# List of top-scoring protein chains for t2k-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 2f22A 144 1.81e-08 1rxqA 178 3.37e-02 a.213.1.1 105118 5eat 548 1.83e+00 5eat a.102.4.1,a.128.1.3 18853,19445 5eau 548 1.91e+00 5eat a.102.4.1,a.128.1.3 18851,19443 1jclA 260 2.11e+00 c.1.10.1 66501 1p1xA 260 3.14e+00 c.1.10.1 104060 1bolA 222 3.15e+00 1bolA d.124.1.1 41120 1t2bA 397 3.73e+00 2gz4A 207 3.88e+00 1f2eA 201 4.09e+00 1a0fA a.45.1.1,c.47.1.5 17745,33039 1io7A 368 4.36e+00 1f4tA a.104.1.1 18971 1tx4A 198 4.78e+00 1tx4A a.116.1.1 19098 1biqA 375 4.90e+00 1xikA a.25.1.2 16786 1gwiA 411 5.52e+00 a.104.1.1 76364 2bzlA 325 5.60e+00 1m12A 84 6.68e+00 a.64.1.1 84745 1l3pA 102 7.06e+00 a.24.17.1 84520 1mioA 534 7.12e+00 1qguA c.92.2.3 35601 2esnA 310 7.12e+00 3ladA 476 7.30e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1y01A 102 7.36e+00 1pmt 203 7.38e+00 1a0fA a.45.1.1,c.47.1.5 17740,33034 1t7lA 766 8.03e+00 1mwmA 320 8.13e+00 c.55.1.1,c.55.1.1 79580,79581 1tn4 159 8.18e+00 1ncx a.39.1.5 17248 1r2rA 248 8.30e+00 c.1.1.1 96875 1f4tA 368 8.57e+00 1f4tA a.104.1.1 18973 1ut8A 291 8.91e+00 a.60.7.1,c.120.1.2 99908,99909 1rz3A 201 8.98e+00 c.37.1.6 98132 1uhkA 191 9.08e+00 1y9iA 178 9.08e+00 1jqcA 375 9.26e+00 1xikA a.25.1.2 63229 1ywzA 175 9.75e+00 1ebdA 455 9.91e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1eemA 241 1.01e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1nw3A 416 1.04e+01 c.66.1.31 86288 1bouB 302 1.07e+01 1bouB c.56.6.1 33859 1b4uB 302 1.07e+01 1bouB c.56.6.1 33861 1mxrA 375 1.08e+01 a.25.1.2 85197 1aw1A 256 1.12e+01 1amk c.1.1.1 28515 1gx3A 284 1.19e+01 d.3.1.5 70678 1l3eB 101 1.20e+01 g.53.1.1 73536 1cmcA 104 1.27e+01 1cmbA a.43.1.5 17462 1tph1 247 1.31e+01 1amk 1idpA 172 1.32e+01 d.17.4.1 83685 3ertA 261 1.32e+01 3erdA a.123.1.1 19292 1ej3A 191 1.34e+01 1ej3A a.39.1.5 17259 1w5rA 278 1.34e+01 1av8A 340 1.37e+01 1xikA a.25.1.2 16796 1on2A 142 1.39e+01 a.4.5.24,a.76.1.1 87103,87104 1mngA 203 1.43e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1nb5I 98 1.44e+01 d.17.1.2 80381 1oe8A 211 1.46e+01 a.45.1.1,c.47.1.5 86905,86906 3tgl 269 1.48e+01 3tgl c.69.1.17 34733 1w5cE 84 1.51e+01 1pbe 394 1.51e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1xikA 375 1.52e+01 1xikA a.25.1.2 16784 2std 172 1.53e+01 3stdA d.17.4.1 38085 1rqlA 267 1.54e+01 c.108.1.3 97750 2gsq 202 1.56e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1sl8A 191 1.60e+01 1pujA 282 1.64e+01 c.37.1.8 88294 1cmbA 104 1.64e+01 1cmbA a.43.1.5 17460 1exnA 290 1.68e+01 1exnA a.60.7.1,c.120.1.2 18088,33358 1uquA 482 1.70e+01 c.87.1.6 99796 1ribA 375 1.73e+01 1xikA a.25.1.2 16788 1am4A 199 1.73e+01 1tx4A a.116.1.1 19100 1swvA 267 1.78e+01 1lyxA 248 1.80e+01 c.1.1.1 78304 1cmaA 104 1.81e+01 1cmbA a.43.1.5 17486 1l2iA 261 1.84e+01 a.123.1.1 