# List of top-scoring protein chains for t04-100-30-str2 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 1lvaA 258 1.26e-02 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1hw5A 210 2.46e-02 2cgpA a.4.5.4 16098 b.82.3.2 28137 1smtA 122 3.18e-02 1smtA a.4.5.5 16109 1r1tA 122 3.94e-02 1lj9A 144 4.01e-02 a.4.5.28 78035 1j5yA 187 5.57e-02 a.4.5.1 71592 d.94.2.1 71593 1bjaA 95 7.68e-02 1bjaA a.4.5.9 16122 1fp2A 352 8.83e-02 1fpxA a.4.5.29 59941 c.66.1.12 59942 1lnwA 147 1.50e-01 a.4.5.28 78104 1in4A 334 1.57e-01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1in6A 334 1.61e-01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1o57A 291 1.67e-01 unknown_sccs -249 c.61.1.1 -7960 1p2fA 220 2.10e-01 a.4.6.1 87720 c.23.1.1 87721 1jhfA 202 2.29e-01 a.4.5.2 63057 b.87.1.1 63058 1okrA 123 2.92e-01 unknown_sccs -235 1aisB 200 3.02e-01 1aisB a.74.1.2 18384 a.74.1.2 18385 1oyiA 82 3.80e-01 a.4.5.19 -292 1j75A 67 4.59e-01 a.4.5.19 62673 1opc 110 4.88e-01 1opc a.4.6.1 16231 1q1hA 110 6.77e-01 unknown_sccs -262 1mkmA 249 8.16e-01 a.4.5.33 79242 d.110.2.2 79243 1s3jA 155 8.23e-01 a.4.5.28 -227 1khyA 148 8.57e-01 a.174.1.1 77410 1rwyA 109 8.69e-01 a.39.1.4 -825 1l9vA 317 8.93e-01 d.13.2.1 73760 d.216.1.1 73761 1res 43 8.98e-01 1ret a.4.1.2 16023 1kgsA 225 9.49e-01 a.4.6.1 68596 c.23.1.1 68597 1rypE 242 1.02e+00 1rypE d.153.1.4 41936 1on2A 142 1.10e+00 a.4.5.24 87103 a.76.1.1 87104 1hw1A 239 1.18e+00 1e2xA a.4.5.6 16111 a.78.1.1 18441 1p4xA 250 1.26e+00 a.4.5.28 87784 a.4.5.28 87785 1fy7A 278 1.30e+00 1fy7A d.108.1.1 40817 1bia 321 1.40e+00 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1k47A 337 1.57e+00 d.14.1.5 72040 d.58.26.4 72041 1cuk 203 1.62e+00 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1gxqA 106 1.87e+00 a.4.6.1 70721 1je8A 82 1.91e+00 a.4.6.2 77108 1regX 122 1.95e+00 1regX d.58.27.1 39406 1nxiA 132 1.96e+00 d.58.47.1 86381 1gvjA 146 2.11e+00 a.4.5.21 -293 1mw9X 592 2.15e+00 e.10.1.1 -11986 1jx4A 352 2.25e+00 unknown_sccs -10188 unknown_sccs -11898 1te5A 257 2.29e+00 1qbjA 81 2.65e+00 1qbjA a.4.5.19 16155 1no4A 97 3.01e+00 h.1.24.1 85918 1azsA 220 3.05e+00 1azsA d.58.29.1 39416 1l3lA 234 3.20e+00 a.4.6.2 73541 d.110.5.1 73542 1pu6A 218 3.26e+00 unknown_sccs -1282 1c7gA 456 3.41e+00 c.67.1.2 -8153 1ub9A 100 3.45e+00 a.4.5.28 -231 1xwl 580 3.63e+00 1xwl c.55.3.5 33708 e.8.1.1 43001 1ng6A 148 3.76e+00 a.182.1.1 85670 