# 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 2ah5A 210 2.67e-05 1pu6A 218 1.43e-01 a.96.1.5 95123 1e19A 314 1.78e-01 1b7bA c.73.1.1 34967 2go7A 207 5.44e-01 1is8A 230 6.58e-01 d.96.1.1 66321 1uc8A 280 6.63e-01 c.30.1.6,d.142.1.7 99165,99166 1eexA 554 7.35e-01 1dioA c.1.19.3 29650 1t5oA 351 7.77e-01 c.124.1.5 106459 1dioA 554 8.13e-01 1dioA c.1.19.3 29656 2f1kA 279 8.99e-01 2f2eA 146 1.02e+00 1cfe 135 1.15e+00 1cfe d.111.1.1 40913 1r0dA 206 1.21e+00 a.216.1.1 104715 1z9hA 290 1.22e+00 1sf8A 126 1.83e+00 d.271.1.1 105472 1wteA 272 2.17e+00 2b49A 287 2.71e+00 1wusA 180 2.75e+00 1i2aA 219 2.81e+00 e.24.1.1 90660 2es4D 332 3.00e+00 1sgmA 191 3.34e+00 a.4.1.9,a.121.1.1 105537,105538 2coiA 386 3.59e+00 2ccjA 205 3.90e+00 1nxuA 333 4.05e+00 c.122.1.1 86389 2a1hA 365 4.17e+00 1kt8A 365 4.24e+00 e.17.1.1 77531 1ktaA 365 4.28e+00 e.17.1.1 77533 2ffjA 300 4.30e+00 1h2rL 534 4.67e+00 1h2rL e.18.1.1 43298 1jnyA 435 4.69e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1bkrA 109 4.75e+00 1bkrA a.40.1.1 17394 1ekfA 365 4.80e+00 1ekfA e.17.1.1 59445 1kzyC 259 4.87e+00 c.15.1.4,c.15.1.4 73383,73384 1c3wA 222 4.98e+00 1c3wA f.13.1.1 43405 1m0kA 262 5.14e+00 f.13.1.1 78344 1smbA 154 5.21e+00 d.111.1.1 105756 1kgbA 231 5.28e+00 f.13.1.1 68581 1aa2 108 5.32e+00 1bkrA a.40.1.1 17395 2a07F 93 5.70e+00 17gsA 210 5.82e+00 1pgtA a.45.1.1,c.47.1.5 17524,32818 1ir6A 424 5.92e+00 c.107.1.2 71342 1b7yA 350 5.94e+00 1pysA d.104.1.1 40776 18gsA 210 6.08e+00 1pgtA a.45.1.1,c.47.1.5 17528,32822 1pysA 350 6.57e+00 1pysA d.104.1.1 40775 1wuiL 534 6.62e+00 1h2aL 567 6.63e+00 1h2rL e.18.1.1 43299 1vgoA 253 6.67e+00 1wzzA 334 6.89e+00 1pgtA 210 7.08e+00 1pgtA a.45.1.1,c.47.1.5 17515,32809 1lbkA 208 7.21e+00 a.45.1.1,c.47.1.5 73809,73810 1aqwA 209 7.23e+00 1pgtA a.45.1.1,c.47.1.5 17517,32811 1dk0A 188 8.04e+00 1b2vA d.35.1.1 38530 1f9zA 135 8.16e+00 1qipA d.32.1.1 38484 2a5vA 213 8.52e+00 1pm6A 72 8.52e+00 a.6.1.7 94894 1glqA 209 8.62e+00 1pgtA a.45.1.1,c.47.1.5 17588,32882 1fjeB 175 8.67e+00 1fj7A d.58.7.1,d.58.7.1 39210,39211 1cjsA 219 8.74e+00 1cjsA e.24.1.1 43354 1a59 378 8.91e+00 1aj8A a.103.1.1 18902 1z6gA 218 9.18e+00 1y8qB 640 9.21e+00 1ubkL 534 9.53e+00 e.18.1.1 88422 1o06A 20 9.56e+00 j.105.1.1 86524 1jwyB 315 9.85e+00 c.37.1.8 67401 1sly 618 9.89e+00 1qsaA a.118.5.1,d.2.1.6 19184,36990 1rh6A 55 1.06e+01 a.6.1.7 104935 1uedA 406 1.08e+01 a.104.1.1 99256 1fj7A 101 1.13e+01 1fj7A d.58.7.1 39209 1dtjA 76 1.14e+01 1dt4A d.51.1.1 38800 1b2vA 188 1.14e+01 1b2vA d.35.1.1 38532 2a5kA 307 1.16e+01 1miwA 