# List of top-scoring protein chains for T0333.t2k-w0.5 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 1iirA 415 1.88e-26 1iirA c.87.1.5 62453 1rrvA 416 1.65e-23 c.87.1.5 105083 1pn3A 404 9.12e-21 c.87.1.5 94938 2acvA 463 8.02e-19 2acwA 465 8.09e-19 2c1xA 456 1.30e-17 1f0kA 364 1.54e-11 1f0kA c.87.1.2 35465 1f6dA 376 9.33e-04 1f6dA c.87.1.3 35467 1vgvA 384 9.70e-04 c.87.1.3 100608 1v4vA 376 1.00e-02 c.87.1.3 100313 2bisA 440 1.50e-02 1o6cA 388 9.27e-02 c.87.1.3 92565 1mejA 223 3.71e-01 c.65.1.1 79029 1t5oA 351 4.63e-01 c.124.1.5 106459 1meoA 209 9.23e-01 c.65.1.1 79035 1zlyA 203 9.26e-01 1w78A 422 1.08e+00 1vjzA 341 1.18e+00 c.1.8.3 100838 1f0jA 377 1.61e+00 1f0jA a.211.1.2 19346 1rorA 378 1.61e+00 1tb5A 381 1.76e+00 a.211.1.2 106735 1xm6A 398 1.82e+00 1gq6A 313 2.30e+00 c.42.1.1 70341 1j9lA 247 4.41e+00 c.106.1.1 62762 1yk0A 480 4.76e+00 1yk1A 479 4.76e+00 2cf2C 342 5.11e+00 2ch1A 396 5.33e+00 1fmtA 314 5.75e+00 1fmtA b.46.1.1,c.65.1.1 25758,34174 1oynA 360 5.95e+00 a.211.1.2 87609 2fm0A 361 6.00e+00 1s1mA 545 6.56e+00 c.23.16.1,c.37.1.10 105201,105202 1jdpA 441 6.66e+00 c.93.1.1 62906 1wb0A 445 7.34e+00 1iugA 352 7.75e+00 c.67.1.3 90699 1dbqA 289 8.13e+00 1qpzA c.93.1.1 35666 1vm6A 228 8.30e+00 c.2.1.3,d.81.1.3 108876,108877 1h3fA 432 8.36e+00 c.26.1.1,d.66.1.4 76631,76632 1a9y 338 8.77e+00 1xel c.2.1.2 29789 1cs0A 1073 8.82e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1vcnA 550 9.07e+00 c.23.16.1,c.37.1.10 108506,108507 1vpwA 340 9.16e+00 1qpzA a.35.1.5,c.93.1.1 17087,35680 1pk8A 422 9.24e+00 c.30.1.5,d.142.1.3 94807,94808 1l2lA 457 9.28e+00 c.72.1.3 77656 1p49A 562 9.36e+00 c.76.1.2 94089 1qpzA 340 9.38e+00 1qpzA a.35.1.5,c.93.1.1 17097,35673 1pfkA 320 9.51e+00 3pfk c.89.1.1 35575 2pfkC 320 9.52e+00 3pfk c.89.1.1 35579 1qqbA 340 9.69e+00 1qpzA a.35.1.5,c.93.1.1 17099,35674 1a9z 338 9.78e+00 1xel c.2.1.2 29795 1vcoA 550 9.94e+00 c.23.16.1,c.37.1.10 108508,108509 1z7bA 358 1.06e+01 1auvA 311 1.07e+01 1auvA c.30.1.5,d.142.1.3 31723,41558 1vdmA 153 1.09e+01 2gsdA 402 1.11e+01 1kvr 338 1.16e+01 1xel c.2.1.2 29793 1oi4A 193 1.20e+01 c.23.16.2 87047 1t9kA 347 1.22e+01 c.124.1.5 106721 2pugA 340 1.24e+01 1qpzA a.35.1.5,c.93.1.1 17088,35683 1z75A 358 1.25e+01 1z74A 358 1.26e+01 1u9jA 358 1.30e+01 1kvq 338 1.30e+01 1xel c.2.1.2 29797 1svb 395 1.33e+01 1svb b.1.18.4,f.10.1.1 21814,43827 1urzA 401 1.37e+01 b.1.18.4,f.10.1.1 99838,99839 2bllA 345 1.44e+01 1kvu 338 1.45e+01 