# List of top-scoring protein chains for t2k-100-30-alpha-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 1wqaA 455 1.45e-03 1lvaA 258 8.90e-02 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1ri7A 171 1.31e-01 a.4.5.32,d.58.4.2 97504,97505 1oz9A 150 1.46e-01 d.92.1.15 93808 1w1wA 430 3.53e-01 1ob8A 135 4.10e-01 1fcyA 236 4.14e-01 2lbd a.123.1.1 19282 1yj7A 171 4.45e-01 2fcr 173 4.51e-01 1rcf c.23.5.1 31151 1wkoA 180 5.11e-01 1ykfA 352 5.29e-01 1pedA b.35.1.2,c.2.1.1 24757,29773 2lbd 267 6.26e-01 2lbd a.123.1.1 19287 1ow1A 195 6.27e-01 b.131.1.3 93625 2u1a 88 6.57e-01 2u1a d.58.7.1 39164 1q7zA 566 7.67e-01 c.1.21.2,c.1.26.1 96090,96091 1hmy 327 8.01e-01 6mhtA c.66.1.26 34229 2fbiA 142 9.19e-01 2cxcA 144 9.27e-01 1x7oA 287 9.87e-01 1pj5A 830 1.10e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1m4vA 204 1.17e+00 b.40.2.2,d.15.6.1 74459,74460 2cuaA 135 1.29e+00 2cuaA b.6.1.2 23039 1ymqA 261 1.37e+00 2cviA 83 1.44e+00 1eudA 311 1.46e+00 2scuA c.2.1.8,c.23.4.1 30312,31140 1ehkB 168 1.46e+00 2cuaA b.6.1.2,f.17.2.1 23041,43625 4lbd 267 1.58e+00 2lbd a.123.1.1 19289 1s0uA 408 1.59e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1rz1A 161 1.67e+00 b.45.1.2 98124 1fjxA 327 1.69e+00 6mhtA c.66.1.26 34228 1vjeA 166 1.72e+00 d.185.1.2 100807 1zpvA 91 1.72e+00 1aisB 200 1.75e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1xx6A 191 1.81e+00 1eucA 311 1.95e+00 2scuA c.2.1.8,c.23.4.1 30311,31139 1jmtA 104 2.02e+00 d.58.7.3 63180 1rzsA 61 2.12e+00 a.35.1.2 105139 1xt5A 135 2.15e+00 3mhtA 327 2.24e+00 6mhtA c.66.1.26 34234 1xn7A 78 2.32e+00 1d3uB 201 2.43e+00 1aisB a.74.1.2,a.74.1.2 18386,18387 2dbbA 151 2.70e+00 1ub9A 100 3.07e+00 a.4.5.28 99159 1vjqA 79 3.08e+00 k.43.1.1 100830 1iyeA 309 3.09e+00 e.17.1.1 83786 1lddA 74 3.09e+00 a.4.5.34 73841 1aoxA 203 3.11e+00 1aoxA c.62.1.1 34151 1geqA 248 3.19e+00 2tysA c.1.2.4 28589 2c9aA 259 3.22e+00 2c7pA 327 3.24e+00 1vq2A 193 3.46e+00 1i1kA 309 3.50e+00 1daaA e.17.1.1 61533 1q1hA 110 3.56e+00 a.4.5.41 95580 1aqm 453 3.57e+00 1smd b.71.1.1,c.1.8.1 27717,28704 1g94A 448 3.59e+00 b.71.1.1,c.1.8.1 65169,65170 1qo0D 196 3.60e+00 1qo0D c.23.1.3 31125 1pswA 348 3.75e+00 c.87.1.7 88287 6mhtA 327 3.85e+00 6mhtA c.66.1.26 34226 1fjgP 88 3.99e+00 1emwA d.27.1.1 38444 1zu4A 320 4.34e+00 1e9rA 437 4.35e+00 c.37.1.11 64827 1tl0D 103 4.37e+00 1vhwA 253 4.50e+00 c.56.2.1 100706 1innA 166 4.76e+00 1j98A d.185.1.2 62608 1rl6A 177 4.89e+00 1rl6A d.141.1.1,d.141.1.1 41473,41474 1srvA 145 4.98e+00 1derA c.8.5.1 30817 2eueA 279 5.12e+00 2d8dA 90 5.22e+00 1f08A 148 5.25e+00 1f08A d.89.1.2 59564 1v7pC 200 5.30e+00 