2dtr 226 3.78e+00 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1fi2A 201 3.92e+00 1fi2A b.82.1.2 59845 1qc7A 101 3.94e+00 1qc7A a.118.14.1 18456 1l2lA 457 4.16e+00 c.72.1.3 77656 1cbs 137 4.36e+00 1hmt b.60.1.2 27201 1rypL 212 4.39e+00 d.153.1.4 41880 1bjt 793 4.57e+00 1bjt e.11.1.1 43249 1i27A 73 4.60e+00 1i27A a.4.5.30 61555 2fokA 579 4.85e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1j3mA 129 5.18e+00 1fx2A 235 5.32e+00 1fx2A d.58.29.1 39430 1ctt 294 5.47e+00 1ctt c.97.1.1 36022 c.97.1.1 36023 1f3vA 179 5.47e+00 1f3vA d.58.22.1 39382 1or7A 194 5.83e+00 a.4.13.2 87332 a.177.1.1 87333 1ku3A 73 6.05e+00 a.4.13.2 73000 1j98A 157 6.14e+00 1j98A d.185.1.2 62755 1k7jA 206 6.23e+00 d.115.1.1 72103 1rypC 244 6.26e+00 1rypC d.153.1.4 41934 1ua4A 455 6.26e+00 c.72.1.3 -8416 1b24A 188 6.45e+00 1b24A d.95.2.1 40573 d.95.2.1 40574 1tlqA 189 6.59e+00 1teaA 299 6.99e+00 1nigA 152 7.12e+00 a.25.2.1 85740 1hg4A 279 7.14e+00 1lbd a.123.1.1 19333 1a8h 500 7.42e+00 1a8h a.27.1.1 16922 c.26.1.1 31589 1g71A 347 7.50e+00 1g71A unknown_sccs 43268 1pylA 97 7.75e+00 1rec 201 7.81e+00 1rec a.39.1.5 17326 1dlwA 116 7.83e+00 1dlyA a.1.1.1 14982 1l3sA 580 7.88e+00 c.55.3.5 84521 e.8.1.1 84522 1nk4A 580 8.19e+00 c.55.3.5 -7625 e.8.1.1 -11875 1q5qA 259 8.46e+00 d.153.1.4 -11433 1burS 123 8.86e+00 1rboC 1abv 134 9.28e+00 1abv a.70.1.1 18317 1pi1A 185 9.32e+00 unknown_sccs -762 1r1uA 106 9.46e+00 8rucI 123 9.52e+00 1rboC d.73.1.1 39629 1k8uA 90 9.87e+00 a.39.1.2 72181 1v33A 366 1.00e+01 unknown_sccs -11384 1gd8A 118 1.02e+01 d.188.1.1 60445 1np7A 489 1.03e+01 a.99.1.1 80677 c.28.1.1 80678 1rypH 205 1.04e+01 d.153.1.4 41876 1r6rA 100 1.07e+01 unknown_sccs -1071 1m1zA 513 1.08e+01 c.26.2.1 78457 d.153.1.1 78458 1v38A 78 1.09e+01 a.60.1.2 -1016 1rypD 241 1.09e+01 1rypD d.153.1.4 41935 1qlpA 394 1.11e+01 1ovaA e.1.1.1 42628 1hbnB 442 1.14e+01 1mroB a.89.1.1 60900 d.58.31.2 60901 1i7dA 659 1.15e+01 1d6mA e.10.1.1 61886 1s7oA 113 1.18e+01 1pueE 89 1.19e+01 1awcA a.4.5.21 16165 1keaA 221 1.19e+01 a.96.1.2 68491 1ucrA 78 1.21e+01 unknown_sccs -308 1top 162 1.21e+01 1ncx a.39.1.5 17223 1mroB 442 1.21e+01 1mroB a.89.1.1 18531 d.58.31.2 39449 1a04A 215 1.21e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1fpzA 212 1.22e+01 1fpzA c.45.1.1 59976 1omrA 201 1.23e+01 a.39.1.5 -854 1j9iA 68 1.24e+01 a.6.1.5 71619 1kk8B 139 1.25e+01 a.39.1.5 77430 1aj8A 371 