# 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 1jpaA 312 4.39e-62 d.144.1.7 67011 1opjA 293 1.52e-60 d.144.1.7 87230 1ir3A 306 5.61e-59 1fmk d.144.1.7 41702 1p4oA 322 2.60e-58 d.144.1.7 87775 1qpcA 279 7.38e-58 1fgkA d.144.1.7 41685 1t46A 313 2.80e-57 d.144.1.7 106397 1fgkA 310 3.89e-57 1fgkA d.144.1.7 41693 1mp8A 281 1.53e-55 d.144.1.7 91384 1fvrA 327 2.57e-55 d.144.1.7 60047 1r0pA 312 4.38e-55 d.144.1.7 96734 1u46A 291 1.56e-54 d.144.1.7 107656 1u59A 287 2.67e-54 d.144.1.7 107681 1xbbA 291 2.00e-53 1ywnA 316 1.00e-52 2b7aA 293 9.88e-51 2evaA 307 5.19e-41 1mq4A 272 7.84e-34 d.144.1.7 91391 1yhvA 297 2.01e-33 1f3mC 297 2.77e-33 1hcl d.144.1.7 41677 2f57A 317 6.72e-33 1xjdA 345 2.85e-32 2c30A 321 8.63e-32 2bfxA 284 2.01e-31 1t4hA 290 5.88e-31 d.144.1.7 106420 2bdwA 362 8.47e-30 1uu3A 310 1.56e-29 d.144.1.7 99999 1vjyA 303 2.02e-29 d.144.1.7 108633 1o6yA 299 2.04e-29 d.144.1.7 81106 2a19B 284 2.54e-29 1ia8A 289 3.06e-29 1ia8A d.144.1.7 62112 1py5A 326 3.20e-29 d.144.1.7 104389 1s9jA 341 3.56e-29 1xh9A 350 3.61e-29 1o6lA 337 4.99e-29 d.144.1.7 81092 1gz8A 299 5.20e-29 d.144.1.7 83405 1h1wA 289 6.06e-29 d.144.1.7 83460 1jksA 294 6.08e-29 d.144.1.7 71710 2bvaA 292 7.05e-29 1zy4A 303 1.75e-28 2eueA 279 1.80e-28 1apmE 350 2.33e-28 1cdkA d.144.1.7 41628 1hcl 298 3.54e-28 1hcl d.144.1.7 41593 1rdqE 350 5.81e-28 d.144.1.7 97314 1p4fA 293 1.26e-27 d.144.1.7 104063 1zrzA 364 1.35e-27 1blxA 326 1.45e-27 1hcl d.144.1.7 41596 1phk 298 2.60e-27 1cdkA d.144.1.7 41635 1pmnA 364 1.05e-26 d.144.1.7 94907 3erk 364 1.37e-26 1hcl d.144.1.7 41654 1tvoA 368 2.58e-26 1x8bA 289 9.21e-26 1omwA 689 9.66e-26 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1vzoA 355 9.97e-26 d.144.1.7 108971 1pme 380 1.15e-25 1hcl d.144.1.7 41653 2b9hA 353 1.72e-25 1xwsA 313 1.86e-25 1r3cA 366 2.75e-25 d.144.1.7 96906 1wbsA 360 2.80e-25 1zzlA 351 3.21e-25 2bikB 313 3.98e-25 1tkiA 321 7.46e-25 1tkiA d.144.1.7 41638 1zz2A 360 1.83e-24 2gfsA 372 2.91e-24 1ywrA 360 8.12e-24 2ac3A 316 1.53e-23 2ac5A 316 4.04e-23 1j1bA 420 6.02e-23 d.144.1.7 90758 1ymiA 334 9.83e-23 1ckiA 317 1.77e-22 1csn d.144.1.7 41660 1z57A 339 7.73e-22 2eu9A 355 5.37e-21 1om1A 332 2.32e-20 d.144.1.7 93347 1m2rA 327 7.09e-20 d.144.1.7 84760 1q8yA 373 2.24e-19 d.144.1.7 96234 1howA 373 2.91e-19 1hcl d.144.1.7 41679 1csn 298 5.64e-18 1csn d.144.1.7 41664 1wbpA 397 3.41e-17 1zarA 282 1.56e-06 1tqmA 282 2.55e-06 a.4.5.56,d.144.1.9 107236,107237 1vdxA 184 2.60e-01 1je0A 236 4.23e-01 c.56.2.1 66581 1btl 263 