404 1.20e+01 a.173.1.1,d.218.1.4 79162,79163 1v54A 514 1.20e+01 f.24.1.1 100321 1mhdA 132 1.20e+01 1mhdA d.164.1.1 42175 1b8zA 90 1.21e+01 1huuA a.55.1.1 17902 2a2fX 325 1.25e+01 1q6aA 107 1.27e+01 a.186.1.1 95966 1ukz 203 1.27e+01 1zin c.37.1.1 31840 2bykB 128 1.28e+01 1fa8A 135 1.30e+01 1qipA d.32.1.1 38486 2a10A 125 1.34e+01 1l7vA 326 1.34e+01 f.22.1.1 73672 1cz4A 185 1.35e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1zclA 180 1.36e+01 1ng1 294 1.40e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 2occA 514 1.43e+01 2occA f.24.1.1 43518 1xrkA 124 1.44e+01 1cg5B 141 1.49e+01 1cg5B a.1.1.2 15585 1wy9A 147 1.50e+01 1vp8A 201 1.51e+01 1z83A 196 1.61e+01 2aqwA 332 1.64e+01 2ng1 293 1.66e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1ffh 294 1.70e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 2axtJ 40 1.77e+01 1dc7A 124 1.79e+01 1dbwA c.23.1.1 31093 1pbwA 216 1.84e+01 1pbwA a.116.1.1 19103 1wxiA 275 1.84e+01 1jx2B 315 1.86e+01 c.37.1.8 67404 1dt4A 73 1.86e+01 1dt4A d.51.1.1 38799 2fsp 124 1.87e+01 1dz3A c.23.1.1 31119 1io1A 398 1.90e+01 1io1A e.32.1.1 62611 1bylA 125 1.91e+01 1bylA d.32.1.2 38495 1ntr 124 1.95e+01 1dbwA c.23.1.1 31092 2cdnA 201 1.97e+01 1k8qA 377 1.98e+01 c.69.1.6 72177 1txdA 385 2.00e+01 a.87.1.1,b.55.1.1 107422,107423 1jpnA 296 2.11e+01 a.24.13.1,c.37.1.10 67039,67040 1nkzB 41 2.14e+01 f.3.1.1 80612 1ku1A 230 2.17e+01 a.118.3.1 72996 1ls1A 295 2.18e+01 a.24.13.1,c.37.1.10 78170,78171 1ft9A 222 2.18e+01 1ft9A a.4.5.4,b.82.3.1 16107,28131 1zckA 154 2.19e+01 1lx8A 55 2.19e+01 a.6.1.7 84734 1rxdA 159 2.19e+01 1sc6A 404 2.22e+01 1ym3A 215 2.23e+01 1yyvA 131 2.25e+01 1v2zA 111 2.27e+01 a.186.1.1 108300 1gks 78 2.30e+01 1cc5 a.3.1.1 15909 1ju3A 583 2.30e+01 b.18.1.13,c.69.1.21 67300,67301 1q2wA 308 2.31e+01 b.47.1.4 88355 1qusA 322 2.35e+01 1ltm d.2.1.6 36991 1ltm 320 2.35e+01 1ltm d.2.1.6 36992 1tx4A 198 2.36e+01 1tx4A a.116.1.1 19098 1s72V 71 2.45e+01 a.2.2.1 105341 1rcuA 195 2.45e+01 c.129.1.1 97295 1d3uB 201 2.47e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 2adoA 196 2.51e+01 1uxtA 501 2.54e+01 c.82.1.1 108125 1alvA 173 2.55e+01 1alvA a.39.1.8 17370 1q1vA 70 2.55e+01 a.159.4.1 104479 2fdsA 352 2.55e+01 2etxA 209 2.57e+01 1odkA 235 2.59e+01 c.56.2.1 86863 1kzuB 41 2.59e+01 1kzuB f.3.1.1 43728 1x24A 180 2.60e+01 1jgsA 138 2.63e+01 a.4.5.28 66683 1q1gA 276 2.64e+01 c.56.2.1 95574 2amdA 311 2.67e+01 1tksA 204 2.67e+01 d.115.1.2 107114 2au5A 139 2.68e+01 1g6wA 261 2.69e+01 1hqoA a.45.1.1,c.47.1.5 17751,33045 1jjvA 206 2.69e+01 c.37.1.1 71698 