# List of top-scoring protein chains for t04-100-30-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 1zj6A 187 1.60e-01 1tqyB 415 6.19e-01 c.95.1.1,c.95.1.1 107247,107248 1aqcA 172 6.70e-01 1x11A b.55.1.2 26983 1sfnA 246 6.88e-01 b.82.1.11 105496 1gtdA 85 8.39e-01 d.284.1.1 76344 1se0A 116 9.13e-01 g.52.1.1 98814 1b1cA 181 1.30e+00 1amoA c.23.5.2 31212 1fa0A 537 1.42e+00 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1zx5A 300 1.42e+00 1tc1A 220 1.51e+00 1tc1A c.61.1.1 34083 1yzgA 179 1.57e+00 1cznA 169 1.88e+00 1rcf c.23.5.1 31181 1ye8A 178 2.05e+00 2bk7B 222 2.47e+00 2bo9B 222 2.47e+00 1ymkA 175 2.86e+00 1vk8A 106 3.05e+00 d.58.48.1 108636 1vhnA 318 3.48e+00 c.1.4.1 100693 1oy3D 282 3.53e+00 d.211.1.1 87554 1vdnA 162 3.55e+00 1xb2B 291 3.85e+00 1v1aA 309 3.94e+00 c.72.1.1 100249 1rreA 200 3.94e+00 d.14.1.10 97791 1x0pA 143 3.99e+00 2a2kA 175 4.07e+00 1n2fA 142 4.07e+00 d.227.1.1 79853 1bn8A 420 4.08e+00 1pcl b.80.1.1 28022 1cdzA 96 4.19e+00 1cdzA c.15.1.1 30925 2fbhA 146 4.86e+00 1mp9A 198 5.13e+00 d.129.1.1,d.129.1.1 91385,91386 1i0lA 221 5.23e+00 c.61.1.1 71096 1qb0A 211 5.75e+00 1c25 c.46.1.1 32699 1kmqA 184 6.04e+00 c.37.1.8 84412 1dfaA 454 6.13e+00 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 1qhdA 398 6.19e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1ja1A 622 6.46e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1vr5A 547 6.89e+00 351c 82 7.68e+00 451c a.3.1.1 15905 451c 82 7.68e+00 451c a.3.1.1 15904 1afwA 393 8.12e+00 1afwA c.95.1.1,c.95.1.1 35900,35901 1alu 186 8.54e+00 1alu a.26.1.1 16826 1qvcA 145 8.66e+00 3ullA b.40.4.3 25284 1jx2B 315 8.74e+00 c.37.1.8 67404 1oaoC 729 8.83e+00 e.26.1.3 86746 1ywmA 200 8.88e+00 1oboA 169 8.94e+00 c.23.5.1 86776 1vplA 256 9.02e+00 1iseA 185 9.31e+00 d.67.3.1 90691 2atzA 180 9.71e+00 1rcf 169 9.86e+00 1rcf c.23.5.1 31170 1c25 161 1.04e+01 1c25 c.46.1.1 32698 1vdeA 454 1.04e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1womA 271 1.07e+01 2cw8A 537 1.14e+01 1qnxA 209 1.14e+01 1qnxA d.111.1.1 40914 1ej8A 140 1.15e+01 1qupA b.1.8.1 22300 1y51A 88 1.16e+01 1f60B 94 1.19e+01 1b64 d.58.12.1 39307 2b25A 336 1.19e+01 1uohA 226 1.19e+01 d.211.1.1 99690 1y81A 138 1.21e+01 1no7A 604 1.22e+01 e.48.1.1 92016 1cjbA 231 1.22e+01 1qk3A c.61.1.1 34079 1lhpA 312 1.23e+01 c.72.1.5 77960 1tx4B 178 1.28e+01 1ctqA c.37.1.8 32045 1hkhA 279 1.35e+01 c.69.1.12 90628 1ek8A 185 1.37e+01 1ek8A d.67.3.1 59444 1bvyF 191 1.43e+01 1bvyF c.23.5.1 31207 2ftrA 108 1.44e+01 1wnhA 225 1.46e+01 1shsA 147 1.51e+01 