5.04e-01 1btl e.3.1.1 42691 1szwA 379 5.14e-01 d.265.1.4 99047 1fm0E 150 5.57e-01 1fmaE d.41.5.1 38629 1bsg 266 5.75e-01 1btl e.3.1.1 42729 1g6aA 271 7.36e-01 1btl e.3.1.1 42704 1ermA 263 7.58e-01 1btl e.3.1.1 42690 1o51A 114 7.78e-01 d.58.5.4 92480 1vgjA 184 8.38e-01 1dsxA 87 8.63e-01 1t1dA d.42.1.2 38644 1m40A 263 9.42e-01 e.3.1.1 74437 1zbfA 142 9.70e-01 1jb3A 131 1.20e+00 1jc7A b.40.3.2 62833 1rybA 212 1.23e+00 c.56.3.1 98098 1t1dA 100 1.28e+00 1t1dA d.42.1.2 38637 1i2sA 282 1.52e+00 e.3.1.1 71104 1jysA 242 1.54e+00 c.56.2.1 77216 1cl8A 276 1.58e+00 1ckqA c.52.1.1 33230 1t4bA 367 1.61e+00 c.2.1.3,d.81.1.1 106406,106407 1a68 95 1.93e+00 1t1dA d.42.1.2 38639 2bfwA 200 2.35e+00 1jhdA 396 2.39e+00 b.122.1.3,c.26.1.5 66712,66713 1gvjA 146 2.45e+00 a.4.5.21 90525 1e25A 282 2.50e+00 1e25A e.3.1.1 42731 1nd4A 264 2.56e+00 d.144.1.6 91815 1tvxA 75 2.60e+00 1tvxA d.9.1.1 37441 1iysA 262 2.67e+00 e.3.1.1 90723 6paxA 133 3.08e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 1b8aA 438 3.16e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1ii7A 333 3.16e+00 1ii7A d.159.1.4 62415 1hzoA 271 3.63e+00 e.3.1.1 71092 1kr4A 125 3.76e+00 d.58.5.2 72889 1zczA 464 3.78e+00 1yljA 263 4.00e+00 1bza 262 4.21e+00 1btl e.3.1.1 42701 1g8iA 190 4.28e+00 1rec a.39.1.5 60363 1q4rA 112 4.31e+00 d.58.4.4 95823 3kvt 115 4.34e+00 1t1dA d.42.1.2 38642 2exrA 524 4.54e+00 1m98A 317 4.60e+00 a.175.1.1,d.17.4.6 78866,78867 1gz2A 142 4.72e+00 d.169.1.1 83392 1vlqA 337 4.95e+00 c.69.1.25 108848 1ntvA 152 5.10e+00 b.55.1.2 86168 2ts1 419 5.27e+00 2ts1 c.26.1.1 31564 1nw1A 429 5.36e+00 d.144.1.8 86286 1zb9A 143 5.37e+00 1yixA 265 5.77e+00 1w19A 160 6.00e+00 2coeA 120 6.33e+00 1z7mA 344 6.43e+00 1txqA 93 6.46e+00 1xknA 355 6.56e+00 1zp4A 304 7.50e+00 2ajrA 331 7.68e+00 1c4xA 285 8.36e+00 1c4xA c.69.1.10 34684 1z5oA 242 8.41e+00 1p1lA 102 8.52e+00 d.58.5.2 87695 2ct9A 208 8.99e+00 2booA 247 9.72e+00 1nlwB 76 9.78e+00 a.38.1.1 80634 1rcwA 231 1.06e+01 a.132.1.4 97299 1u7kA 131 1.06e+01 1bueA 265 1.07e+01 1btl e.3.1.1 42727 1dkzA 219 1.07e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1jtaA 361 1.09e+01 b.80.1.1 71859 1ys4A 354 1.12e+01 1lehA 364 1.15e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1nkpB 83 1.15e+01 a.38.1.1 80574 1b35B 255 1.16e+01 1b35B b.121.4.1 23334 1e17A 150 1.17e+01 2hfh a.4.5.14 16143 2fa1A 160 1.19e+01 1jffA 451 1.20e+01 c.32.1.1,d.79.2.1 62932,62933 1a8q 274 1.21e+01 1brt c.69.1.12 34702 1wlgA 299 1.23e+01 1zkdA 387 1.24e+01 1d2zB 153 