73503 1dq3A 454 1.87e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1k0iA 394 1.89e+01 c.3.1.2,d.16.1.2 67942,67943 1lki 180 1.90e+01 1lki a.26.1.1 16829 1rlkA 117 1.91e+01 c.131.1.1 97651 1y8oA 419 1.92e+01 1gd8A 118 1.93e+01 d.188.1.1 60445 2gnxA 365 1.94e+01 1f7lA 121 1.96e+01 1f7lA d.150.1.2 59666 1k1xA 659 2.02e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1fmcA 255 2.05e+01 1cydA c.2.1.2 29856 1xiuA 230 2.06e+01 1jcjA 260 2.06e+01 c.1.10.1 66499 1std 172 2.07e+01 3stdA d.17.4.1 38089 2ahjB 212 2.09e+01 2ahjB b.34.4.4 24599 3stdA 165 2.10e+01 3stdA d.17.4.1 38073 3crxA 343 2.13e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 2a65A 519 2.14e+01 2etsA 128 2.19e+01 2genA 197 2.33e+01 1kbuA 349 2.36e+01 a.60.9.1,d.163.1.1 72284,72285 1v7nV 163 2.37e+01 a.26.1.2 100476 2cz1B 212 2.44e+01 1zs3A 182 2.46e+01 1qqtA 551 2.57e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 1rl0A 255 2.61e+01 1mtpA 323 2.66e+01 e.1.1.1 85107 2phh 394 2.67e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1g5yA 238 2.70e+01 1lbd a.123.1.1 60294 2axtE 84 2.72e+01 1j8yF 297 2.75e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1f44A 324 2.75e+01 a.60.9.1,d.163.1.1 64982,64983 1pea 385 2.76e+01 1pea c.93.1.1 35662 1cj3A 392 2.78e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1uqtA 482 2.82e+01 c.87.1.6 99794 1oxa 403 2.88e+01 1f4tA a.104.1.1 18965 4crxA 322 2.91e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1xpcA 248 2.96e+01 1z8uA 102 2.96e+01 1orrA 347 3.02e+01 c.2.1.2 93460 1xo0A 324 3.02e+01 2gyqA 175 3.04e+01 1ncx 162 3.08e+01 1ncx a.39.1.5 17222 1aw2A 256 3.08e+01 1amk c.1.1.1 28523 1hv2A 99 3.09e+01 d.42.1.1 61287 1xdpA 687 3.10e+01 1w0uA 55 3.12e+01 1ahjB 212 3.14e+01 2ahjB b.34.4.4 24601 1vf1A 229 3.20e+01 2bykB 128 3.21e+01 1lp8A 254 3.23e+01 d.165.1.1 91082 1l8cA 95 3.23e+01 g.53.1.1 73685 1fts 295 3.25e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1ydgA 211 3.29e+01 1lgyA 269 3.30e+01 3tgl c.69.1.17 34758 1cfpA 92 3.30e+01 1b4cA a.39.1.2 17172 1nlwB 76 3.33e+01 a.38.1.1 80634 1h49A 512 3.35e+01 c.1.8.4 83477 1exnB 290 3.35e+01 1exnA a.60.7.1,c.120.1.2 18089,33359 1cpcB 172 3.39e+01 1qgwC a.1.1.3 15644 1pioA 257 3.40e+01 1btl e.3.1.1 42719 1cqwA 295 3.45e+01 1b6g c.69.1.8 34679 1bn7A 294 3.46e+01 1bn6A c.69.1.8 34677 1tadA 324 3.50e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1top 162 3.53e+01 1ncx a.39.1.5 17223 1jb1A 205 3.53e+01 1jb1A c.91.1.2 62832 1s5lF 45 3.54e+01 1qhtA 775 3.58e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1a52A 258 3.63e+01 3erdA a.123.1.1 19296 1xmeA 568 3.65e+01 1z0xA 220 3.78e+01 1z6oM 191 3.79e+01 1a7m 180 3.81e+01 1lki a.26.1.1 16830 2c31A 568 3.83e+01 1art 396 3.85e+01 1ajsA c.67.1.1 34285 1kptA 105 3.91e+01 1kptA d.70.1.1 39588 117eA 286 3.95e+01 1wgjA