# List of top-scoring protein chains for t2k-100-30-dssp-ehl2 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 1jgsA 138 2.36e-03 a.4.5.28 66683 1fp2A 352 3.35e-02 1fpxA a.4.5.29 59941 c.66.1.12 59942 1fpxA 352 6.77e-02 1fpxA a.4.5.29 59950 c.66.1.12 59951 1lj9A 144 8.55e-02 a.4.5.28 78035 1lvaA 258 9.06e-02 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1i1sA 96 9.24e-02 1bjaA a.4.5.9 16124 1bjaA 95 1.95e-01 1bjaA a.4.5.9 16122 1j5yA 187 2.20e-01 a.4.5.1 71592 d.94.2.1 71593 1r1tA 122 3.25e-01 1smtA 122 3.83e-01 1smtA a.4.5.5 16109 1oyiA 82 4.91e-01 a.4.5.19 -292 1hw5A 210 5.05e-01 2cgpA a.4.5.4 16098 b.82.3.2 28137 1cjtA 217 5.09e-01 1azsA d.58.29.1 39419 1aisB 200 5.33e-01 1aisB a.74.1.2 18384 a.74.1.2 18385 1q1hA 110 5.46e-01 unknown_sccs -262 1culA 217 5.48e-01 1azsA d.58.29.1 39417 1lnwA 147 5.62e-01 a.4.5.28 78104 2cgpA 210 5.63e-01 2cgpA a.4.5.4 16102 b.82.3.2 28141 1opc 110 5.81e-01 1opc a.4.6.1 16231 1j75A 67 6.06e-01 a.4.5.19 62673 1p2fA 220 6.28e-01 a.4.6.1 87720 c.23.1.1 87721 1smtB 122 6.41e-01 1smtA a.4.5.5 16110 1lea 84 7.33e-01 1lea a.4.5.2 16085 1d3uB 201 7.46e-01 1aisB a.74.1.2 18386 a.74.1.2 18387 1jhfA 202 8.35e-01 a.4.5.2 63057 b.87.1.1 63058 1res 43 8.76e-01 1ret a.4.1.2 16023 1odd 118 9.88e-01 1opc a.4.6.1 16232 1okrA 123 1.05e+00 unknown_sccs -235 1azsA 220 1.08e+00 1azsA d.58.29.1 39416 1ret 43 1.11e+00 1ret a.4.1.2 16024 1jmoA 480 1.12e+00 e.1.1.1 77138 1khyA 148 1.25e+00 a.174.1.1 77410 1teaA 299 1.27e+00 1mkmA 249 1.33e+00 a.4.5.33 79242 d.110.2.2 79243 1l9vA 317 1.38e+00 d.13.2.1 73760 d.216.1.1 73761 1rwyA 109 1.49e+00 a.39.1.4 -825 1tplA 426 1.57e+00 1ax4A c.67.1.2 34387 1oz9A 150 1.73e+00 unknown_sccs -10588 1fx4A 231 1.84e+00 1fx2A d.58.29.1 39431 1tfb 208 1.90e+00 1tfb a.74.1.2 18382 a.74.1.2 18383 1c7gA 456 1.97e+00 c.67.1.2 -8153 1f0jA 377 2.00e+00 1f0jA a.125.1.1 19346 1volA 204 2.04e+00 1tfb a.74.1.2 18370 a.74.1.2 18371 1a5t 334 2.23e+00 1a5t a.80.1.1 18450 c.37.1.20 32423 1gvjA 146 2.27e+00 a.4.5.21 -293 1o57A 291 2.30e+00 unknown_sccs -249 c.61.1.1 -7960 1p41A 291 2.30e+00 1bia 321 2.32e+00 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1j2rA 199 2.39e+00 unknown_sccs -6799 1je8A 82 2.61e+00 a.4.6.2 77108 1fx2A 235 2.72e+00 1fx2A d.58.29.1 39430 1an7A 136 2.76e+00 1seiA d.140.1.1 41465 9apiA 347 2.88e+00 1ovaA e.1.1.1 42630 1np7A 489 2.98e+00 a.99.1.1 80677 c.28.1.1 80678 1cuk 203 3.15e+00 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1rypE 242 3.37e+00 1rypE d.153.1.4 41936 1bib 321 3.45e+00 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1dpuA 99 3.50e+00 1dpuA a.4.5.16 16150 1dbs 224 3.57e+00 1byi c.37.1.10 32209 1g71A 347 3.73e+00 1g71A unknown_sccs 43268 1kbuA 349 3.86e+00 a.60.9.1 72284 d.163.1.1 72285 1dts 221 3.89e+00 