# List of top-scoring protein chains for t04-100-30-str2-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 1dnlA 199 2.60e-17 1ci0A b.45.1.1 25753 1g79A 218 2.71e-17 1ci0A b.45.1.1 25752 1rfeA 162 4.17e-17 2fhqA 141 9.79e-15 2asfA 137 1.79e-14 1t9mA 214 2.33e-14 1nrgA 261 5.85e-14 b.45.1.1 80694 1ty9A 222 3.73e-13 1xxoA 147 6.44e-13 2aq6A 147 7.47e-13 1w9aA 147 1.32e-12 1vl7A 157 1.58e-11 b.45.1.1 108732 2arzA 247 4.62e-11 2fg9A 178 3.02e-10 2furA 209 1.13e-08 1flmA 122 8.50e-08 1axj b.45.1.1 25747 1xhnA 184 8.93e-08 1w3oA 216 2.39e-07 1ejeA 192 8.60e-03 1ejeA b.45.1.2 25757 2d37A 176 3.71e-01 1i0rA 169 4.17e-01 1i0rA b.45.1.2 61489 1i0sA 169 4.17e-01 1i0rA b.45.1.2 61491 1ko3A 230 4.76e-01 d.157.1.1 90974 2fauA 341 5.09e-01 1rz1A 161 1.04e+00 b.45.1.2 98124 1y08A 323 1.45e+00 1agqA 135 1.49e+00 1agqA g.17.1.2 44789 1am2 199 1.65e+00 1am2 b.86.1.2 28381 1b8aA 438 1.69e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 2cw5A 255 2.07e+00 1qrrA 394 2.08e+00 1qrrA c.2.1.2 29824 1i24A 404 2.15e+00 c.2.1.2 83663 1llnA 262 2.38e+00 d.165.1.1 84625 1oa4A 222 3.33e+00 b.29.1.11 86731 1widA 130 3.99e+00 1pysA 350 4.10e+00 1pysA d.104.1.1 40775 1aszB 490 4.63e+00 1b8aA b.40.4.1,d.104.1.1 25241,40762 1aisA 182 4.71e+00 1ytbA d.129.1.1,d.129.1.1 41288,41289 1a7cA 379 4.71e+00 1sek e.1.1.1 42660 1ye8A 178 4.86e+00 1v5wA 343 5.22e+00 c.37.1.11 108387 2bgiA 272 5.53e+00 2f06A 144 5.69e+00 1q2lA 939 5.87e+00 1lrzA 426 6.04e+00 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1b7yA 350 6.10e+00 1pysA d.104.1.1 40776 1q40B 219 6.35e+00 d.17.4.2 95771 1wvhA 134 6.47e+00 2phlA 397 7.05e+00 1dgwA b.82.1.2,b.82.1.2 28082,28083 1qm4A 396 7.39e+00 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1j5kA 89 7.70e+00 d.51.1.1 71565 1j5yA 187 7.92e+00 a.4.5.1,d.94.2.1 71592,71593 1vclA 432 8.14e+00 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1wmmA 145 8.32e+00 1xipA 388 8.32e+00 1ag6 99 8.82e+00 1plc b.6.1.1 22857 1tdzA 272 9.36e+00 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1nnjA 271 9.60e+00 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1at0 145 9.88e+00 1at0 b.86.1.1 28374 1ta8A 332 1.01e+01 2gibA 103 1.03e+01 1jtdB 273 1.06e+01 b.69.5.2 67265 1pjjA 271 1.09e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1hfuA 503 1.15e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1ylnA 252 1.20e+01 1zd7A 159 1.23e+01 1lj5A 379 1.24e+01 e.1.1.1 73928 1a65A 504 1.28e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 2b4wA 315 1.34e+01 1cruA 454 1.35e+01 1c9uA b.68.2.1 27617 2camA 127 1.38e+01 1swuA b.61.1.1 27407 1rlmB 271 1.43e+01 1lbvA 252 1.43e+01 e.7.1.1 73813 2culA 232 1.46e+01 1q74A 303 1.51e+01 c.134.1.1 96019 1ei1A 391 1.53e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1jj2E 177 1.56e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1uscA 178 1.57e+01 b.45.1.2 99860 1bfg 146 1.59e+01 1bfg b.42.1.1 25485 1wbiA 129 1.64e+01 4fgf 146 1.64e+01 1bfg b.42.1.1 25486 1pvl 301 1.65e+01 1pvl f.6.1.1 43819 1z4xA 532 1.66e+01 1z4vA 532 1.68e+01 1s72E 178 1.68e+01 d.141.1.1,d.141.1.1 105323,105324 1y55X 126 1.70e+01 1xqbA 247 