c.62.1.1 108408 1yreA 197 5.31e+00 3chbD 104 5.31e+00 3chbD b.40.2.1 24970 1fnlA 175 5.33e+00 2fcbA b.1.1.4,b.1.1.4 21783,21784 1ksyA 154 5.48e+00 d.89.1.2 72948 1a3gA 308 5.65e+00 1daaA e.17.1.1 43286 2ch8A 201 5.72e+00 1xc3A 302 5.85e+00 1nfn 191 6.06e+00 1nfn a.24.1.1 16523 1yfqA 342 6.06e+00 1tqmA 282 6.35e+00 a.4.5.56,d.144.1.9 107236,107237 2ffuA 501 6.57e+00 1k2fA 190 6.78e+00 b.8.1.2 68054 1kid 203 6.82e+00 1derA c.8.5.1 30771 1hcrA 52 6.93e+00 1hcrA a.4.1.2 16020 1ejeA 192 7.14e+00 1ejeA b.45.1.2 25757 1g3qA 237 7.21e+00 1hyqA c.37.1.10 60237 2c0nA 203 7.21e+00 2fsqA 243 7.28e+00 1vkfA 188 7.46e+00 c.1.29.1 108656 1ursA 402 7.47e+00 c.94.1.1 99833 1qwdA 177 7.75e+00 b.60.1.1 96471 1lea 84 7.79e+00 1lea a.4.5.2 16085 1lylA 504 7.81e+00 1lylA b.40.4.1,d.104.1.1 25261,40717 2f5gA 133 7.88e+00 1fsz 372 7.93e+00 1fsz c.32.1.1,d.79.2.1 31750,39802 1hw1A 239 8.00e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 2bz1A 196 8.01e+00 1gegA 256 8.19e+00 1ybvA c.2.1.2 29888 1ymiA 334 8.38e+00 2bolA 314 8.38e+00 1wi9A 72 8.54e+00 1repC 251 8.68e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1k3pA 426 8.89e+00 a.103.1.1 77237 1tin 69 8.93e+00 2sniI d.40.1.1 38580 1bbpA 173 9.26e+00 1bbpA b.60.1.1 27147 1ooeA 236 9.29e+00 c.2.1.2 87196 1ckeA 227 9.42e+00 1ckeA c.37.1.1 31846 1qt9A 98 9.56e+00 1awd d.15.4.1 37647 1czpA 98 9.66e+00 1awd d.15.4.1 37645 2fiqA 420 9.66e+00 1mit 69 9.81e+00 1hymA d.40.1.1 38582 2ff4A 388 9.83e+00 2dexX 671 9.98e+00 1gveA 327 1.00e+01 c.1.7.1 70597 1tdj 514 1.00e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 1u4cA 349 1.01e+01 b.69.4.2 107666 1qc5A 192 1.02e+01 1aoxA c.62.1.1 34147 2fliA 220 1.02e+01 1u8sA 192 1.02e+01 d.58.18.5,d.58.18.5 107737,107738 1pjqA 457 1.02e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1ka2A 499 1.03e+01 d.92.1.5 77305 1ebmA 317 1.05e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 1pt6A 213 1.06e+01 c.62.1.1 95091 1lp3A 519 1.07e+01 b.121.5.2 74169 1a9nB 96 1.07e+01 1urnA d.58.7.1 39165 1zowA 313 1.08e+01 1qb2A 109 1.10e+01 1qb2A a.36.1.1 17125 1xhbA 472 1.11e+01 1zkdA 387 1.12e+01 1k4mA 213 1.14e+01 c.26.1.3 77258 1vjjA 692 1.15e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 2anuA 255 1.17e+01 2gjsA 176 1.19e+01 1e2xA 243 1.20e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1mfqC 129 1.21e+01 a.36.1.1 79046 1szqA 483 1.21e+01 e.44.1.1 99045 1i8tA 367 1.22e+01 c.4.1.3,d.16.1.7 66094,66095 2wsyA 268 1.22e+01 2tysA c.1.2.4 28588 1k3eA 156 1.23e+01 d.198.1.1 68103 1cjsA 219 1.23e+01 1cjsA e.24.1.1 43354 1zarA 282 1.23e+01 1vbuA 328 1.25e+01 1fnnA 389 