1xel c.2.1.2 29794 5reqA 727 1.48e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 2pucA 340 1.51e+01 1qpzA a.35.1.5,c.93.1.1 17094,35684 1id1A 153 1.51e+01 1id1A c.2.1.9 62286 1reqA 727 1.51e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1z73A 358 1.52e+01 1m6vA 1073 1.52e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 74536,74537,74538,74539,74540,74541 1e1cA 727 1.54e+01 1reqA c.1.19.1,c.23.6.1 29636,31263 1wcv1 257 1.55e+01 2gwrA 238 1.55e+01 1ilzA 275 1.56e+01 f.4.2.1 66209 1zejA 293 1.57e+01 1sovA 328 1.57e+01 1qyrA 252 1.63e+01 c.66.1.24 104657 1a9xA 1073 1.64e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 2bekA 257 1.64e+01 1lssA 140 1.68e+01 c.2.1.9 74246 1krhA 338 1.71e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1z7eA 660 1.73e+01 1p3wA 404 1.79e+01 c.67.1.3 87752 4sknE 223 1.80e+01 3eugA c.18.1.1 31013 1qe3A 489 1.82e+01 2bce c.69.1.1 34630 1u8xX 472 1.86e+01 c.2.1.5,d.162.1.2 107741,107742 1mzbA 136 1.91e+01 a.4.5.42 91497 1ktbA 405 1.93e+01 b.71.1.1,c.1.8.1 72960,72961 1nscA 390 1.98e+01 2qwc b.68.1.1 27591 1i35A 95 1.98e+01 d.15.1.5 66017 1udc 338 2.00e+01 1xel c.2.1.2 29785 2cv9A 252 2.01e+01 1xvlA 321 2.02e+01 1np3A 338 2.05e+01 a.100.1.2,c.2.1.6 85946,85947 1c7jA 489 2.07e+01 2bce c.69.1.1 34631 2bjrA 368 2.07e+01 1qd5A 275 2.12e+01 1qd5A f.4.2.1 43748 7timA 247 2.13e+01 1amk c.1.1.1 28457 1tdj 514 2.14e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 1zd3A 555 2.16e+01 1kvt 338 2.16e+01 1xel c.2.1.2 29798 1fw3A 275 2.16e+01 1qd5A f.4.2.1 60054 1h6vA 499 2.32e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 60693,60694,60695 1k8rB 110 2.35e+01 d.15.1.5 72180 1f25A 402 2.36e+01 1rom a.104.1.1 18952 1pswA 348 2.36e+01 c.87.1.7 88287 1tbbA 332 2.38e+01 a.211.1.2 106741 1qfjA 232 2.40e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1o60A 292 2.42e+01 c.1.10.4 92532 1hyqA 263 2.42e+01 1hyqA c.37.1.10 61412 1ulwA 402 2.46e+01 1cmnA 402 2.46e+01 1rom a.104.1.1 18958 1ehgA 403 2.46e+01 1rom a.104.1.1 18956 1ve1A 304 2.49e+01 1f26A 402 2.50e+01 1rom a.104.1.1 18951 1udb 338 2.51e+01 1xel c.2.1.2 29787 1zknA 334 2.51e+01 1m2hA 249 2.52e+01 c.31.1.5 84751 1y2kA 349 2.53e+01 1cl6A 402 2.54e+01 1rom a.104.1.1 18960 1gejA 403 2.54e+01 1rom a.104.1.1 18954 1jfbA 404 2.54e+01 a.104.1.1 66624 1cmjA 402 2.58e+01 1rom a.104.1.1 18959 1ehfA 403 2.58e+01 1rom a.104.1.1 18957 1f24A 402 2.63e+01 1rom a.104.1.1 18953 1xqdA 403 2.63e+01 1jhzA 