1.78e+01 2h1tA 188 1.84e+01 1zzkA 82 1.88e+01 1d2eA 397 1.89e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1dqiA 124 1.93e+01 1do6A b.1.13.1 22357 1exmA 405 1.95e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1plc 99 1.99e+01 1plc b.6.1.1 22846 1a6cA 513 2.01e+01 1a6cA b.121.4.2,b.121.4.2,b.121.4.2 23296,23297,23298 1ha3A 405 2.01e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1rloA 271 2.03e+01 1o98A 511 2.06e+01 c.105.1.1,c.76.1.3 86684,86685 1yoaA 159 2.06e+01 2bitX 165 2.07e+01 1w6sA 599 2.09e+01 1eluA 390 2.12e+01 1elqA c.67.1.3 34434 1rocA 155 2.12e+01 b.1.22.1 97673 1ravA 127 2.14e+01 1swuA b.61.1.1 27409 2bu3A 254 2.18e+01 1mhnA 59 2.20e+01 b.34.9.1 84964 1elqA 390 2.21e+01 1elqA c.67.1.3 34436 1b7gO 340 2.24e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1sotA 320 2.25e+01 b.36.1.4,b.47.1.1 105852,105853 1n9lA 109 2.30e+01 d.110.3.6 85468 1v1qA 134 2.32e+01 1rlmA 271 2.32e+01 1vqoE 178 2.34e+01 2sli 679 2.35e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1jjtA 228 2.38e+01 1a7tA d.157.1.1 63139 1pvtA 238 2.38e+01 c.74.1.1 95189 1ixcA 294 2.41e+01 a.4.5.37,c.94.1.1 83764,83765 1zuoA 186 2.44e+01 2bjfA 329 2.50e+01 1do6A 124 2.53e+01 1do6A b.1.13.1 22361 1ztcA 221 2.54e+01 1lfdA 87 2.54e+01 1lfdA d.15.1.5 37622 2f15A 96 2.55e+01 1v0wA 506 2.64e+01 d.136.1.2,d.136.1.2 108220,108221 1z90A 469 2.68e+01 1vk8A 106 2.69e+01 d.58.48.1 108636 1wj9A 211 2.70e+01 1f0iA 504 2.71e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 2f4mA 295 2.73e+01 1vyoA 128 2.76e+01 2asuB 234 2.81e+01 1rliA 184 2.81e+01 c.23.5.6 97647 1eqjA 511 2.82e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 2coqA 108 2.84e+01 1ockA 412 2.86e+01 c.117.1.1 86802 1njhA 119 2.89e+01 b.128.1.1 85787 2bc4A 211 2.89e+01 1v3eA 431 2.89e+01 b.68.1.1 100287 1wgbA 159 2.90e+01 2gjgA 248 2.93e+01 2i1b 153 3.00e+01 2i1b b.42.1.2 25538 1knb 196 3.01e+01 1qhvA b.21.1.1 23841 2a6zA 222 3.03e+01 1yliA 153 3.03e+01 1jyoA 130 3.05e+01 d.198.1.1 67483 1ywxA 102 3.07e+01 1yqbA 100 3.14e+01 1q6uA 245 3.15e+01 d.26.1.1 95998 1wsrA 375 3.17e+01 1kv7A 488 3.17e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1f60A 458 3.18e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1qsoA 149 3.21e+01 1qsmA d.108.1.1 40812 1hr0W 71 3.22e+01 1ah9 b.40.4.5 25329 1plq 258 3.24e+01 1plq d.131.1.2,d.131.1.2 41388,41389 2fggA 101 3.24e+01 1nbcA 155 3.27e+01 1nbcA b.2.2.2 22390 1d8hA 311 3.28e+01 1d8iA d.63.1.1 39544 1u0kA 288 3.36e+01 d.21.1.2,d.21.1.2 107547,107548 1q42A 201 3.38e+01 d.17.4.2 95776 1mg7A 417 3.42e+01 d.14.1.6,d.58.26.6 84954,84955 1v0aA 178 3.42e+01 1pne 140 3.45e+01 1pne d.110.1.1 40866 1qs1A 462 3.48e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1ej1A 190 3.56e+01 1ejhA d.86.1.1 40144 1l8bA 190 3.62e+01 d.86.1.1 73683 2gukA 120 3.63e+01 2c78A 405 3.64e+01 1a0i 348 3.66e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1mjc 69 3.67e+01 1mjc b.40.4.5 25319 1ojrA 274 3.75e+01 c.74.1.1 93147 7pcy 98 3.76e+01 1plc b.6.1.1 22863 1qy1A 174 3.78e+01 b.60.1.1 96568 2f9zC 159 3.88e+01 1fnuA 221 3.89e+01 3seb b.40.2.2,d.15.6.1 25212,37801 1nlnA 204 3.89e+01 