# List of top-scoring protein chains for t04-100-30-bys-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 1twiA 434 5.59e-02 b.49.2.3,c.1.6.1 107399,107400 1tufA 434 1.27e-01 b.49.2.3,c.1.6.1 107335,107336 1i4jA 110 2.12e-01 d.55.1.1 76734 1a12A 413 2.36e-01 1a12A b.69.5.1 27663 1bxeA 113 2.38e-01 1bxeA d.55.1.1 38898 1rlzA 369 3.30e-01 c.31.1.1 104989 1nh9A 87 3.69e-01 d.68.6.1 91878 1xnkA 196 5.03e-01 1h1aA 191 6.69e-01 b.29.1.11 83450 1u2eA 289 6.91e-01 1dhs 344 8.22e-01 1dhs c.31.1.1 31727 1s14A 194 1.08e+00 d.122.1.2 98329 1neiA 60 1.14e+00 d.253.1.1 91843 1mgtA 174 1.22e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1uwkA 557 1.26e+00 e.51.1.1 108065 1wp1A 474 1.38e+00 2au5A 139 1.40e+00 1s7zA 117 1.59e+00 a.159.3.1 98715 1zyeA 220 1.76e+00 1axn 323 1.91e+00 1avc a.65.1.1 18149 1womA 271 1.92e+00 1wy6A 172 2.16e+00 1s7iA 124 2.48e+00 d.58.4.9 105353 1p97A 114 2.79e+00 d.110.3.7 94382 2bkyA 97 2.86e+00 1to2I 64 3.14e+00 1to6A 371 3.14e+00 c.141.1.1 107170 1lw6I 64 3.15e+00 d.40.1.1 74294 1xuqA 212 3.25e+00 1h0xA 100 3.36e+00 d.68.6.1 76451 1fc6A 388 3.53e+00 1fc6A b.36.1.3,c.14.1.2 64738,64739 2bhoA 130 3.65e+00 1g26A 31 3.70e+00 1g26A g.3.16.1 44381 1ekgA 127 4.14e+00 1dlxA d.82.2.1 40021 1ir3A 306 4.27e+00 1fmk d.144.1.7 41702 1c7qA 445 4.36e+00 2pgi c.80.1.2 35307 1guqA 348 4.96e+00 1guqA d.13.1.2,d.13.1.2 37522,37523 1xqoA 256 5.00e+00 1nm8A 616 5.37e+00 c.43.1.3,c.43.1.3 85872,85873 1ew6A 137 5.52e+00 1ewaA a.1.1.2 15637 1y60A 169 5.59e+00 1u14A 172 5.81e+00 c.51.4.3 107579 1r9kA 172 6.10e+00 a.168.1.1 104869 2bcqA 335 6.21e+00 2bzpA 226 6.26e+00 1h6kZ 98 6.55e+00 d.58.7.1 60686 2abqA 306 7.07e+00 1k7cA 233 7.34e+00 c.23.10.4 68267 1k24A 253 7.44e+00 f.4.4.2 72002 2au3A 407 7.50e+00 2aqwA 332 7.74e+00 1xpjA 126 7.79e+00 1sjdA 368 7.92e+00 c.1.11.2,d.54.1.1 105632,105633 1lxa 262 8.13e+00 1lxa b.81.1.1 28052 1edqA 540 8.21e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 2d4rA 147 8.24e+00 1li5B 461 8.33e+00 a.27.1.1,c.26.1.1 73914,73915 2occG 84 8.49e+00 2occG f.23.2.1 43522 1jtdB 273 8.72e+00 b.69.5.2 67265 1idaA 99 8.95e+00 1fmb b.50.1.1 26715 1eu1A 780 9.22e+00 1dmr b.52.2.2,c.81.1.1 26903,35311 2kfnA 605 9.35e+00 1xwl c.55.3.5,e.8.1.1 33682,42975 2axwA 134 9.49e+00 1pyaB 228 9.54e+00 1pyaB 1wyuB 474 9.55e+00 1pk1B 89 9.62e+00 1deoA 233 9.74e+00 1deoA c.23.10.4 31345 1s0pA 176 1.01e+01 a.192.1.1 98300 2fdsA 352 1.01e+01 1ybzA 91 1.09e+01 1e94F 449 1.09e+01 1do0A c.37.1.20 32443 1mugA 168 1.11e+01 1mugA c.18.1.2 31030 1p4oA 322 1.11e+01 d.144.1.7 87775 1rztA 331 1.13e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1rwrA 301 1.13e+01 b.80.1.11 97990 1uadC 99 1.15e+01 b.1.18.18 88379 1ctn 540 1.17e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1v30A 124 1.18e+01 1kssA 571 