1.25e+01 1d2zB a.77.1.2 18439 1y6nL 145 1.27e+01 1ukuA 102 1.29e+01 d.58.5.2 99533 1tif 78 1.33e+01 1tif d.15.8.1 37836 1so7A 382 1.34e+01 1usmA 80 1.38e+01 d.74.1.1 99876 1kdxB 28 1.41e+01 1z5nA 242 1.42e+01 2bgzA 299 1.47e+01 2bdeA 470 1.48e+01 7a3hA 303 1.56e+01 7a3hA c.1.8.3 28817 1j7lA 264 1.56e+01 d.144.1.6 62697 1sfp 114 1.59e+01 1sfp b.23.1.1 23895 1n2fA 142 1.63e+01 d.227.1.1 79853 1psrA 100 1.67e+01 1psrA a.39.1.2 17180 1rzhH 260 1.74e+01 b.41.1.1,f.23.10.1 98162,98163 1lyvA 306 1.76e+01 c.45.1.2 74348 1z9lA 128 1.79e+01 2ezh 75 1.82e+01 2ezh a.4.1.2 16029 2b4yA 271 1.82e+01 2ftzA 284 1.85e+01 1ako 268 1.86e+01 1ako d.151.1.1 41779 1gudA 288 1.86e+01 c.93.1.1 83326 1rypC 244 1.88e+01 1rypC d.153.1.4 41934 1rxwA 336 1.91e+01 a.60.7.1,c.120.1.2 98059,98060 1jilA 420 1.91e+01 c.26.1.1 66745 1vrpA 381 1.92e+01 2ahqA 76 1.94e+01 1zkeA 83 1.94e+01 1vjzA 341 1.95e+01 c.1.8.3 100838 1t1uA 639 1.96e+01 1nx8A 273 2.00e+01 b.82.2.8 86374 1rqjA 299 2.11e+01 a.128.1.1 97744 1wjnA 97 2.18e+01 2bkkA 264 2.18e+01 2a5lA 200 2.20e+01 1x67A 146 2.31e+01 1o8rA 94 2.33e+01 d.234.1.1 86677 1jl2A 156 2.35e+01 c.55.3.1 66822 1m4lA 307 2.38e+01 c.56.5.1 78604 2c6yA 111 2.42e+01 1ad4A 266 2.44e+01 1aj2 c.1.21.1 29670 1jqnA 883 2.48e+01 c.1.12.3 77159 1hxhA 253 2.48e+01 c.2.1.2 76725 1jj2E 177 2.50e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1ytw 306 2.52e+01 1ytw c.45.1.2 32689 1g0hA 252 2.60e+01 1dk4A e.7.1.1 60171 4blmA 265 2.61e+01 1btl e.3.1.1 42721 1sffA 426 2.64e+01 c.67.1.4 105482 1q7zA 566 2.64e+01 c.1.21.2,c.1.26.1 96090,96091 1qjpA 171 2.67e+01 1bxwA f.4.1.1 43742 1s72E 178 2.71e+01 d.141.1.1,d.141.1.1 105323,105324 1pe9A 361 2.72e+01 b.80.1.1 94595 1b5tA 275 2.76e+01 1b5tA c.1.23.1 29676 2a07F 93 2.76e+01 1fiy 883 2.82e+01 1fiy c.1.12.3 29307 2gdnA 267 2.84e+01 1qovH 260 2.85e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1szoA 257 2.85e+01 c.14.1.3 106164 1g2bA 62 2.87e+01 1tud b.34.2.1 24488 1o6dA 163 2.88e+01 c.116.1.3 92567 1y08A 323 2.91e+01 1te2A 226 2.91e+01 c.108.1.6 106792 1hzdA 272 2.94e+01 c.14.1.3 65969 2az0A 73 2.94e+01 1tcvA 287 2.98e+01 1w1wA 430 2.99e+01 1l7aA 318 3.00e+01 c.69.1.25 77772 2gmqA 118 3.04e+01 1x99A 145 3.10e+01 1vqb 87 3.11e+01 1gvp b.40.4.7 25370 1tqhA 247 3.13e+01 c.69.1.29 107225 1e8gA 560 3.15e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1vns 609 3.15e+01 1vns a.111.1.3 19061 2ctc 307 3.27e+01 1aye c.56.5.1 33802 1gjjA 168 3.31e+01 a.140.1.1,a.140.1.1 83291,83292 1vqoE 178 3.33e+01 