d.3.1.7 91962 1m4vA 204 3.89e+01 b.40.2.2,d.15.6.1 74459,74460 2abqA 306 3.92e+01 1vrtA 560 3.92e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1ze3C 205 3.94e+01 1a2vA 655 3.97e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1xyiA 66 3.99e+01 1x99A 145 4.01e+01 1cr5A 189 4.03e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1l0gA 358 4.03e+01 e.3.1.1 73400 2bklA 695 4.07e+01 1kkcA 221 4.09e+01 a.2.11.1,d.44.1.1 68660,68661 2ganA 190 4.09e+01 1ysjA 404 4.10e+01 4bcl 366 4.14e+01 4bcl b.75.1.1 27968 1azpA 66 4.16e+01 1azpA b.34.13.1 37467 2ffyA 358 4.20e+01 1y8oA 419 4.22e+01 1mc0A 368 4.25e+01 d.110.2.1,d.110.2.1 78937,78938 1z84A 351 4.27e+01 1k3eA 156 4.30e+01 d.198.1.1 68103 1k8kD 300 4.33e+01 d.198.2.1,d.198.2.1 68309,68310 1nqnA 122 4.38e+01 b.61.1.1 86042 2fvgA 340 4.40e+01 1txyA 104 4.41e+01 1uch 230 4.51e+01 1uch d.3.1.6 37129 1u6mA 199 4.55e+01 2axoA 270 4.57e+01 1uteA 313 4.61e+01 1uteA d.159.1.1 42078 1v1pA 211 4.61e+01 b.40.2.2,d.15.6.1 108268,108269 1wubA 178 4.66e+01 1qa7A 217 4.75e+01 1havA b.47.1.4 26425 1umwA 237 4.75e+01 d.223.1.2,d.223.1.2 99631,99632 1jjeA 222 4.76e+01 1a7tA d.157.1.1 63117 1f7zA 233 4.80e+01 5ptp b.47.1.2 59681 1fhgA 154 4.85e+01 1tlk b.1.1.4 21706 1xrtA 467 4.89e+01 1qniA 581 4.95e+01 1qniA b.6.1.4,b.69.3.1 23042,27642 1yna 194 5.07e+01 1axkA b.29.1.11 24335 1i50K 120 5.08e+01 d.74.3.2 61765 1wznA 252 5.09e+01 3seb 238 5.11e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1qh7A 207 5.12e+01 1axkA b.29.1.11 24317 1fwxA 595 5.16e+01 b.6.1.4,b.69.3.1 60069,60070 1h4gA 207 5.18e+01 b.29.1.11 70863 1rypF 233 5.28e+01 1rypF d.153.1.4 41937 2gp4A 628 5.29e+01 1reqB 637 5.30e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1q6hA 224 5.40e+01 d.26.1.1 95975 1tdhA 364 5.48e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1z0mA 96 5.53e+01 1xkpC 143 5.55e+01 1xf1A 926 5.56e+01 1zboA 210 5.58e+01 1kskA 234 5.58e+01 d.66.1.5,d.265.1.3 72920,90389 2bnfB 241 5.59e+01 1zx8A 136 5.61e+01 1xygD 359 5.65e+01 1avpA 204 5.66e+01 1avpA d.3.1.7 37132 1ekeA 230 5.67e+01 1ekeA c.55.3.1 33572 1winA 143 5.68e+01 2arpA 116 5.70e+01 1zybA 232 5.77e+01 2fgtA 417 5.79e+01 1em2A 229 5.85e+01 1em2A d.129.3.2 41321 2a5hA 416 5.85e+01 1z0nA 96 5.87e+01 1zndA 174 5.88e+01 1w5fA 353 5.89e+01 1e39A 571 5.91e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 2d13A 227 5.94e+01 1vajA 214 5.95e+01 1e6pA 499 5.96e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1wxxA 382 6.01e+01 1q9iA 571 6.05e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1s9jA 341 6.05e+01 1tr8A 102 6.05e+01 1vjpA 394 6.08e+01 c.2.1.3,d.81.1.3 100828,100829 1x1fA 149 6.11e+01 1u07A 90 6.13e+01 1fsyA 358 6.13e+01 1gceA e.3.1.1 60016 1bkcE 256 6.14e+01 1bkcA d.92.1.10 40333 1pi4A 358 6.15e+01 e.3.1.1 94700 2fsqA 243 6.19e+01 1jj2R 84 6.19e+01 1ffkP d.12.1.1 63103 1s72S 85 6.21e+01 d.12.1.1 105338 1h1aA 191 6.22e+01 b.29.1.11 83450 1i8aA 189 6.23e+01 1i82A b.1.9.2 61951 1dhr 241 6.35e+01 1dhr c.2.1.2 29832 1bkcI 256 6.36e+01 1bkcA d.92.1.10 40334 2glfA 450 6.40e+01 1feuA 206 6.41e+01 1feuA b.53.1.1 59801 1jhjA 171 6.45e+01 b.18.1.9 66714 