1.20e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1fh9A 312 1.21e+01 1taxA c.1.8.3 28913 1n7eA 97 1.22e+01 b.36.1.1 91691 1twjA 84 1.25e+01 d.284.1.1 107407 1y43A 39 1.28e+01 1bco 327 1.31e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1iuqA 367 1.32e+01 c.112.1.1 90703 2a5lA 200 1.34e+01 2ghjA 118 1.36e+01 1u8vA 490 1.41e+01 1li5A 461 1.41e+01 a.27.1.1,c.26.1.1 73912,73913 1rgyA 360 1.44e+01 e.3.1.1 97456 1k1vA 41 1.47e+01 a.37.1.1 71999 2cu3A 64 1.51e+01 1t4aA 84 1.54e+01 d.284.1.1 106404 1qopA 268 1.60e+01 2tysA c.1.2.4 28570 1g99A 408 1.63e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1gegA 256 1.64e+01 1ybvA c.2.1.2 29888 1d2rA 326 1.69e+01 1d2rB c.26.1.1 31572 1udvA 89 1.71e+01 d.68.6.1 99224 1k68A 140 1.71e+01 c.23.1.1 90943 1x8mA 288 1.74e+01 b.82.1.13 109516 1p2hA 571 1.75e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1nogA 177 1.81e+01 a.25.2.2 85923 1q9iA 571 1.86e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1y0pA 571 1.86e+01 1g55A 343 1.87e+01 1g55A c.66.1.26 34247 1allA 160 1.90e+01 1qgwC a.1.1.3 15647 1p0hA 318 1.92e+01 d.108.1.1 93866 1wzlA 585 1.94e+01 1nriA 306 1.95e+01 c.80.1.3 86123 1fhdA 312 1.97e+01 1taxA c.1.8.3 28915 1dm5A 315 2.01e+01 1avc a.65.1.1 18186 1lb3A 182 2.02e+01 a.25.1.1 77873 1h96A 182 2.02e+01 2fha a.25.1.1 60811 1h03P 125 2.03e+01 g.18.1.1,g.18.1.1 83411,83412 2his 312 2.05e+01 1taxA c.1.8.3 28918 1n7fA 97 2.09e+01 b.36.1.1 91692 2bsjA 133 2.18e+01 1viaA 175 2.19e+01 c.37.1.2 100754 1wwiA 148 2.22e+01 1xsnA 335 2.24e+01 1paqA 189 2.28e+01 a.118.1.14 94413 1tp5A 119 2.31e+01 2viuA 328 2.33e+01 1hgeA b.19.1.2 23797 1hxiA 121 2.37e+01 1hxiA a.118.8.1 61366 1lghB 45 2.38e+01 1lghB f.3.1.1 43734 1jcfA 344 2.38e+01 c.55.1.1,c.55.1.1 62878,62879 1xruA 282 2.41e+01 1b0nA 111 2.41e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1zq1A 438 2.41e+01 1gv3A 248 2.46e+01 a.2.11.1,d.44.1.1 70585,70586 1na6A 404 2.55e+01 b.142.1.1,c.52.1.22 91748,91749 1m48A 133 2.60e+01 a.26.1.2 74443 2bshA 125 2.67e+01 1hm6A 346 2.74e+01 1avc a.65.1.1 18147 1ti6A 875 2.77e+01 b.52.2.2,c.81.1.1 106974,106975 2d2mD 145 2.82e+01 1xhkA 187 2.83e+01 1wxrA 1048 2.85e+01 2dnjA 260 2.86e+01 3dni d.151.1.1 41790 1omp 370 2.87e+01 4mbp c.94.1.1 35778 1v54G 85 2.94e+01 f.23.2.1 100328 1pp7U 131 3.03e+01 a.4.5.44 94973 2f9dA 125 3.03e+01 1zvnA 99 3.06e+01 1ytvA 366 3.11e+01 1i4dA 224 3.13e+01 h.4.7.1 61682 2a40B 260 3.22e+01 1tx2A 297 3.31e+01 c.1.21.1 107420 1e39A 571 3.33e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1ewnA 219 3.41e+01 1bnkA b.46.1.2 25762 1d0qA 103 3.44e+01 1d0qA g.41.3.2 45208 1hjxA 362 3.45e+01 c.1.8.5,d.26.3.1 83512,83513 1th8A 145 3.49e+01 d.122.1.3 106908 4mbp 370 3.52e+01 4mbp c.94.1.1 35777 2aehA 369 3.53e+01 2gmyA 153 3.54e+01 1dgnA 89 3.56e+01 1dgnA a.77.1.3 