289 2.66e+01 c.93.1.1 66731 1jh9A 340 2.69e+01 a.35.1.5,c.93.1.1 66710,66711 1wglA 59 2.74e+01 1pwhA 327 2.80e+01 c.79.1.1 95224 1c7iA 489 2.81e+01 1thg c.69.1.1 34632 1yxyA 234 2.85e+01 2c4nA 250 2.89e+01 2sspE 223 2.91e+01 3eugA c.18.1.1 31012 1mkdA 328 2.92e+01 a.211.1.2 84982 1lrkA 338 2.95e+01 c.2.1.2 74225 1y0zA 330 3.01e+01 1rcuA 195 3.02e+01 c.129.1.1 97295 1akz 223 3.03e+01 3eugA c.18.1.1 31007 1v8gA 329 3.04e+01 a.46.2.1,c.27.1.1 100505,100506 1q44A 326 3.09e+01 c.37.1.5 95779 1jfsA 340 3.10e+01 a.35.1.5,c.93.1.1 66650,66651 1f9yA 158 3.25e+01 d.58.30.1 83249 2bi7A 384 3.26e+01 1jftA 340 3.29e+01 a.35.1.5,c.93.1.1 66652,66653 1urmA 172 3.31e+01 2f1kA 279 3.33e+01 1wamA 384 3.34e+01 1t8pA 267 3.42e+01 c.60.1.1 106667 1q6zA 528 3.43e+01 1kvs 338 3.45e+01 1xel c.2.1.2 29799 1hq2A 158 3.45e+01 d.58.30.1 83620 1ihuA 589 3.45e+01 c.37.1.10,c.37.1.10 62394,62395 1pi3A 528 3.46e+01 1ynoA 527 3.49e+01 2arjA 211 3.50e+01 1bfd 528 3.50e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1b41A 539 3.52e+01 2bce c.69.1.1 34621 1u1iA 392 3.55e+01 c.2.1.3,d.81.1.3 107582,107583 2g36A 340 3.56e+01 1qv9A 283 3.59e+01 c.127.1.1 96356 2a6pA 208 3.63e+01 1lhpA 312 3.63e+01 c.72.1.5 77960 1fw8A 416 3.66e+01 16pk c.86.1.1 60058 1st9A 143 3.68e+01 c.47.1.10 98987 1yuoA 223 3.68e+01 1yioA 208 3.72e+01 1o1yA 239 3.73e+01 c.23.16.1 86554 2f9sA 151 3.82e+01 1t64A 377 3.82e+01 c.42.1.2 106543 1g7uA 284 3.86e+01 1d9eA c.1.10.4 60334 1zbqA 327 3.89e+01 1y1pA 342 3.92e+01 1nulA 152 3.92e+01 1nulA c.61.1.1 34011 1tmmA 158 3.92e+01 1qmhA 347 3.93e+01 1qmhA c.47.2.1,d.68.2.1 33082,39568 3ypiA 247 3.94e+01 1amk c.1.1.1 28463 1cqxA 403 3.95e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1uzmA 247 3.95e+01 1akw 147 3.97e+01 5nul c.23.5.1 31153 1f9hA 158 3.98e+01 d.58.30.1 83248 2ac2A 309 4.02e+01 1phwA 284 4.03e+01 c.1.10.4 104155 2ajpA 326 4.07e+01 1c1hA 310 4.07e+01 1ak1 c.92.1.1 35593 1oi7A 288 4.08e+01 c.2.1.8,c.23.4.1 87049,87050 1a6aB 187 4.12e+01 1iakB b.1.1.2,d.19.1.1 21616,38190 1dozA 309 4.12e+01 1ak1 c.92.1.1 35592 1nu5A 370 4.16e+01 c.1.11.2,d.54.1.1 92183,92184 1hd2A 161 4.18e+01 c.47.1.10 60962 1vqoI 162 4.21e+01 1c9eA 306 4.27e+01 1ak1 c.92.1.1 35595 1a98A 152 4.28e+01 1nulA c.61.1.1 34021 2bw0A 329 4.30e+01 1ecfA 504 4.44e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ybfA 268 4.50e+01 1uzlA 247 4.58e+01 1tqnA 486 4.61e+01 a.104.1.1 107238 1k30A 368 4.64e+01 c.112.1.1 68067 1w0fA 