b.40.5.1 25401 1mznA 240 3.96e+01 a.123.1.1 79704 1yppA 286 3.96e+01 1wgjA b.40.5.1 25407 8prkB 287 3.99e+01 1wgjA b.40.5.1 25396 2g7sA 194 4.00e+01 1g5aA 628 4.08e+01 b.71.1.1,c.1.8.1 65152,65153 1nhyA 219 4.08e+01 a.45.1.1,c.47.1.5 80520,80521 1bn6A 294 4.12e+01 1bn6A c.69.1.8 34678 1wy1A 172 4.13e+01 1ac5 483 4.13e+01 1ac5 c.69.1.5 34653 1pfvA 551 4.17e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1f4lA 551 4.18e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1yr2A 741 4.18e+01 1z8oA 404 4.19e+01 1q7sA 117 4.19e+01 c.131.1.1 96055 1xg1A 67 4.19e+01 1bgj 394 4.22e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1w0bA 102 4.26e+01 a.7.11.1 108985 1wgjA 286 4.28e+01 1wgjA b.40.5.1 25397 1gz5A 456 4.34e+01 c.87.1.6 76406 1b79A 119 4.35e+01 1b79A a.81.1.1 18451 1mvcA 240 4.41e+01 a.123.1.1 79499 1tazA 365 4.44e+01 a.211.1.2 106734 3blm 257 4.46e+01 1btl e.3.1.1 42709 1ykjA 394 4.51e+01 1avsA 90 4.66e+01 1cll a.39.1.5 17226 1f7tA 122 4.70e+01 1f7lA d.150.1.2 59667 1ud0A 113 4.71e+01 a.8.4.1 99198 2a5yA 204 4.79e+01 1ehkA 562 4.82e+01 1ehkA f.24.1.1 43624 1of8A 370 4.83e+01 c.1.10.4 92819 1ahxA 396 4.87e+01 1ajsA c.67.1.1 34293 1qqiA 104 4.98e+01 1opc a.4.6.1 16233 1qisA 396 5.01e+01 1ajsA c.67.1.1 34284 1spa 396 5.04e+01 1ajsA c.67.1.1 34291 1ffh 294 5.07e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1e55A 512 5.10e+01 1e70M c.1.8.4 28934 1pi1A 185 5.10e+01 a.29.7.1 94699 1w2xA 758 5.14e+01 c.14.1.4,c.14.1.4 109134,109135 1fecA 490 5.15e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 3erdA 261 5.17e+01 3erdA a.123.1.1 19293 1zx4A 192 5.18e+01 1pv1A 299 5.18e+01 1yvoA 172 5.18e+01 1k8kA 418 5.28e+01 c.55.1.1,c.55.1.1 68305,68306 1is1A 185 5.31e+01 d.67.3.1 83704 1arhA 396 5.32e+01 1ajsA c.67.1.1 34321 1h12A 405 5.34e+01 a.102.1.2 83447 1x46A 150 5.36e+01 8prkA 287 5.38e+01 1wgjA b.40.5.1 25395 1cxqA 162 5.43e+01 1cxqA c.55.3.2 33621 1twfB 1224 5.45e+01 1fp3A 402 5.48e+01 1fp3A a.102.1.3 18842 1e9gB 286 5.49e+01 1wgjA b.40.5.1 59394 1uj2A 252 5.49e+01 c.37.1.6 99452 1e1dA 553 5.50e+01 1e1dA e.26.1.1 43363 1ljrA 244 5.52e+01 1ljrA a.45.1.1,c.47.1.5 17707,33001 1nthA 458 5.57e+01 c.1.25.1 80730 1dkfA 233 5.60e+01 3erdA a.123.1.1 19280 1l3iA 192 5.72e+01 c.66.1.22 77676 1aiaA 396 5.72e+01 1ajsA c.67.1.1 34306 2gjlA 328 5.73e+01 1za0A 275 5.74e+01 1w5cF 44 5.75e+01 2ng1 293 5.79e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1tam 132 5.81e+01 1hiwA a.61.1.1 18128 1xtzA 264 5.85e+01 1cll 148 5.91e+01 1cll a.39.1.5 17263 1ariA 396 5.93e+01 1ajsA c.67.1.1 34331 1wu3I 161 5.96e+01 1xrsA 516 6.05e+01 1tzlA 622 6.09e+01 1ghpA 258 6.09e+01 1btl e.3.1.1 60520 1a0i 348 6.10e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1o5xA 248 6.12e+01 c.1.1.1 92528 1ghr 306 6.19e+01 1aq0A c.1.8.3 28844 1a0fA 201 6.24e+01 1a0fA