1latA 82 2.70e+01 2nllB g.39.1.2 45122 1qsaA 618 2.71e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 2g7sA 194 2.73e+01 1n1jA 93 2.75e+01 a.22.1.3 79813 1vhqA 232 2.75e+01 c.23.16.2 100696 1jeqA 609 2.84e+01 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 1qguB 519 2.87e+01 1qguB c.92.2.3 35626 1g8lA 411 2.87e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 2gx9A 129 2.87e+01 1oaoA 674 2.88e+01 e.26.1.2 86744 2f02A 323 2.91e+01 2evaA 307 2.97e+01 1zkrA 153 2.98e+01 1qh8B 519 2.99e+01 1qguB c.92.2.3 35634 1wa8B 95 3.01e+01 1am4A 199 3.04e+01 1tx4A a.116.1.1 19100 1jysA 242 3.06e+01 c.56.2.1 77216 2fiqA 420 3.06e+01 2g7gA 213 3.09e+01 1jj2U 70 3.14e+01 1ffkS a.2.2.1 63106 1vqoV 71 3.15e+01 1jwwA 80 3.15e+01 d.58.17.1 71919 2bykA 140 3.17e+01 1oqcA 125 3.19e+01 a.24.15.1 87264 1lmzA 187 3.19e+01 a.96.1.4 74037 1srrA 124 3.23e+01 1dz3A c.23.1.1 31110 1elrA 131 3.23e+01 1a17 a.118.8.1 19209 1bd3A 243 3.31e+01 1bd3A c.61.1.1 34098 1bw0A 416 3.34e+01 1bw0A c.67.1.1 34385 1e3yA 104 3.37e+01 1fadA a.77.1.2 18426 1b0nA 111 3.38e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1z5oA 242 3.38e+01 1pmi 440 3.39e+01 1pmi b.82.1.3 28114 1vhtA 218 3.39e+01 c.37.1.1 100700 1kv4A 42 3.42e+01 j.4.1.3 73051 174lA 164 3.44e+01 1l92 d.2.1.3 36956 1aisB 200 3.44e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 2aebA 322 3.48e+01 1oeyA 83 3.53e+01 d.15.2.2 92800 1v32A 101 3.55e+01 a.42.1.1 100277 1q18A 332 3.55e+01 c.55.1.7,c.55.1.7 104470,104471 2gh1A 301 3.57e+01 1z5nA 242 3.65e+01 1ufiA 64 3.65e+01 a.30.4.1 99336 2gtsA 86 3.65e+01 1k0dA 260 3.67e+01 a.45.1.1,c.47.1.5 67930,67931 1qh4A 380 3.70e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1ffkS 70 3.73e+01 1ffkS a.2.2.1 15692 1b33A 160 3.74e+01 1qgwC a.1.1.3 15649 1hbnB 442 3.75e+01 1mroB a.89.1.1,d.58.31.2 60900,60901 1t2bA 397 3.80e+01 1mroB 442 3.85e+01 1mroB a.89.1.1,d.58.31.2 18531,39449 1x6vA 630 3.89e+01 1g2cK 52 3.96e+01 1g2cK h.3.2.1 45772 1l9mA 692 3.98e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 73732,73733,73734,73735 1twuA 139 4.02e+01 d.32.1.8 107413 2btoA 473 4.02e+01 2f6lA 166 4.04e+01 1bsg 266 4.06e+01 1btl e.3.1.1 42729 1rypF 233 4.07e+01 1rypF d.153.1.4 41937 2bsxA 253 4.07e+01 2fbqA 235 4.09e+01 1g2cI 52 4.11e+01 1g2cI h.3.2.1 45771 1r8sE 203 4.14e+01 a.118.3.1 97248 1t33A 224 4.15e+01 a.4.1.9,a.121.1.1 106295,106296 1gdvA 85 4.20e+01 1ctj a.3.1.1 60458 1g2cA 52 4.20e+01 1g2cA h.3.2.1 45767 1gyfA 62 4.31e+01 1gyfA d.76.1.1 39749 1vjjA 692 4.32e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1oy1A 