1.26e+01 1aj8A a.103.1.1 18900 1omiA 248 1.31e+01 a.4.5.4 87079 b.82.3.3 87080 1ecsA 126 1.33e+01 1ecsA d.32.1.2 59407 1a5t 334 1.33e+01 1a5t a.80.1.1 18450 c.37.1.20 32423 1th8A 145 1.35e+01 1ii7A 333 1.36e+01 1ii7A d.159.1.4 62415 1rypA 243 1.36e+01 1pmaA d.153.1.4 41932 4crxA 322 1.36e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1o0iA 138 1.42e+01 d.38.1.5 86532 6paxA 133 1.42e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1pvmA 184 1.44e+01 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1pzlA 237 1.44e+01 1ufmA 84 1.48e+01 1iw7C 1119 1.48e+01 e.29.1.1 71474 1a48 306 1.54e+01 1a48 d.143.1.1 41590 1b79A 119 1.55e+01 1b79A a.81.1.1 18451 1bl0A 129 1.57e+01 1d5yA a.4.1.8 16053 a.4.1.8 16054 1l6rA 227 1.59e+01 c.108.1.10 77768 1ckiA 317 1.60e+01 1csn d.144.1.7 41660 1mvcA 240 1.60e+01 a.123.1.1 79499 1l4dB 122 1.61e+01 d.15.5.1 77684 1fts 295 1.65e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1k78A 149 1.67e+01 a.4.1.5 68255 a.4.1.5 68256 5pal 109 1.70e+01 1a75A a.39.1.4 17215 1f44A 324 1.73e+01 a.60.9.1 64982 d.163.1.1 64983 5eau 548 1.80e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1obdA 306 1.84e+01 d.143.1.1 86767 1s9pA 227 1.86e+01 1a9xA 1058 1.88e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1bed 181 1.88e+01 1fvkA unknown_sccs -7444 1vkeA 133 1.91e+01 1nb8A 353 1.92e+01 d.3.1.9 80385 1ezvA 430 1.92e+01 1be3A d.185.1.1 59541 d.185.1.1 59542 1rypG 244 1.94e+01 d.153.1.4 41938 1octC 156 1.94e+01 1au7A a.4.1.1 15991 a.35.1.1 17017 1rypI 222 1.95e+01 d.153.1.4 41877 2gsaA 432 1.96e+01 2gsaA c.67.1.4 34446 1kb9A 431 1.96e+01 d.185.1.1 77311 d.185.1.1 77312 1csn 298 1.99e+01 1csn d.144.1.7 41664 1opr 213 1.99e+01 1opr c.61.1.1 34091 1dc1A 323 2.00e+01 1dc1A c.52.1.11 33321 1gy8A 397 2.03e+01 c.2.1.2 83376 1fjgD 209 2.05e+01 1c05A d.66.1.2 39553 1j6wA 175 2.05e+01 1j98A d.185.1.2 62663 1rqtA 37 2.09e+01 a.108.1.1 -1473 1e3oC 160 2.15e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1rh5A 436 2.15e+01 unknown_sccs -12298 1phnA 162 2.18e+01 1cpcA a.1.1.3 15641 1p4wA 99 2.21e+01 a.4.6.2 87783 1jrrA 382 2.31e+01 e.1.1.1 63256 1ift 263 2.35e+01 1mrj d.165.1.1 42211 1udxA 416 2.36e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 2ahjB 212 2.38e+01 2ahjB b.34.4.4 24599 1oroA 213 2.45e+01 1opr c.61.1.1 34093 1cm5A 759 2.46e+01 1cm5A c.7.1.1 30671 1qhtA 775 2.47e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1k9uA 