1shsA b.15.1.1 23675 1j0aA 325 1.56e+01 c.79.1.1 83871 1bi5A 389 1.61e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1v5rA 97 1.65e+01 2gatA 66 1.66e+01 1gatA g.39.1.1 45102 1a8y 367 1.66e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1hurA 180 1.74e+01 1hurA c.37.1.8 32052 1f7cA 231 1.76e+01 1f7cA a.116.1.1 19107 1v6tA 255 1.79e+01 1r31A 428 1.83e+01 d.58.20.1,d.179.1.1 96897,96898 2bkyA 97 1.85e+01 1nox 205 1.94e+01 1nox d.90.1.1 40242 1qoiA 177 1.95e+01 2cpl b.62.1.1 27490 1i88A 389 1.97e+01 c.95.1.2,c.95.1.2 66070,66071 1cvrA 435 1.98e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1mtpA 323 1.99e+01 e.1.1.1 85107 2fsjA 346 2.11e+01 1wvfA 520 2.18e+01 1guzA 310 2.20e+01 c.2.1.5,d.162.1.1 65586,65587 1y8oB 128 2.26e+01 1e1oA 504 2.29e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1sqlA 146 2.31e+01 d.96.1.3 105925 1nrzA 164 2.32e+01 c.38.1.1 86131 2d00A 109 2.33e+01 1fzqA 181 2.34e+01 1hurA c.37.1.8 32060 1r45A 204 2.38e+01 1eexA 554 2.39e+01 1dioA c.1.19.3 29650 1xtoA 311 2.40e+01 1e8cA 498 2.40e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1ynfA 458 2.45e+01 1czaN 917 2.47e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1tedA 393 2.48e+01 c.95.1.2 106807 1trkA 680 2.55e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 2bjvA 265 2.55e+01 1azwA 313 2.63e+01 1qtrA c.69.1.7 34658 1rzhL 281 2.64e+01 f.26.1.1 98164 2gh1A 301 2.64e+01 2g2cA 167 2.68e+01 1ywfA 296 2.70e+01 1v71A 323 2.72e+01 1lylA 504 2.77e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1tyjA 170 2.77e+01 1m6dA 214 2.83e+01 d.3.1.1 84849 1ef1A 294 2.85e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1j0sA 157 2.91e+01 b.42.1.2 90747 1eejA 216 2.96e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1qkkA 155 2.99e+01 1dbwA c.23.1.1 31104 1xxlA 239 3.04e+01 1gsa 316 3.27e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1tw7A 99 3.27e+01 1xtnA 120 3.28e+01 1yrtA 364 3.34e+01 1y7rA 133 3.35e+01 2av5A 120 3.43e+01 1h0xA 100 3.44e+01 d.68.6.1 76451 1gpr 162 3.47e+01 1gpr b.84.3.1 28267 1w25A 459 3.52e+01 1vljA 407 3.59e+01 e.22.1.2 108832 1r5tA 142 3.59e+01 c.97.1.1 104812 1ryoA 327 3.59e+01 c.94.1.2 98108 1oh4A 179 3.60e+01 b.18.1.18 92978 1xeaA 323 3.61e+01 c.2.1.3,d.81.1.5 109572,109573 2phlA 397 3.63e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1f3iA 481 3.66e+01 1b7eA 1qo0D 196 3.68e+01 1qo0D c.23.1.3 31125 1qfjA 232 3.68e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1of4A 179 3.81e+01 b.18.1.18 86932 1w6uA 302 3.82e+01 1kicA 339 