1.25e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1wi1A 126 1.27e+01 2cvlA 124 1.27e+01 1b7eA 420 1.31e+01 1b7eA c.55.3.4 33680 1on3A 523 1.33e+01 c.14.1.4,c.14.1.4 87107,87108 1nbwB 117 1.33e+01 c.51.3.2 80396 1pot 325 1.33e+01 1pot c.94.1.1 35807 1thg 544 1.36e+01 1thg c.69.1.17 34763 1svsA 353 1.38e+01 c.37.1.8 106051 2azpA 318 1.39e+01 1ku3A 73 1.40e+01 a.4.13.2 73000 1ww9A 392 1.41e+01 1buoA 121 1.41e+01 1buoA d.42.1.1 38631 1pme 380 1.42e+01 1hcl d.144.1.7 41653 2jdxA 385 1.43e+01 1jdw d.126.1.2 41139 2bp1A 360 1.46e+01 1m1hA 248 1.50e+01 b.114.1.1,d.58.42.1 78415,78416 2b0jA 358 1.51e+01 2cfxA 144 1.52e+01 1b34A 119 1.55e+01 1d3bA b.38.1.1 24796 1i2aA 219 1.60e+01 e.24.1.1 90660 2gjgA 248 1.60e+01 1xfoA 357 1.61e+01 1l9mA 692 1.61e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 73732,73733,73734,73735 1e0tA 470 1.62e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1y02A 120 1.63e+01 1jkoC 52 1.65e+01 a.4.1.2 66809 1sg4A 260 1.65e+01 1bfd 528 1.67e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1b44D 129 1.69e+01 3chbD b.40.2.1 24960 1oi7A 288 1.71e+01 c.2.1.8,c.23.4.1 87049,87050 1m3qA 317 1.73e+01 a.96.1.3,d.129.1.2 91184,91185 1zbsA 291 1.74e+01 1yiyA 429 1.76e+01 1wteA 272 1.77e+01 2cu1A 103 1.78e+01 1efpB 252 1.78e+01 1efvB c.26.2.3 31636 1yemA 179 1.80e+01 1wwiA 148 1.81e+01 1ja9A 274 1.85e+01 c.2.1.2 62817 1nglA 179 1.86e+01 1nglA b.60.1.1 27146 1tvoA 368 1.86e+01 1jj2A 239 1.90e+01 1rl2A b.34.5.3,b.40.4.5 63084,63085 1pk9A 237 1.90e+01 c.56.2.1 94823 1jhfA 202 1.91e+01 a.4.5.2,b.87.1.1 63057,63058 1vqoA 240 1.93e+01 1phd 414 1.94e+01 1phd a.104.1.1 18913 1vdyA 140 1.96e+01 1aoa 275 2.00e+01 1aoa a.40.1.1,a.40.1.1 17396,17397 1hq1A 105 2.01e+01 1dulA a.36.1.1 17120 1vqsA 116 2.03e+01 1d3yA 301 2.04e+01 1d3yA e.12.1.1 43252 1ea0A 1479 2.06e+01 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 1tkaA 678 2.07e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31815,31816,33096 1sc6A 404 2.08e+01 1lwyA 324 2.08e+01 a.96.1.3,d.129.1.2 78285,78286 2gm3A 175 2.08e+01 1i05A 180 2.09e+01 1mup b.60.1.1 27130 2fiyA 309 2.09e+01 1foaA 348 2.09e+01 1foaA c.68.1.10 59929 1qmqA 414 2.09e+01 1phd a.104.1.1 18907 2ag9A 164 2.09e+01 1nmuB 104 2.10e+01 d.79.3.1 80666 1sa3A 262 2.12e+01 c.52.1.23 105400 1j5kA 89 2.12e+01 d.51.1.1 71565 1r5tA 142 2.12e+01 c.97.1.1 104812 1w4tA 299 2.13e+01 1kxrA 339 2.19e+01 d.3.1.3 73175 2dcnA 311 2.20e+01 1xfcA 384 2.20e+01 1q6zA 528 2.21e+01 2ghpA 292 2.21e+01 1d2eA 397 2.24e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1kqqA 139 2.27e+01 a.4.3.1 72885 1i6xA 209 2.27e+01 a.4.5.4,b.82.3.2 83673,83674 