1kb5B 117 6.45e+01 1kb5B b.1.1.1 20632 2ar1A 172 6.46e+01 1vqoS 85 6.51e+01 1ff4A 65 6.53e+01 g.7.1.1 83251 1vcaA 202 6.54e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1l2hA 153 6.60e+01 b.42.1.2 77655 1uh4A 637 6.61e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1ksiA 642 6.65e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1fthA 122 6.66e+01 d.150.1.2 60028 1eyqA 222 6.66e+01 1eypA d.36.1.1 38534 1xneA 113 6.69e+01 1pm4A 119 6.74e+01 b.135.1.1 94891 1viaA 175 6.85e+01 c.37.1.2 100754 1z0sA 278 6.86e+01 1vzyA 291 6.88e+01 1havA 217 6.90e+01 1havA b.47.1.4 26423 2db2A 119 6.91e+01 1rdr 461 6.92e+01 1rdr e.8.1.4 43116 2bneA 241 6.95e+01 2bv5A 282 6.95e+01 1jhdA 396 6.95e+01 b.122.1.3,c.26.1.5 66712,66713 1u1wA 298 7.02e+01 1mkp 144 7.05e+01 1vhrA c.45.1.1 32654 2gwnA 452 7.11e+01 1zvkA 358 7.11e+01 1zarA 282 7.14e+01 1quqB 121 7.16e+01 1quqB b.40.4.3 25305 1yarA 233 7.17e+01 1suwA 249 7.19e+01 e.52.1.1 106027 2eueA 279 7.22e+01 1nt0A 286 7.23e+01 b.23.1.1,b.23.1.1,g.3.11.1 86143,86144,86145 1yioA 208 7.24e+01 1hdr 244 7.26e+01 1dhr c.2.1.2 29837 2bb3A 221 7.30e+01 1r5mA 425 7.35e+01 1kr4A 125 7.38e+01 d.58.5.2 72889 1nlfA 279 7.39e+01 c.37.1.11 85850 2a5vA 213 7.39e+01 1qhdA 398 7.45e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1a34A 159 7.45e+01 1a34A b.121.7.1 23286 2grrA 161 7.48e+01 1q87A 221 7.49e+01 e.47.1.1 96192 1x54A 434 7.53e+01 1qexA 288 7.55e+01 1qexA b.32.1.1 24425 1frpA 335 7.55e+01 1frpA e.7.1.1 42875 1lkfA 299 7.56e+01 1pvl f.6.1.1 43821 2bh8A 101 7.57e+01 1rowA 109 7.58e+01 b.1.11.2 97676 1g8yA 279 7.60e+01 1g8yA c.37.1.11 32302 1n6aA 259 7.65e+01 b.76.2.1,b.85.7.1 80121,80122 1djnA 729 7.66e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1xg9A 260 7.71e+01 1zghA 260 7.71e+01 1zvhA 134 7.75e+01 1p2hA 571 7.77e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1eajA 126 7.80e+01 1f5wA b.1.1.1 59401 1s28A 132 7.83e+01 d.198.1.1 105223 1hm9A 468 7.89e+01 b.81.1.4,c.68.1.5 65866,65867 2f2hA 773 7.96e+01 1obpA 159 7.96e+01 1obpA b.60.1.1 27092 2govA 195 7.97e+01 1qhvA 195 8.06e+01 1qhvA b.21.1.1 23842 1e4fT 419 8.17e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1x0oA 119 8.17e+01 1mup 166 8.26e+01 1mup b.60.1.1 27133 1u9aA 160 8.30e+01 1u9aA d.20.1.1 38333 1ofuA 320 8.31e+01 c.32.1.1,d.79.2.1 86972,86973 1k3rA 268 8.33e+01 b.40.4.10,c.116.1.2 72018,72019 1xubA 298 8.36e+01 2bltA 361 8.45e+01 1gceA e.3.1.1 42739 1y0pA 571 8.49e+01 1kwgA 645 8.50e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1zsoA 164 8.52e+01 1so7A 382 8.52e+01 1ji1A 637 8.53e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1fi4A 416 8.55e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 1jv4A 162 8.57e+01 b.60.1.1 67343 1h7zA 194 8.60e+01 1qhvA b.21.1.1 60733 1qf6A 642 8.60e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1r9hA 135 8.61e+01 d.26.1.1 97260 2fexA 188 8.65e+01 1zwxA 301 8.65e+01 2acaA 189 8.66e+01 1cqqA 180 8.93e+01 1cqqA b.47.1.4 26422 1cwvA 492 8.93e+01 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 1ga0A 364 8.95e+01 1gceA e.3.1.1 60410 1ybiA 288 8.96e+01 1mjfA 281 9.00e+01 c.66.1.17 79198