1hqz1 141 3.36e+01 1e8aA 91 3.37e+01 1b4cA a.39.1.2 17188 1pinA 163 3.40e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 1vheA 373 3.40e+01 b.49.3.1,c.56.5.4 100669,100670 1voqa 90 3.42e+01 1ggzA 148 3.44e+01 a.39.1.5 70176 1gvp 87 3.48e+01 1gvp b.40.4.7 25369 2f02A 323 3.53e+01 1g4yR 148 3.54e+01 1cll a.39.1.5 60252 1x42A 232 3.66e+01 2cxxA 190 3.71e+01 2awdA 323 3.71e+01 1mdyA 68 3.72e+01 1mdyA a.38.1.1 17132 1d4aA 273 3.73e+01 1d4aA c.23.5.3 31219 1g0oA 283 3.76e+01 1ybvA c.2.1.2 60181 1zthA 258 3.77e+01 1v7lA 163 3.85e+01 1l3iA 192 3.87e+01 c.66.1.22 77676 1yd0A 96 3.91e+01 1j5yA 187 3.98e+01 a.4.5.1,d.94.2.1 71592,71593 1et9A 204 4.07e+01 1an8 b.40.2.2,d.15.6.1 25204,37793 1qgoA 264 4.11e+01 1qgoA c.92.1.2 35596 1r1dA 247 4.14e+01 c.69.1.29 96813 2feaA 236 4.26e+01 1j9bA 141 4.27e+01 c.47.1.12 66459 1ursA 402 4.27e+01 c.94.1.1 99833 1wvhA 134 4.34e+01 2b7oA 464 4.36e+01 1xjvA 294 4.37e+01 1vajA 214 4.44e+01 2f4qA 346 4.46e+01 1rie 129 4.47e+01 1rie b.33.1.1 24427 1k9sA 237 4.65e+01 c.56.2.1 68359 2be4A 272 4.66e+01 1qnrA 344 4.71e+01 1qnoA c.1.8.3 28834 1qbgA 272 4.72e+01 1d4aA c.23.5.3 31227 1vjjA 692 4.73e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1v5tA 90 4.75e+01 d.15.1.1 108385 1wlzA 105 4.83e+01 1zk7A 467 4.89e+01 1o5zA 442 4.90e+01 c.59.1.2,c.72.2.2 92530,92531 2bc2A 227 4.92e+01 1a7tA d.157.1.1 42031 2cwcA 303 4.99e+01 1k4mA 213 5.00e+01 c.26.1.3 77258 1d5yA 292 5.03e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1rh5B 74 5.05e+01 f.23.28.1 97465 1f3uA 118 5.09e+01 1f3uA b.65.1.1 27521 1wmhA 89 5.13e+01 1dykA 394 5.14e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1wn2A 121 5.16e+01 1t6t1 118 5.18e+01 1lci 550 5.19e+01 1lci e.23.1.1 43349 2az2A 73 5.25e+01 1s3cA 141 5.27e+01 1pm4A 119 5.31e+01 b.135.1.1 94891 1f3vA 179 5.32e+01 1f3vA d.58.22.1 39382 1ej6D 418 5.33e+01 i.7.1.1 45970 3fivA 116 5.33e+01 1fmb b.50.1.1 26768 1q44A 326 5.39e+01 c.37.1.5 95779 1p97A 114 5.40e+01 d.110.3.7 94382 1yqbA 100 5.46e+01 1eh6A 207 5.52e+01 1sfe a.4.2.1,c.55.7.1 16076,33751 1vd2A 89 5.62e+01 d.15.2.2 108517 1fjgN 61 5.70e+01 1fjfN g.39.1.7 45154 1k78A 149 5.71e+01 a.4.1.5,a.4.1.5 68255,68256 1y7pA 223 5.72e+01 1quqA 129 5.72e+01 1quqA b.40.4.3 25303 1nszA 347 5.74e+01 b.30.5.4 80724 1cuk 203 5.81e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1is1A 185 5.85e+01 d.67.3.1 83704 2aeeA 211 5.94e+01 2aaoA 166 5.96e+01 1n9bA 265 6.04e+01 e.3.1.1 85463 1kutA 230 6.12e+01 d.143.1.1 73017 1nox 205 6.13e+01 1nox