3.83e+01 c.70.1.1 72510 3znf 30 3.86e+01 g.37.1.1 45049 2f3yA 148 3.92e+01 2au5A 139 3.92e+01 1h4vB 421 3.98e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1fp2A 352 3.98e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1qgoA 264 4.01e+01 1qgoA c.92.1.2 35596 1hxrA 115 4.01e+01 1fwqA b.88.1.1 28392 1k8wA 327 4.05e+01 b.122.1.1,d.265.1.2 83094,90388 1kshA 186 4.09e+01 c.37.1.8 72914 1un7A 400 4.09e+01 b.92.1.5,c.1.9.10 99657,99658 1i36A 264 4.13e+01 a.100.1.8,c.2.1.6 71108,71109 1yruA 364 4.20e+01 1r8sA 164 4.23e+01 c.37.1.8 97247 1z0wA 207 4.23e+01 1y0hA 105 4.30e+01 1vj7A 393 4.46e+01 a.211.1.1,d.218.1.8 100801,100802 1g4yR 148 4.46e+01 1cll a.39.1.5 60252 1a8e 329 4.50e+01 1cb6A c.94.1.2 35888 1xfxO 149 4.51e+01 1ru3A 732 4.58e+01 e.26.1.3 97835 2a5jA 191 4.59e+01 1xrhA 351 4.59e+01 1x3lA 440 4.63e+01 1jg5A 83 4.76e+01 d.205.1.1 66666 1zotA 358 4.79e+01 1oc0B 51 4.80e+01 g.64.1.1 86791 1c3mA 147 4.80e+01 1jotA b.77.3.1 27983 5rubA 490 4.86e+01 1burA c.1.14.1,d.58.9.1 29382,39288 2fhwA 24 4.92e+01 1zavA 180 4.98e+01 1pvvA 315 5.00e+01 c.78.1.1,c.78.1.1 95190,95191 1io2A 213 5.01e+01 1ekeA c.55.3.1 62612 1t5rA 284 5.02e+01 f.6.1.1 106465 1hufA 140 5.05e+01 1hufA d.195.1.1 61272 1bueA 265 5.06e+01 1btl e.3.1.1 42727 2b3yA 888 5.08e+01 1nh1A 330 5.12e+01 e.45.1.1 91871 2fmr 65 5.13e+01 2fmr d.51.1.1 38808 1b79A 119 5.14e+01 1b79A a.81.1.1 18451 1wwzA 159 5.21e+01 1tv8A 340 5.22e+01 c.1.28.3 107352 1ehs 48 5.24e+01 1ehs g.2.1.1 43998 1n0qA 93 5.28e+01 k.37.1.1 79754 1eayC 74 5.30e+01 1eayC d.58.24.1 39386 1jm6A 407 5.32e+01 a.29.5.1,d.122.1.4 66876,66877 7odcA 424 5.34e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1eluA 390 5.35e+01 1elqA c.67.1.3 34434 1qycA 308 5.38e+01 c.2.1.2 96581 1j5sA 463 5.40e+01 c.1.9.8 71580 1uh6A 100 5.42e+01 d.15.1.1 99394 1vjtA 483 5.45e+01 c.2.1.5,d.162.1.2 100833,100834 1o59A 355 5.47e+01 b.18.1.22,b.18.1.22 92495,92496 2bmoA 447 5.50e+01 2cfeA 162 5.53e+01 1d2zB 153 5.54e+01 1d2zB a.77.1.2 18439 1a48 306 5.56e+01 1a48 d.143.1.1 41590 2fflA 756 5.64e+01 1vl5A 260 5.71e+01 c.66.1.41 108720 1ogqA 313 5.86e+01 c.10.2.8 86996 2cxvA 219 5.89e+01 1elqA 390 5.91e+01 1elqA c.67.1.3 34436 1vcc 77 5.94e+01 1vcc d.121.1.1 41092 1wmdA 434 5.98e+01 b.18.1.20,c.41.1.1 109408,109409 1ez0A 510 6.05e+01 1eyyA c.82.1.1 35385 1mvlA 209 6.09e+01 c.34.1.1 85146 1kmvA 186 6.11e+01 c.71.1.1 72757 1pzqA 60 6.17e+01 a.34.3.1 95466 1gpuA 680 6.18e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1nbwA 607 6.20e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 