485 4.65e+01 a.104.1.1 108987 1iuqA 367 4.65e+01 c.112.1.1 90703 1g2iA 166 4.68e+01 1g2iA c.23.16.2 31438 1a97A 148 4.74e+01 1nulA c.61.1.1 34023 1s3iA 310 4.75e+01 b.46.1.1,c.65.1.1 98435,98436 1i5nA 146 4.77e+01 1i5nA a.24.10.3 61805 1bax 94 4.81e+01 1bax a.61.1.3 18133 1i1oA 147 4.86e+01 5nul c.23.5.1 61542 2reb 352 4.86e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1ml4A 308 4.88e+01 c.78.1.1,c.78.1.1 79255,79256 2recA 353 4.89e+01 2reb i.2.1.1 45879 1vjoA 393 4.94e+01 c.67.1.3 100827 1u94A 356 4.97e+01 c.37.1.11,d.48.1.1 107743,107744 1xjdA 345 5.02e+01 1azl 147 5.03e+01 5nul c.23.5.1 31154 1cbkA 160 5.04e+01 1hka d.58.30.1 39435 1qolA 173 5.06e+01 1qmyA d.3.1.2 37097 1xuuA 349 5.15e+01 1f8uA 583 5.18e+01 2bce c.69.1.1 34620 1akr 147 5.25e+01 1rcf c.23.5.1 31152 2etvA 346 5.38e+01 1i7nA 309 5.41e+01 c.30.1.5,d.142.1.3 83681,83682 1p4cA 380 5.42e+01 c.1.4.1 94100 1faiH 221 5.45e+01 1mfa b.1.1.1,b.1.1.2 19845,20949 1vkjA 285 5.47e+01 c.37.1.5 108666 1c7fA 147 5.49e+01 5nul c.23.5.1 31163 1oc3A 172 5.49e+01 c.47.1.10 92767 1neyA 247 5.52e+01 c.1.1.1 80449 1j9eA 147 5.52e+01 c.23.5.1 62756 1fjgB 256 5.61e+01 1fjfB c.23.15.1 31400 1i45A 248 5.63e+01 1amk c.1.1.1 61665 1t8sA 484 5.66e+01 c.56.2.1 106679 1o5iA 249 5.69e+01 c.2.1.2 92499 1uaaA 673 5.71e+01 1pjr c.37.1.19,c.37.1.19 32401,32402 2c1oA 254 5.80e+01 1dms 781 5.82e+01 1dmr b.52.2.2,c.81.1.1 26906,35314 1qpaA 345 5.83e+01 1arv a.93.1.1 18585 1p53A 266 5.84e+01 b.1.1.3,b.1.1.4,b.1.1.4 94118,94119,94120 1bn7A 294 5.84e+01 1bn6A c.69.1.8 34677 1l9xA 315 5.87e+01 c.23.16.1 73762 1j8qA 147 5.88e+01 c.23.5.1 62744 1c2yA 156 5.89e+01 1rvv1 c.16.1.1 30972 1bu5A 147 5.92e+01 5nul c.23.5.1 31155 1akt 147 5.94e+01 5nul c.23.5.1 31157 1cqwA 295 5.95e+01 1b6g c.69.1.8 34679 2fi9A 128 5.97e+01 1i2dA 573 5.97e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 61556,61557,61558 1iciA 256 5.98e+01 1iciA c.31.1.5 62266 1hxjA 507 6.05e+01 c.1.8.4 76729 2es7A 142 6.17e+01 1h49A 512 6.18e+01 c.1.8.4 83477 1e1eA 512 6.18e+01 1e70M c.1.8.4 28944 1v08A 512 6.18e+01 c.1.8.4 108202 1inf 390 6.25e+01 2qwc b.68.1.1 27602 2cfyA 521 6.25e+01 1tx2A 297 6.27e+01 c.1.21.1 107420 1i94B 255 6.27e+01 1fjfB c.23.15.1 61991 1qmyA 167 6.28e+01 1qmyA d.3.1.2 37094 1b9vA 390 6.41e+01 2qwc b.68.1.1 27603 1akq 147 6.46e+01 5nul c.23.5.1 31159 1vcjA 389 6.50e+01 b.68.1.1 100559 1vkzA 412 6.59e+01 b.84.2.1,c.30.1.1,d.142.1.2 108698,108699,108700 1rzuA 485 