d.90.1.1 40242 1omrA 201 6.18e+01 a.39.1.5 93349 1h2vC 771 6.23e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1odkA 235 6.25e+01 c.56.2.1 86863 1vk6A 269 6.32e+01 d.113.1.4,d.113.1.4 100851,100852 1h6kA 757 6.37e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1rec 201 6.44e+01 1rec a.39.1.5 17326 1vkhA 273 6.47e+01 c.69.1.32 108662 1xb3A 128 6.55e+01 1wkuA 254 6.57e+01 1widA 130 6.58e+01 1yymG 313 6.62e+01 1dtdA 303 6.68e+01 1aye c.56.5.1 33823 1ppjE 196 6.81e+01 b.33.1.1,f.23.12.1 104260,104261 2brqA 97 6.89e+01 1whsA 255 6.94e+01 1ivyA c.69.1.5 34649 1ecpA 238 6.94e+01 1ecpA c.56.2.1 33775 1b5pA 385 6.97e+01 c.67.1.1 90403 1uxaA 194 6.98e+01 b.21.1.1 108091 1pmmA 466 7.03e+01 c.67.1.6 94901 2ilk 160 7.04e+01 2ilk a.26.1.3 16885 1t64A 377 7.04e+01 c.42.1.2 106543 1tfuA 157 7.05e+01 c.26.1.3 106859 2a13A 166 7.13e+01 1pdo 135 7.15e+01 1pdo c.54.1.1 33376 2cohA 202 7.20e+01 1y13A 181 7.22e+01 1jnyA 435 7.24e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1whtA 256 7.25e+01 1ivyA c.69.1.5 34646 1ejxA 100 7.28e+01 d.8.1.1 83182 1eh8A 207 7.32e+01 1sfe a.4.2.1,c.55.7.1 16077,33752 1d3bA 75 7.38e+01 1d3bA b.38.1.1 24798 1twdA 256 7.42e+01 c.1.30.1 107397 1vk0A 206 7.51e+01 c.55.3.5 100839 2anxA 146 7.53e+01 2f3yA 148 7.60e+01 1vmeA 410 7.63e+01 c.23.5.1,d.157.1.3 108893,108894 1k3sA 113 7.88e+01 d.198.1.1 68120 1rl2A 137 7.91e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1lvwA 295 7.95e+01 c.68.1.6 84723 1a32 88 7.99e+01 1a32 a.16.1.2 16384 1kblA 873 8.08e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1v9sA 208 8.08e+01 1r89A 437 8.11e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1s7bA 110 8.12e+01 f.39.1.1 98634 1uouA 474 8.15e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1nm8A 616 8.30e+01 c.43.1.3,c.43.1.3 85872,85873 1uf2C 421 8.32e+01 a.115.1.3,b.19.1.1 99291,99292 1ja1A 622 8.34e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1jekA 42 8.34e+01 1jekA h.3.2.1 62920 1yxcA 292 8.41e+01 2a6lA 292 8.41e+01 2aeuA 374 8.45e+01 2a6nA 292 8.54e+01 1iw7C 1119 8.55e+01 e.29.1.1 71474 1es9A 232 8.58e+01 1wab c.23.10.3 31340 1ohtA 215 8.59e+01 d.118.1.1 87036 1nzaA 103 8.62e+01 d.58.5.2 86444 1iseA 185 8.62e+01 d.67.3.1 90691 1c3pA 375 8.73e+01 1c3pA c.42.1.2 32606 1ucnA 152 8.78e+01 d.58.6.1 99183 1wk2A 121 8.90e+01 1o2dA 371 8.91e+01 e.22.1.2 86591 1kekA 1231 8.92e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1fp1D 372 8.93e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1z54A 132 8.93e+01