78 2.49e+01 a.39.1.10 84348 1b4pA 217 2.49e+01 a.45.1.1 83158 c.47.1.5 83159 1apyB 141 2.50e+01 1apyB 1nfp 228 2.51e+01 1nfp c.1.16.2 29555 1rfzA 168 2.60e+01 unknown_sccs -1206 1r1mA 164 2.61e+01 unknown_sccs -10431 1foeA 377 2.67e+01 1foeA a.87.1.1 18517 b.55.1.1 26969 1e0nA 27 2.72e+01 b.72.1.1 27807 1heiA 451 2.75e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 1scfA 273 2.76e+01 1exzA a.26.1.2 16873 1l3aA 228 2.77e+01 d.18.1.2 73531 1obwA 175 2.80e+01 2prd b.40.5.1 25416 1sviA 195 2.80e+01 1q87A 221 2.82e+01 unknown_sccs -12028 1nnvA 110 2.86e+01 unknown_sccs -9309 1h16A 759 2.88e+01 c.7.1.1 76462 1jw2A 72 2.93e+01 a.23.5.1 67372 1k1vA 41 2.97e+01 a.37.1.1 71999 1s9rA 410 2.98e+01 unknown_sccs -10989 1i40A 175 2.98e+01 b.40.5.1 66024 1o2dA 371 2.99e+01 e.22.1.2 86591 1q8bA 105 3.05e+01 unknown_sccs -9958 1cpcA 162 3.25e+01 1cpcA a.1.1.3 15643 1dwkA 156 3.26e+01 1dw9A a.35.1.4 17075 d.72.1.1 39606 1vin 268 3.27e+01 1vin a.74.1.1 18354 a.74.1.1 18355 2ran 316 3.27e+01 1avc a.65.1.1 18170 1e6yB 433 3.29e+01 1mroB a.89.1.1 18535 d.58.31.2 39453 1tbxA 99 3.34e+01 1jzgA 128 3.36e+01 b.6.1.1 67855 1qd1A 325 3.39e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1tbmA 326 3.43e+01 1nthA 458 3.46e+01 c.1.25.1 80730 1qqrA 138 3.47e+01 1bmlC d.15.5.1 37721 1fseA 74 3.49e+01 1fseA a.4.6.2 60000 1dd3C 32 3.51e+01 1dd3C a.108.1.1 19033 1o70A 324 3.51e+01 b.118.1.1 81115 b.118.1.1 81116 1a99A 344 3.51e+01 1pot c.94.1.1 35812 1it2A 146 3.52e+01 a.1.1.2 66365 1a79A 171 3.52e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1lh0A 213 3.54e+01 c.61.1.1 73896 1f2aA 215 3.57e+01 1cs8A d.3.1.1 37040 1c52 131 3.58e+01 1c52 a.3.1.1 15810 1q7bA 244 3.62e+01 c.2.1.2 -5826 1gntA 553 3.63e+01 e.26.1.1 70290 1me4A 215 3.66e+01 d.3.1.1 79023 1lfkA 398 3.66e+01 a.104.1.1 77926 1q06A 135 3.74e+01 a.6.1.3 -375 1hm6A 346 3.75e+01 1avc a.65.1.1 18147 1rypB 250 3.76e+01 1rypB d.153.1.4 41933 1a8b 318 3.77e+01 1avc a.65.1.1 18171 1bby 69 3.81e+01 2bby a.4.5.15 16149 1e2uA 553 3.82e+01 1e1dA e.26.1.1 43362 2tct 207 3.84e+01 2tct a.4.1.9 16063 a.121.1.1 19240 1g2nA 264 3.90e+01 1lbd a.123.1.1 60227 1avaA 403 3.90e+01 1jdc b.71.1.1 27797 c.1.8.1 28784 4kbpA 432 3.90e+01 4kbpA b.1.12.1 22345 d.159.1.1 42064 1ef1C 90 3.91e+01 1ef1C a.137.5.1 19642 1o08A 221 3.94e+01 c.108.1.6 86525 1hr6B 443 4.00e+01 1be3A d.185.1.1 61166 d.185.1.1 61167