6.63e+01 c.87.1.8 105140 1qrdA 273 6.78e+01 1d4aA c.23.5.3 31217 1w44A 331 6.87e+01 1mv8A 436 7.02e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1xupO 487 7.07e+01 2b87B 58 7.07e+01 2czcA 334 7.10e+01 1m8pA 573 7.15e+01 b.122.1.3,c.26.1.5,c.37.1.15 78777,78778,78779 1m2jA 249 7.21e+01 c.31.1.5 84753 1q0yH 221 7.34e+01 b.1.1.1,b.1.1.2 95521,95522 1qpg 415 7.39e+01 16pk c.86.1.1 35450 2ac4A 309 7.43e+01 1rkqA 282 7.44e+01 c.108.1.10 97621 1q5zA 177 7.46e+01 a.196.1.1 95954 1qhuA 460 7.54e+01 1qhuA b.66.1.1,b.66.1.1 27530,27531 2cts 437 7.56e+01 1csh a.103.1.1 18896 1f20A 435 7.56e+01 b.43.4.1,c.25.1.4 64932,64933 1pq4A 291 7.58e+01 c.92.2.2 94995 1cts 437 7.59e+01 1csh a.103.1.1 18897 1wiiA 85 7.59e+01 1e18A 823 7.66e+01 1dmr b.52.2.2,c.81.1.1 26907,35315 1bgxT 832 7.67e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18083,33353,33699,42992 1t4cA 427 7.76e+01 c.123.1.1 106410 1d5zB 192 7.81e+01 1iakB b.1.1.2,d.19.1.1 21620,38194 2gk4A 232 7.84e+01 1d5mB 192 7.88e+01 1iakB b.1.1.2,d.19.1.1 21618,38192 1l0bA 229 7.88e+01 c.15.1.3,c.15.1.3 73391,73392 1lrzA 426 7.88e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1t3zA 427 7.90e+01 c.123.1.1 106388 1xwfA 431 7.91e+01 1gcuA 295 7.91e+01 1gcuA c.2.1.3,d.81.1.4 30063,39978 1lc0A 294 7.91e+01 c.2.1.3,d.81.1.4 73823,73824 1vmaA 306 7.96e+01 a.24.13.1,c.37.1.10 108887,108888 1taq 832 7.97e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1vgrA 427 8.01e+01 c.123.1.1 108625 1rtzA 152 8.06e+01 d.58.30.1 97831 2fuvA 549 8.08e+01 1p5hA 428 8.09e+01 c.123.1.1 87802 1q7zA 566 8.09e+01 c.1.21.2,c.1.26.1 96090,96091 1t4cB 427 8.10e+01 c.123.1.1 106411 1e61A 823 8.12e+01 1dmr b.52.2.2,c.81.1.1 26908,35316 1vgqA 427 8.12e+01 c.123.1.1 108623 1kqfA 1015 8.17e+01 b.52.2.2,c.81.1.1 72871,72872 4dmr 823 8.22e+01 1dmr b.52.2.2,c.81.1.1 26905,35313 1dmr 823 8.22e+01 1dmr b.52.2.2,c.81.1.1 26904,35312 2aefA 234 8.33e+01 1s1fA 406 8.41e+01 1t93A 406 8.41e+01 2d09A 407 8.41e+01 1se6A 406 8.43e+01 2d0eA 407 8.44e+01 1q5pA 269 8.50e+01 c.41.1.1 95903 1iyxA 432 8.52e+01 c.1.11.1,d.54.1.1 83815,83816 1tllA 688 8.52e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1hjqA 332 8.55e+01 c.1.8.3 83491 1f4pA 147 8.56e+01 5nul c.23.5.1 59651 1w30A 201 8.65e+01 1r59O 505 8.67e+01 1y56B 382 8.72e+01 1j9gA 147 8.80e+01 c.23.5.1 62757 1wswA 148 8.81e+01 1v0eA 666 8.81e+01 1xpjA 126 8.86e+01 1vl8A 267 8.94e+01 c.2.1.2 108733 1o4sA 389 8.94e+01 c.67.1.1 86620