1byi c.37.1.10 32200 1jfkA 134 3.91e+00 a.39.1.5 66639 1j3mA 129 3.93e+00 1in4A 334 4.11e+00 1hqcA a.4.5.11 62597 c.37.1.20 62598 1byi 224 4.16e+00 1byi c.37.1.10 32199 1qlpA 394 4.16e+00 1ovaA e.1.1.1 42628 1in6A 334 4.20e+00 1hqcA a.4.5.11 62601 c.37.1.20 62602 1dad 224 4.21e+00 1byi c.37.1.10 32204 1hqcA 324 4.53e+00 1hqcA a.4.5.11 16127 c.37.1.20 32424 1g0oA 283 4.76e+00 1ybvA c.2.1.2 60181 1nxiA 132 4.97e+00 d.58.47.1 86381 1p4xA 250 5.11e+00 a.4.5.28 87784 a.4.5.28 87785 1jpdX 324 5.12e+00 c.1.11.2 67014 d.54.1.1 67015 1hleA 345 5.22e+00 1ovaA e.1.1.1 42618 7a3hA 303 5.36e+00 7a3hA c.1.8.3 28817 1a3h 300 5.36e+00 7a3hA c.1.8.3 28819 1cbs 137 6.15e+00 1hmt b.60.1.2 27201 1ybvA 283 6.24e+00 1ybvA c.2.1.2 29948 1xwl 580 6.36e+00 1xwl c.55.3.5 33708 e.8.1.1 43001 1i27A 73 6.43e+00 1i27A a.4.5.30 61555 1rypC 244 6.44e+00 1rypC d.153.1.4 41934 3crxA 343 6.61e+00 4crxA a.60.9.1 18101 d.163.1.1 42161 1k47A 337 7.09e+00 d.14.1.5 72040 d.58.26.4 72041 1pueE 89 7.28e+00 1awcA a.4.5.21 16165 1abv 134 7.28e+00 1abv a.70.1.1 18317 1fi4A 416 7.62e+00 1fi4A d.14.1.5 59847 d.58.26.2 59848 1v33A 366 7.75e+00 unknown_sccs -11384 1pylA 97 7.85e+00 1f44A 324 7.87e+00 a.60.9.1 64982 d.163.1.1 64983 4crxA 322 7.97e+00 4crxA a.60.9.1 18095 d.163.1.1 42155 1vjzA 341 8.01e+00 c.1.8.3 -5318 1d0sA 356 8.08e+00 1d0vA c.39.1.1 32477 1r4wA 226 8.10e+00 unknown_sccs -7447 3bdpA 580 8.12e+00 1xwl c.55.3.5 33711 e.8.1.1 43004 1ctt 294 8.36e+00 1ctt c.97.1.1 36022 c.97.1.1 36023 1nk4A 580 8.46e+00 c.55.3.5 -7625 e.8.1.1 -11875 2pec 353 8.57e+00 1air b.80.1.1 28019 1hw1A 239 8.66e+00 1e2xA a.4.5.6 16111 a.78.1.1 18441 1d0vA 356 8.74e+00 1d0vA c.39.1.1 32476 1lj5A 379 8.94e+00 e.1.1.1 73928 1l3sA 580 8.97e+00 c.55.3.5 84521 e.8.1.1 84522 1l5oA 356 9.03e+00 c.39.1.1 77711 1dguA 183 9.07e+00 1dguA a.39.1.5 17333 1ua4A 455 9.87e+00 c.72.1.3 -8416 2bdpA 580 9.88e+00 1xwl c.55.3.5 33709 e.8.1.1 43002 1qbjA 81 9.94e+00 1qbjA a.4.5.19 16155 1mjnA 179 1.03e+01 c.62.1.1 79210 1o88A 353 1.04e+01 b.80.1.1 81178 1air 353 1.04e+01 1air b.80.1.1 28018 1crxA 322 1.07e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1jr3E 334 1.07e+01 a.80.1.1 63253 c.37.1.20 63254 1qgpA 77 1.08e+01 1qbjA a.4.5.19 16158 1a7cA 379 1.10e+01 1sek e.1.1.1 42660 1e2xA 243 1.11e+01 1e2xA a.4.5.6 16113 a.78.1.1 18443 1ng6A 148 1.13e+01 a.182.1.1 85670 1no4A 97 1.13e+01 h.1.24.1 85918 1pu6A 218 1.14e+01 unknown_sccs -1282 1mi3A 322 1.18e+01 c.1.7.1 -5257 1k8cA 322 1.18e+01 c.1.7.1 72172 1d6mA 653 1.20e+01 1d6mA e.10.1.1 43248 1rboC 123 1.23e+01 1rboC d.73.1.1 39634 8rucI 123 1.23e+01 1rboC d.73.1.1 39629 1j3wA 163 1.23e+01 unknown_sccs -10870 1l2lA 457 1.24e+01 c.72.1.3 77656 1jh8A 356 1.34e+01 c.39.1.1 63052 2tct 207 1.35e+01 2tct a.4.1.9 16063 a.121.1.1 19240 