1xjvA 294 7.37e+01 1oxxK 353 7.40e+01 b.40.6.3,c.37.1.12 93715,93716 1kmvA 186 7.44e+01 c.71.1.1 72757 1hw1A 239 7.48e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1zybA 232 7.48e+01 1j5pA 253 7.52e+01 d.81.1.3,c.2.1.3 71577,83092 1z5oA 242 7.60e+01 1sfdA 105 7.61e+01 b.6.1.1 105480 2bhvA 246 7.65e+01 1yy6A 155 7.68e+01 1th0A 226 7.70e+01 d.3.1.7 106903 1h2eA 207 7.72e+01 c.60.1.1 70857 1t3iA 420 7.77e+01 c.67.1.3 106354 1uyrA 737 7.84e+01 c.14.1.4,c.14.1.4 100188,100189 1hz6A 72 7.86e+01 2ptl d.15.7.1 61429 1jysA 242 7.91e+01 c.56.2.1 77216 1lnzA 342 7.91e+01 b.117.1.1,c.37.1.8 78112,78113 1koiA 184 7.98e+01 b.60.1.1 68725 1mzbA 136 8.02e+01 a.4.5.42 91497 1vc3B 97 8.05e+01 1fkqA 124 8.08e+01 3lzt d.2.1.2 36601 1semA 58 8.17e+01 1ckaA b.34.2.1 24544 1z3eA 132 8.23e+01 2fhqA 141 8.30e+01 1nkqA 259 8.31e+01 d.177.1.1 103862 1pg5A 299 8.34e+01 c.78.1.1,c.78.1.1 104146,104147 1o54A 277 8.35e+01 c.66.1.13 92482 1tif 78 8.36e+01 1tif d.15.8.1 37836 1kqpA 271 8.36e+01 c.26.2.1 72883 2an9A 207 8.39e+01 1ys7A 233 8.43e+01 1oktA 211 8.44e+01 a.45.1.1,c.47.1.5 93272,93273 1px5A 349 8.44e+01 a.160.1.2,d.218.1.6 95277,95278 1mmsA 140 8.49e+01 1mmsA a.4.7.1,d.47.1.1 16247,38766 1cl1A 395 8.58e+01 1cl2A c.67.1.3 34395 1r61A 207 8.60e+01 c.8.8.1 97138 1wdiA 345 8.69e+01 2bhmA 164 8.72e+01 1sy3A 184 8.76e+01 b.60.1.1 106110 1ycoA 279 8.78e+01 1vl5A 260 8.82e+01 c.66.1.41 108720 1bxvA 91 8.90e+01 1aac b.6.1.1 22875 2furA 209 8.97e+01