18436 1xrxA 50 3.56e+01 1wozA 177 3.59e+01 1ldg 316 3.67e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1t2dA 322 3.75e+01 c.2.1.5,d.162.1.1 99084,99085 1bmdA 327 3.89e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1b78A 193 3.91e+01 1b78A c.51.4.1 33221 2b1yA 104 3.92e+01 2gcuA 245 3.96e+01 2bkyX 89 3.96e+01 3dni 260 4.01e+01 3dni d.151.1.1 41791 1iscA 192 4.02e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1mhnA 59 4.02e+01 b.34.9.1 84964 1ja9A 274 4.03e+01 c.2.1.2 62817 2ajgA 196 4.06e+01 1ve2A 235 4.06e+01 1r7jA 95 4.11e+01 a.4.5.49 104836 1nu0A 138 4.13e+01 c.55.3.8 92165 1thg 544 4.13e+01 1thg c.69.1.17 34763 1qwrA 319 4.18e+01 b.82.1.3 96491 1i2tA 61 4.19e+01 1i2tA a.144.1.1 61582 1yarO 237 4.22e+01 1iz0A 302 4.26e+01 b.35.1.2,c.2.1.1 83821,83822 2gtsA 86 4.28e+01 2c27A 315 4.28e+01 1oo4A 111 4.38e+01 d.93.1.1 87185 1be9A 119 4.38e+01 1pdr b.36.1.1 24774 1lnsA 763 4.39e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1sbzA 197 4.45e+01 1pfvA 551 4.46e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1mp1A 111 4.47e+01 a.188.1.1 91382 2f2gA 221 4.47e+01 2b5aA 77 4.58e+01 1nmeA 146 4.59e+01 c.17.1.1 85874 2bw8A 227 4.63e+01 2govA 195 4.65e+01 1np7A 489 4.66e+01 a.99.1.1,c.28.1.1 80677,80678 1gzsB 165 4.71e+01 a.168.1.1 76425 1s12A 94 4.75e+01 1q4mA 221 4.76e+01 a.132.1.3 95805 1f4lA 551 4.80e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1uteA 313 4.81e+01 1uteA d.159.1.1 42078 2acaA 189 4.87e+01 1kn1A 160 4.87e+01 a.1.1.3 77455 1x6zA 123 4.87e+01 1ypcI 64 4.90e+01 2sniI d.40.1.1 38570 1bouA 139 4.91e+01 1bouA a.88.1.1 18521 1ojaA 520 5.04e+01 c.3.1.2,d.16.1.5 93096,93097 1xmxA 385 5.14e+01 1mtyD 512 5.16e+01 1mhyD a.25.1.2 16742 1yeyA 444 5.18e+01 1y7tA 327 5.19e+01 1q06A 135 5.23e+01 a.6.1.3 95493 1ppn 212 5.26e+01 1cs8A d.3.1.1 37004 1x92A 199 5.32e+01 2nlrA 234 5.35e+01 2nlrA b.29.1.11 24344 2d0eA 407 5.35e+01 1anf 370 5.36e+01 4mbp c.94.1.1 35776 1bdmA 327 5.38e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 2bzvA 181 5.39e+01 2ae8A 221 5.53e+01 2f46A 156 5.54e+01 1guzA 310 5.54e+01 c.2.1.5,d.162.1.1 65586,65587 1xzoA 174 5.57e+01 1cyj 90 5.66e+01 1ctj a.3.1.1 15805 1n8vA 112 5.69e+01 a.118.21.1 85457 1s3eA 520 5.75e+01 c.3.1.2,d.16.1.5 98426,98427 1puzA 82 5.79e+01 a.218.1.1 104320 1ibrB 462 5.81e+01 1qgrA a.118.1.1 19120 1xreA 217 5.94e+01 2aw4Q 117 5.98e+01 1mrj 247 6.02e+01 1mrj d.165.1.1 42177 1i6lA 328 6.03e+01 c.26.1.1 66041 1h7wA 1025 6.09e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1zkiA 133 6.09e+01 4tmkA 213 6.10e+01 5tmpA c.37.1.1 31930 1ox3A 109 6.10e+01 h.1.17.1 93668 1k04A 162 6.14e+01 a.24.14.1 67904 1egpA 45 6.16e+01 1egpA d.40.1.1 38561 2cwcA 303 6.22e+01 2cyjA 118 6.24e+01 2cioA 212 6.24e+01 1uxjA 309 6.26e+01 c.2.1.5,d.162.1.1 108112,108113 