a.45.1.1,c.47.1.5 17737,33031 1hfbA 370 6.24e+01 c.1.10.4 76706 1iyhA 198 6.36e+01 a.45.1.1,c.47.1.5 83790,83791 1a2xA 159 6.42e+01 1ncx a.39.1.5 17251 2amlA 373 6.47e+01 2f3yA 148 6.51e+01 1e9gA 286 6.54e+01 1wgjA b.40.5.1 59393 1qjbA 245 6.55e+01 1qjaA a.118.7.1 19202 1colA 204 6.71e+01 1a87 f.1.1.1 43378 1n1jA 93 6.75e+01 a.22.1.3 79813 1ars 396 6.76e+01 1ajsA c.67.1.1 34287 1asg 396 6.78e+01 1ajsA c.67.1.1 34335 1yyaA 250 6.78e+01 1q74A 303 6.78e+01 c.134.1.1 96019 1fwkA 296 6.79e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1cei 94 6.81e+01 1cei a.28.2.1 16939 1s5lE 84 6.85e+01 2g2dA 193 6.87e+01 1mh3A 421 6.88e+01 a.4.1.1,c.94.1.1 79112,79113 1xsvA 113 6.95e+01 1s2xA 206 7.02e+01 a.47.3.1 105229 1xd7A 145 7.03e+01 a.4.5.55 109566 1nkpB 83 7.09e+01 a.38.1.1 80574 2fwtA 125 7.12e+01 2frvB 536 7.12e+01 1h2rL e.18.1.1 43291 2cvdA 198 7.18e+01 1bw0A 416 7.20e+01 1bw0A c.67.1.1 34385 1yirA 408 7.20e+01 1zupA 315 7.25e+01 1jeoA 180 7.33e+01 c.80.1.3 66611 2axtF 45 7.33e+01 1j8mF 297 7.36e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1db3A 372 7.36e+01 1db3A c.2.1.2 29813 1uwcA 261 7.39e+01 c.69.1.17 100101 2c3nA 247 7.45e+01 2f5vA 595 7.49e+01 1ukfA 188 7.53e+01 d.3.1.10 99488 1d2fA 390 7.55e+01 1d2fA c.67.1.3 34411 1jipA 403 7.58e+01 a.104.1.1 66748 1gxqA 106 7.59e+01 a.4.6.1 70721 1efyA 350 7.69e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 2fq4A 192 7.77e+01 1w41A 101 7.85e+01 1ezfA 340 7.87e+01 1ezfA a.128.1.2 19440 1tt0A 623 7.88e+01 1ecxA 384 7.97e+01 1ecxA c.67.1.3 34431 1mjoA 104 7.97e+01 1cmbA a.43.1.5 17466 1a26 361 7.98e+01 1a26 a.41.1.1,d.166.1.2 17412,42274 1fgqA 839 8.04e+01 1yge a.119.1.1,b.12.1.1 59826,59827 1eupA 403 8.04e+01 1rom a.104.1.1 18967 1h72C 296 8.06e+01 d.14.1.5,d.58.26.1 60712,60713 1rfzA 168 8.07e+01 a.195.1.1 97411 2czlA 272 8.08e+01 1f8nA 839 8.09e+01 1yge a.119.1.1,b.12.1.1 59703,59704 1ctt 294 8.10e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1ayl 541 8.12e+01 1ayl c.91.1.1,c.109.1.1 64718,64719 1hs6A 611 8.14e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1f16A 192 8.16e+01 1f16A f.1.4.1 43400 2afdA 88 8.20e+01 1sfcB 83 8.24e+01 1sfcB h.1.15.1 45644 1lw7A 365 8.24e+01 c.26.1.3,c.37.1.1 74295,74296 1jweA 114 8.30e+01 1b79A a.81.1.1 18455 1eg5A 384 8.35e+01 1ecxA c.67.1.3 34429 1klxA 138 8.40e+01 a.118.18.1 77440 1qx2A 76 8.42e+01 a.39.1.1 104622 1tlqA 189 8.43e+01 a.195.1.1 107134 2fh5A 185 8.43e+01 1tgoA 773 8.43e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1bxeA 113 8.46e+01 1bxeA d.55.1.1 38898 2bptA 861 8.53e+01 1glqA 209 8.54e+01 1pgtA a.45.1.1,c.47.1.5 17588,32882 1unkA 87 8.56e+01 1cei a.28.2.1 16935 1ebbA 202 8.70e+01 c.60.1.1 64900 1alq 266 8.79e+01 1btl e.3.1.1 42707 1h5yA 253 8.84e+01 c.1.2.1 65638 1zjcA 418 8.88e+01 1l2qA 458 8.96e+01 c.1.25.1 73510