1df3A 162 2.29e+01 1mup b.60.1.1 27134 1zndA 174 2.31e+01 1td4A 115 2.31e+01 1y0nA 78 2.31e+01 1ujpA 271 2.32e+01 c.1.2.4 99462 1qy1A 174 2.33e+01 b.60.1.1 96568 1ro5A 201 2.33e+01 d.108.1.3 105023 1kpgA 287 2.33e+01 c.66.1.18 68735 2ethA 154 2.33e+01 1dz4A 414 2.33e+01 1phd a.104.1.1 18903 1jdw 423 2.34e+01 1jdw d.126.1.2 41129 1x42A 232 2.35e+01 1wstA 417 2.36e+01 1k9sA 237 2.39e+01 c.56.2.1 68359 1hbxG 157 2.41e+01 1awcA a.4.5.21 60934 1lvwA 295 2.41e+01 c.68.1.6 84723 2oneA 436 2.42e+01 4enl c.1.11.1,d.54.1.1 29203,38847 1y0yA 353 2.44e+01 1emwA 88 2.45e+01 1emwA d.27.1.1 38448 3erk 364 2.48e+01 1hcl d.144.1.7 41654 1uirA 314 2.49e+01 c.66.1.17 99429 1f0iA 504 2.51e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 2cobA 70 2.51e+01 1xt9A 212 2.51e+01 1lqpA 135 2.52e+01 d.32.1.2 78151 2dri 271 2.53e+01 2dri c.93.1.1 35637 2ag4A 164 2.53e+01 1ojxA 263 2.55e+01 c.1.10.1 93164 1nkiA 135 2.56e+01 d.32.1.2 91941 1yrgB 385 2.57e+01 1yrgA c.10.1.2 30855 1ozhA 566 2.58e+01 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1pu5A 164 2.58e+01 b.95.1.1 104310 1yizA 429 2.59e+01 1tr1A 447 2.61e+01 1e70M c.1.8.4 28957 1gpuA 680 2.61e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1ordA 730 2.65e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1g41A 444 2.65e+01 1do0A c.37.1.20 32450 1yucA 255 2.65e+01 1y9aA 360 2.69e+01 1gm6A 175 2.71e+01 b.60.1.1 70272 2gauA 232 2.71e+01 1or7A 194 2.73e+01 a.4.13.2,a.177.1.1 87332,87333 1sayA 361 2.74e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 1ay0A 680 2.78e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31823,31824,33100 1tl9A 339 2.79e+01 1gx3A 284 2.80e+01 d.3.1.5 70678 2bhvA 246 2.80e+01 1ecfA 504 2.80e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1v8gA 329 2.81e+01 a.46.2.1,c.27.1.1 100505,100506 1f3lA 321 2.82e+01 1g6q2 c.66.1.6 59630 2faoA 309 2.86e+01 1u4nA 310 2.89e+01 1m2rA 327 2.91e+01 d.144.1.7 84760 2d1sA 548 2.93e+01 1rm4A 337 2.94e+01 c.2.1.3,d.81.1.1 105000,105001 1jrmA 104 2.96e+01 d.206.1.1 67136 1skoA 143 2.96e+01 d.110.7.1 105676 1jajA 174 2.96e+01 d.218.1.2 66471 1trkA 680 2.96e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 1fjrA 195 2.97e+01 1fjrA b.102.1.1 59855 1ty0A 211 2.98e+01 b.40.2.2,d.15.6.1 107440,107441 2bkrA 212 2.98e+01 1v5eA 590 2.98e+01 1wvqA 167 2.99e+01 1wdaA 670 3.00e+01 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 1v9nA 360 3.02e+01 1r29A 127 3.03e+01 d.42.1.1 96856 1eluB 390 3.03e+01 1elqA c.67.1.3 34435 2bvaA 292 3.03e+01 1volA 204 3.04e+01 1tfb a.74.1.2,a.74.1.2 18370,18371 1dik 874 3.07e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1ihcA 