228 4.32e+01 c.23.16.2 87548 1gmwA 143 4.34e+01 b.107.1.1,d.58.38.1 65347,65348 1ar1A 558 4.35e+01 2occA f.24.1.1 43618 1sz2A 332 4.35e+01 3adk 195 4.36e+01 1zin c.37.1.1 31885 1gln 468 4.36e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1l0lG 81 4.39e+01 f.23.13.1 84493 2grrB 170 4.42e+01 1hlgA 371 4.48e+01 1hlgA c.69.1.6 34656 1ihfB 94 4.52e+01 1huuA a.55.1.1 17894 1zd8A 227 4.52e+01 1su8A 636 4.54e+01 e.26.1.2 98999 1ozjA 144 4.54e+01 d.164.1.1 93846 1g2cQ 52 4.64e+01 1g2cQ h.3.2.1 45775 1ybzA 91 4.64e+01 1v1rA 400 4.66e+01 c.36.1.11 108272 1ihgA 370 4.66e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1g2cO 52 4.69e+01 1g2cO h.3.2.1 45774 2fnaA 357 4.71e+01 2ctoA 93 4.78e+01 1ujmA 342 4.79e+01 2gfhA 260 4.90e+01 1nu7D 282 4.93e+01 a.8.6.1,a.8.6.1 92191,92192 1azwA 313 4.95e+01 1qtrA c.69.1.7 34658 1syxB 86 4.97e+01 1dvkA 173 5.04e+01 1dvkA a.72.1.1 18319 1j09A 468 5.08e+01 a.97.1.1,c.26.1.1 77025,77026 1rvgA 305 5.09e+01 c.1.10.2 97920 2ax4A 198 5.11e+01 1fcqA 350 5.12e+01 c.1.8.9 65006 1u3dA 509 5.13e+01 a.99.1.1,c.28.1.1 107638,107639 1x3lA 440 5.18e+01 1hnr 47 5.25e+01 1hnr a.155.1.1 17896 1szqA 483 5.28e+01 e.44.1.1 99045 1jjyA 636 5.32e+01 1jjyA 1nnsA 326 5.37e+01 c.88.1.1 85910 1wx1A 335 5.42e+01 1tx4B 178 5.48e+01 1ctqA c.37.1.8 32045 1wfyA 104 5.49e+01 1cxzB 86 5.51e+01 1cxzB a.2.6.1 15705 2at9 247 5.54e+01 1c3wA f.13.1.1 43427 1cd9C 175 5.62e+01 1bgc a.26.1.1 16816 1q0vA 81 5.63e+01 j.105.1.1 95514 1cpt 412 5.66e+01 1cpt a.104.1.1 18968 1skyB 502 5.70e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1vekA 84 5.73e+01 1b72B 87 5.78e+01 1akhA a.4.1.1 16001 192l 164 5.89e+01 1l92 d.2.1.3 36815 2awdA 323 6.15e+01 2g7lA 243 6.18e+01 1i58A 189 6.23e+01 1b3qA d.122.1.3 61773 1g59A 468 6.26e+01 a.97.1.1,c.26.1.1 60257,60258 1rlaA 323 6.27e+01 1d3vA c.42.1.1 32561 1kanA 253 6.32e+01 1knyA a.24.16.1,d.218.1.1 75878,75879 1cnt2 187 6.32e+01 1cnt3 1jr8A 117 6.34e+01 a.24.15.1 67115 1or0A 160 6.40e+01 d.153.1.2 93445 1h3lA 87 6.44e+01 a.177.1.1 76639 1f4tA 368 6.49e+01 1f4tA a.104.1.1 18973 1urfA 81 6.49e+01 a.2.6.1 99827 1lfkA 398 6.56e+01 a.104.1.1 77926 1x42A 232 6.73e+01 1zac 90 6.73e+01 1ncx a.39.1.5 17236 1knvA 293 6.75e+01 c.52.1.7 68707 1r1hA 696 6.76e+01 d.92.1.4 104756 1owfB 94 6.76e+01 a.55.1.1 87488 1gmuA 143 6.84e+01 b.107.1.1,d.58.38.1 65335,65336 1fioA 196 6.90e+01 1fioA a.47.2.1 17773 2cz2A 223 6.91e+01 1pq1A 196 6.98e+01 f.1.4.1 94986 1pufB 73 7.07e+01 a.4.1.1 95132 1t3tA 1303 7.12e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1pbv 