1eyqA 222 6.26e+01 1eypA d.36.1.1 38534 1ecmA 109 6.29e+01 1ecmA a.130.1.1 19492 1xnb 185 6.30e+01 1axkA b.29.1.11 24308 2dcyA 185 6.35e+01 1j7gA 144 6.41e+01 c.110.1.1 84130 1nrwA 288 6.41e+01 c.108.1.10 86128 1cnoA 87 6.47e+01 a.3.1.1 15814 1wu7A 434 6.47e+01 1gteA 1025 6.47e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1xfsA 178 6.57e+01 d.129.3.5 109589 1h4pA 408 6.60e+01 c.1.8.3 90617 1laxA 370 6.66e+01 c.94.1.1 84576 1wmwA 330 6.67e+01 1zud2 66 6.68e+01 1qnrA 344 6.68e+01 1qnoA c.1.8.3 28834 2afaA 425 6.70e+01 1n0qA 93 6.78e+01 k.37.1.1 79754 2aa4A 289 6.82e+01 1o0pA 104 6.93e+01 d.58.7.1 86535 1pgjA 478 6.93e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1w6sB 74 7.01e+01 1nxqA 251 7.03e+01 c.2.1.2 86388 2fug5 207 7.05e+01 1j8bA 112 7.05e+01 d.222.1.1 77101 1i1iP 681 7.16e+01 1i1iP d.92.1.5 40297 1qpcA 279 7.23e+01 1fgkA d.144.1.7 41685 1yn8A 59 7.24e+01 1a48 306 7.25e+01 1a48 d.143.1.1 41590 1sg4A 260 7.26e+01 2al6A 375 7.30e+01 1jfxA 217 7.33e+01 c.1.8.8 62943 1uayA 242 7.36e+01 c.2.1.2 88390 1zmmA 33 7.43e+01 2b33A 140 7.45e+01 1std 172 7.47e+01 3stdA d.17.4.1 38089 1sur 215 7.49e+01 1sur c.26.2.2 31620 1u55A 188 7.50e+01 d.278.1.1 107677 1idpA 172 7.52e+01 d.17.4.1 83685 2bhvA 246 7.56e+01 2b1xA 470 7.59e+01 1quuA 250 7.62e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 1gl4B 98 7.66e+01 b.1.1.4 65288 1kblA 873 7.67e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 2d09A 407 7.73e+01 1qhfA 240 7.73e+01 1qhfA c.60.1.1 33960 1sknP 92 7.74e+01 1sknP a.37.1.1 17127 1khqA 212 7.75e+01 d.3.1.1 90964 1v7rA 186 7.77e+01 c.51.4.1 100482 2a19B 284 7.84e+01 1xxnA 185 7.84e+01 1r5iD 216 7.88e+01 a.202.1.1 97091 1zavU 30 7.90e+01 1uch 230 7.90e+01 1uch d.3.1.6 37129 1pg5A 299 7.95e+01 c.78.1.1,c.78.1.1 104146,104147 1gz8A 299 7.98e+01 d.144.1.7 83405 1wnlA 235 8.00e+01 1uozA 315 8.01e+01 1a05A 358 8.02e+01 1cnzA c.77.1.1 35059 1ur3M 319 8.13e+01 c.1.7.1 99806 1yksA 440 8.16e+01 2ch7A 309 8.22e+01 1g0uL 241 8.25e+01 d.153.1.4 41894 2sli 679 8.25e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1tu5A 746 8.28e+01 1t15A 214 8.32e+01 c.15.1.3,c.15.1.3 99067,99068 1xyn 178 8.33e+01 1axkA b.29.1.11 24322 1j7lA 264 8.39e+01 d.144.1.6 62697 1ad4A 266 8.40e+01 1aj2 c.1.21.1 29670 2gj0A 31 8.46e+01 1u5tB 169 8.52e+01 a.4.5.54,a.4.5.54 107686,107687 1u6mA 199 8.57e+01 1u9lA 70 8.57e+01 a.60.4.2 107751 1ei1A 391 8.60e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1kv4A 42 8.63e+01 j.4.1.3 73051 1v71A 323 8.67e+01 1x0oA 119 8.68e+01 1m6pA 152 8.70e+01 1m6pA b.64.1.1 27519 1z7mA 344 8.70e+01 1fgkA 310 8.72e+01 1fgkA d.144.1.7 41693 2g9zA 348 8.86e+01 1r9cA 139 8.94e+01 d.32.1.2 97255 1cpcA 162 8.96e+01 1cpcA a.1.1.3 15643 1hcl 298 8.97e+01 1hcl d.144.1.7 41593 1udh 244 8.98e+01 3eugA c.18.1.1 31015