188 3.11e+01 1di6A c.57.1.1 62379 1ko9A 345 3.12e+01 a.96.1.3,d.129.1.2 68717,68718 1ass 159 3.14e+01 1a6dA c.8.5.2 30818 1p4xA 250 3.15e+01 a.4.5.28,a.4.5.28 87784,87785 1jv4A 162 3.17e+01 b.60.1.1 67343 1yal 218 3.17e+01 1cs8A d.3.1.1 37025 1qouA 181 3.18e+01 1qouA b.17.1.1 23707 1uquA 482 3.19e+01 c.87.1.6 99796 1ecfB 504 3.23e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1vl6A 388 3.23e+01 c.2.1.7,c.58.1.3 108724,108725 1kepA 348 3.24e+01 c.2.1.2 68536 1oq9A 363 3.25e+01 a.25.1.2 87257 1z15A 344 3.26e+01 2as9A 210 3.28e+01 2fuvA 549 3.28e+01 1pvvA 315 3.34e+01 c.78.1.1,c.78.1.1 95190,95191 1nrwA 288 3.36e+01 c.108.1.10 86128 1rgyA 360 3.37e+01 e.3.1.1 97456 2al2A 436 3.38e+01 1qysA 106 3.42e+01 k.41.1.1 96603 2bogX 286 3.43e+01 2c07A 285 3.43e+01 1x89A 178 3.43e+01 1wnaA 131 3.47e+01 1zjrA 211 3.49e+01 1fa0B 537 3.49e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 1wgzA 510 3.51e+01 1cpt 412 3.55e+01 1cpt a.104.1.1 18968 1b6rA 355 3.57e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1fhuA 320 3.62e+01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1de4C 640 3.62e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1su8A 636 3.63e+01 e.26.1.2 98999 2gsaA 432 3.66e+01 2gsaA c.67.1.4 34446 1nhcA 336 3.67e+01 b.80.1.3 91879 1rfkA 98 3.69e+01 2cg4A 152 3.72e+01 1oaa 259 3.74e+01 1oaa c.2.1.2 29829 2f57A 317 3.75e+01 1vgjA 184 3.78e+01 1oc2A 348 3.79e+01 c.2.1.2 92765 1lx7A 253 3.80e+01 c.56.2.1 74329 1oneA 436 3.80e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1b6sA 355 3.81e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28242,31649,41494 1zip 217 3.82e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1jjoC 261 3.83e+01 1tph1 247 3.83e+01 1amk 1rxyA 253 3.84e+01 c.56.2.1 98065 1hymA 45 3.84e+01 1hymA d.40.1.1 38581 1mc0A 368 3.84e+01 d.110.2.1,d.110.2.1 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g.3.11.2,g.3.11.2,g.3.11.2 44326,44327,44328 1mhxA 65 8.62e+01 d.15.7.1 79134 1hbq 183 8.62e+01 1aqb b.60.1.1 27078 1h2kA 349 8.63e+01 b.82.2.6 76572 2f9sA 151 8.64e+01 3bifA 468 8.68e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1wznA 252 8.69e+01 1a4uA 254 8.72e+01 1b16A c.2.1.2 29878 1n3bA 216 8.75e+01 c.37.1.1 79959 1zs4A 83 8.77e+01 256bA 106 8.79e+01 256bA a.24.3.1 16539 1ve5A 311 8.79e+01 1ypfA 336 8.82e+01 1xbl 107 8.84e+01 1bqz a.2.3.1 15697 1lqc 56 8.85e+01 1pru a.35.1.5 17109 2bifA 469 8.86e+01 1bif c.37.1.7,c.60.1.4 31963,34009 2adgA 214 8.87e+01 1v6tA 255 8.88e+01 2au3A 407 8.89e+01 1mkzA 172 8.90e+01 c.57.1.1 84998 1z7dA 433 8.91e+01 1ni9A 338 8.93e+01 e.7.1.2 85739