2fokA 579 1.35e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1au7A 146 1.38e+01 1au7A a.4.1.1 15995 a.35.1.1 17021 1or7A 194 1.38e+01 a.4.13.2 87332 a.177.1.1 87333 1gdtA 183 1.39e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1nnvA 110 1.41e+01 unknown_sccs -9309 1g65K 211 1.45e+01 d.153.1.4 41907 1rypL 212 1.46e+01 d.153.1.4 41880 1ufmA 84 1.55e+01 1b79A 119 1.55e+01 1b79A a.81.1.1 18451 1ekeA 230 1.55e+01 1ekeA c.55.3.1 33572 1e87A 118 1.58e+01 1b6e d.169.1.1 42327 1q5qA 259 1.61e+01 d.153.1.4 -11433 1tikA 213 1.62e+01 1o0iA 138 1.62e+01 d.38.1.5 86532 2hdhA 293 1.64e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1i7dA 659 1.66e+01 1d6mA e.10.1.1 61886 1qqiA 104 1.66e+01 1opc a.4.6.1 16233 1pysB 785 1.68e+01 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1l58 164 1.71e+01 1l92 d.2.1.3 36635 1te5A 257 1.73e+01 1bpyA 335 1.74e+01 1bpyA a.60.6.1 17980 a.60.12.1 75819 d.218.1.2 75820 1bi0 226 1.80e+01 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 1vj7A 393 1.80e+01 unknown_sccs -1265 unknown_sccs -9814 1o98A 511 1.80e+01 c.105.1.1 86684 c.76.1.3 86685 1l3lA 234 1.83e+01 a.4.6.2 73541 d.110.5.1 73542 1oeyJ 107 1.83e+01 d.15.2.2 -9168 1dxeA 256 1.84e+01 1dxeA c.1.12.5 29310 1lbd 282 1.84e+01 1lbd a.123.1.1 19279 1fy7A 278 1.85e+01 1fy7A d.108.1.1 40817 1qoxN 449 1.85e+01 1qoxN c.1.8.4 28978 1b7yB 785 1.85e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1m41A 380 1.85e+01 c.1.16.4 78595 1guxA 218 1.86e+01 1guxA a.74.1.3 18388 1f0yA 302 1.86e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1pioA 257 1.86e+01 1btl e.3.1.1 42719 1i1gA 141 1.88e+01 a.4.5.32 65982 d.58.4.2 65983 1dgnA 89 1.90e+01 1dgnA a.77.1.3 18436 1fi2A 201 1.90e+01 1fi2A b.82.1.2 59845 1ass 159 1.90e+01 1a6dA c.8.5.2 30818 1rypI 222 1.95e+01 d.153.1.4 41877 1blr 137 1.97e+01 1hmt b.60.1.2 27208 1eqjA 511 1.97e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1kgsA 225 1.97e+01 a.4.6.1 68596 c.23.1.1 68597 1rro 108 1.99e+01 1a75A a.39.1.4 17195 1lccA 51 1.99e+01 1pru a.35.1.5 17110 1lcdA 51 1.99e+01 1pru a.35.1.5 17111 1h5vA 304 2.05e+01 c.1.8.3 70898 1jrrA 382 2.13e+01 e.1.1.1 63256 1eesA 178 2.14e+01 1eesA c.37.1.8 32073 1fobA 334 2.14e+01 c.1.8.3 83255 1v9dA 340 2.16e+01 unknown_sccs -1762 1c3oE 1073 2.17e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1avyB 74 2.18e+01 1avyB h.1.17.1 45657 1oaoA 674 2.21e+01 e.26.1.2 86744 1rgyA 360 2.26e+01 e.3.1.1 -11768 119l 164 2.26e+01 1l92 d.2.1.3 36622 1on2A 142 2.30e+01 a.4.5.24 87103 a.76.1.1 87104 1alq 266 2.34e+01 1btl e.3.1.1 42707 1qc7A 101 2.35e+01 1qc7A a.118.14.1 18456 1ihfB 94 2.41e+01 1huuA a.55.1.1 17894 1lw9A 164 2.44e+01 d.2.1.3 84727 1edg 380 2.45e+01 1edg c.1.8.3 28807 1jx4A 352 2.49e+01 unknown_sccs -10188 unknown_sccs -11898 