195 7.13e+01 1pbv a.118.3.1 19179 1wosA 364 7.16e+01 b.44.2.1,d.250.1.1 109468,109469 1mq4A 272 7.22e+01 d.144.1.7 91391 1w0mA 226 7.23e+01 c.1.1.1 109027 1f1eA 154 7.32e+01 a.22.1.2 64927 1k4iA 233 7.35e+01 d.115.1.2 72056 1jekA 42 7.38e+01 1jekA h.3.2.1 62920 1b3bA 415 7.42e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1jraA 117 7.43e+01 a.24.15.1 67117 3mddA 385 7.44e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 1jjrA 151 7.44e+01 a.140.2.1 66772 1fnnA 389 7.48e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1x6mA 196 7.49e+01 3pga1 337 7.49e+01 4pgaA 1sfkA 76 7.51e+01 a.190.1.1 105488 1w41A 101 7.53e+01 1z7lA 276 7.54e+01 1odoA 408 7.54e+01 a.104.1.1 92783 1h05A 146 7.55e+01 c.23.13.1 76433 1iomA 377 7.58e+01 a.103.1.1 83698 1hqoA 258 7.59e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1opc 110 7.60e+01 1opc a.4.6.1 16231 1q1fA 151 7.60e+01 a.1.1.2 104476 1ncx 162 7.66e+01 1ncx a.39.1.5 17222 1oz9A 150 7.70e+01 d.92.1.15 93808 1y1oA 203 7.72e+01 1be3G 81 7.73e+01 1be3G f.23.13.1 43669 2ahjA 206 7.74e+01 2ahjA d.149.1.1 41772 1t0qB 330 7.75e+01 a.25.1.2 106221 1iso 416 7.87e+01 1iso c.77.1.1 35065 1jc4A 148 7.90e+01 1jc4A d.32.1.4 62863 1qzzA 374 7.92e+01 a.4.5.29,c.66.1.12 96719,96720 2cfuA 658 7.93e+01 1qcrG 70 7.94e+01 1be3G f.23.13.1 43677 1kfuS 184 7.98e+01 a.39.1.8 68574 1fc3A 120 8.01e+01 1fc3A a.4.6.3 16237 1a6i 217 8.03e+01 2tct a.4.1.9,a.121.1.1 16066,19243 2cy0A 263 8.13e+01 1qhqA 140 8.25e+01 1qhqA b.6.1.1 63326 1wxdA 263 8.27e+01 1lkyA 77 8.27e+01 a.60.1.1 73985 1top 162 8.28e+01 1ncx a.39.1.5 17223 1pw4A 451 8.30e+01 f.38.1.1 95198 2d5cA 263 8.31e+01 1hwxA 501 8.36e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1k4nA 192 8.38e+01 d.32.1.5 72059 1sr9A 644 8.44e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1vhxA 150 8.45e+01 c.55.3.8 100712 2aorA 223 8.46e+01 3mdeA 385 8.47e+01 3mdeA a.29.3.1,e.6.1.1 16594,42855 2ch4A 320 8.53e+01 1k8kG 151 8.53e+01 a.118.13.1 68313 2ao0A 324 8.54e+01 189l 164 8.55e+01 1l92 d.2.1.3 36960 1g63A 181 8.64e+01 1g5qA c.34.1.1 60299 1pb1A 416 8.69e+01 c.77.1.1 88014 1dxeA 256 8.76e+01 1dxeA c.1.12.5 29310 1xgsA 295 8.78e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1zccA 248 8.80e+01 1puoA 170 8.81e+01 a.101.1.1,a.101.1.1 95134,95135 7icd 416 8.81e+01 1iso c.77.1.1 35072 2bw3A 534 8.81e+01 1t7lA 766 8.83e+01 2dhqA 146 8.87e+01 2dhqA c.23.13.1 31382 1m5yA 408 8.91e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 2f46A 156 8.92e+01 1x7yA 400 8.95e+01 2c31A 568 8.96e+01 2amxA 376 8.98e+01