2b8nA 429 6.23e+01 1ssqA 267 6.48e+01 b.81.1.6 105993 1yadA 221 6.50e+01 1ru4A 400 6.53e+01 b.80.1.9 97836 2gmfA 127 6.55e+01 2gmfA a.26.1.2 16849 1z8sA 146 6.58e+01 1kyqA 274 6.61e+01 c.2.1.11,e.37.1.1 73281,73282 1obbA 480 6.61e+01 c.2.1.5,d.162.1.2 86760,86761 1tbaA 67 6.63e+01 1tbaA a.15.1.1 16380 1mugA 168 6.75e+01 1mugA c.18.1.2 31030 1o0uA 429 6.96e+01 c.118.1.1 80743 1q48A 134 6.98e+01 d.224.1.2 95783 1yjsA 419 6.99e+01 1xteA 154 7.02e+01 1jv2A 957 7.04e+01 b.1.15.1,b.1.15.1,b.1.15.1,b.69.8.1 67334,67335,67336,67337 1qfoA 119 7.06e+01 1qfoA b.1.1.1 19708 1neeA 138 7.09e+01 d.241.1.1,g.59.1.1 91841,91842 1e20A 209 7.11e+01 1e20A c.34.1.1 31759 1aisA 182 7.12e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1n83A 270 7.16e+01 a.123.1.1 80276 1yqtA 538 7.20e+01 1mgtA 174 7.29e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1nh9A 87 7.36e+01 d.68.6.1 91878 2bfdB 345 7.39e+01 1b78A 193 7.41e+01 1b78A c.51.4.1 33221 1vrpA 381 7.44e+01 1j5pA 253 7.46e+01 d.81.1.3,c.2.1.3 71577,83092 1tg7A 971 7.50e+01 1smtA 122 7.53e+01 1smtA a.4.5.5 16109 1zcbA 362 7.54e+01 1ub0A 258 7.57e+01 c.72.1.2 88394 1kl1A 419 7.57e+01 c.67.1.4 72663 1ile 821 7.62e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1v4pA 157 7.62e+01 2fliA 220 7.65e+01 1fnnA 389 7.68e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1nxiA 132 7.82e+01 d.58.47.1 86381 1as4B 37 7.94e+01 1as4B 1qahA 136 7.95e+01 d.79.1.1 96338 1ri6A 343 7.95e+01 b.69.11.1 97503 1exrA 148 8.00e+01 1cll a.39.1.5 17299 1l9vA 317 8.02e+01 d.13.2.1,d.216.1.1 73760,73761 1le6A 123 8.04e+01 a.133.1.2 73862 1zkeA 83 8.05e+01 1obdA 306 8.10e+01 d.143.1.1 86767 1nn7A 105 8.15e+01 d.42.1.2 85894 1x7yB 342 8.19e+01 1pfzA 380 8.22e+01 1smrA b.50.1.2 26881 2fbaA 492 8.31e+01 1odkA 235 8.34e+01 c.56.2.1 86863 1hw7A 255 8.39e+01 1i7fA d.193.1.1 61297 1dp4A 435 8.44e+01 1dp4A c.93.1.1 35710 1vd2A 89 8.45e+01 d.15.2.2 108517 1usmA 80 8.51e+01 d.74.1.1 99876 1ayx 492 8.53e+01 1ayx a.102.1.1 18825 1q40B 219 8.55e+01 d.17.4.2 95771 1eonA 245 8.56e+01 1rvaA c.52.1.2 33238 1dykA 394 8.56e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1kl7A 514 8.59e+01 c.79.1.1 72678 1b35C 282 8.62e+01 1b35C 2c4nA 250 8.66e+01 1gkpA 458 8.68e+01 b.92.1.3,c.1.9.6 70231,70232 1clxA 347 8.71e+01 1taxA c.1.8.3 28899 1yakA 263 8.78e+01 1q2hA 69 8.82e+01 a.34.4.1 104498 2aifA 135 8.83e+01 1v1rB 342 8.83e+01 c.36.1.7,c.48.1.2 108273,108274 2gvhA 288 8.85e+01 1nriA 306 8.93e+01 c.80.1.3 86123 1xesA 413 8.95e+01 1xfkA 336 8.99e+01