1regX 122 2.49e+01 1regX d.58.27.1 39406 1jlm 192 2.50e+01 1ido c.62.1.1 34140 1qnf 484 2.53e+01 1qnf a.99.1.1 18777 c.28.1.1 31632 1owlA 484 2.54e+01 a.99.1.1 -1296 c.28.1.1 -6646 1aj8A 371 2.54e+01 1aj8A a.103.1.1 18900 1lfaA 187 2.59e+01 1ido c.62.1.1 34122 1a8h 500 2.62e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1mf7A 194 2.66e+01 c.62.1.1 84937 1om0A 274 2.68e+01 c.1.8.5 87058 1jk0A 419 2.68e+01 a.25.1.2 63142 1p36A 164 2.69e+01 d.2.1.3 -8840 1k8uA 90 2.73e+01 a.39.1.2 72181 1uwsA 489 2.73e+01 1o7xB 377 2.73e+01 a.103.1.1 81172 1a04A 215 2.75e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1im4A 221 2.83e+01 unknown_sccs 62581 1dgqA 188 2.84e+01 1ido c.62.1.1 34131 1c9kB 180 2.88e+01 1c9kB c.37.1.11 32364 6cts 433 2.89e+01 1csh a.103.1.1 18891 1dc1A 323 2.89e+01 1dc1A c.52.1.11 33321 1hg4A 279 2.89e+01 1lbd a.123.1.1 19333 1fr1A 361 2.94e+01 1gceA e.3.1.1 42734 1pmaA 233 2.94e+01 1pmaA d.153.1.4 41918 3blm 257 3.01e+01 1btl e.3.1.1 42709 1r6rA 100 3.03e+01 unknown_sccs -1071 1qy1A 174 3.04e+01 b.60.1.1 -4445 1kzhA 555 3.13e+01 c.89.1.1 73361 1nigA 152 3.16e+01 a.25.2.1 85740 1pvaA 110 3.18e+01 1a75A a.39.1.4 17207 1gd8A 118 3.19e+01 d.188.1.1 60445 1s7oA 113 3.19e+01 1lqc 56 3.21e+01 1pru a.35.1.5 17109 1ghpA 258 3.24e+01 1btl e.3.1.1 60520 1me3A 215 3.26e+01 d.3.1.1 79022 1iqrA 420 3.27e+01 a.99.1.1 66275 c.28.1.1 66276 1tml 286 3.32e+01 1tml c.6.1.1 30656 2wsyA 268 3.33e+01 2tysA c.1.2.4 28588 1phnA 162 3.37e+01 1cpcA a.1.1.3 15641 1i06A 180 3.43e+01 1mup b.60.1.1 27131 1gy8A 397 3.45e+01 c.2.1.2 83376 6paxA 133 3.46e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1m6dA 214 3.47e+01 d.3.1.1 84849 1ub9A 100 3.49e+01 a.4.5.28 -231 1scfA 273 3.49e+01 1exzA a.26.1.2 16873 1bjz 207 3.52e+01 2tct a.4.1.9 16065 a.121.1.1 19242 1tiiD 99 3.53e+01 1tiiD b.40.2.1 24965 2dtr 226 3.56e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1qb5D 99 3.57e+01 b.40.2.1 88357 1ejjA 511 3.60e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1v7nV 163 3.66e+01 a.26.1.2 -715 1b24A 188 3.68e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 1o8rA 94 3.79e+01 d.234.1.1 86677 1jdbB 1073 3.79e+01 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1p4wA 99 3.81e+01 a.4.6.2 87783 1c3oG 1073 3.83e+01 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1jn5B 250 3.87e+01 d.17.4.2 66922 1keeA 1073 3.91e+01 a.92.1.1 68492 c.24.1.1 68493 c.30.1.1 68494 c.30.1.1 68495 d.142.1.2 68496 d.142.1.2 68497 1a27 289 3.91e+01 1fds c.2.1.2 29839 1oheA 348 3.91e+01 c.45.1.1 87013 c.45.1.1 87014 1k7jA 206 3.92e+01 d.115.1.1 72103 1jkgB 250 3.92e+01 d.17.4.2 66796 1nqkA 381 3.94e+01 c.1.16.4 -5607 1pdnC 128 3.95e+01 6paxA a.4.1.5 16047 1fokA 568 3.98e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325