# List of top-scoring protein chains for t2k-100-30-alpha 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 1yasA 257 2.80e-02 1qj4A c.69.1.20 34801 1qj4A 257 3.07e-02 1qj4A c.69.1.20 34796 1b3jA 274 1.38e-01 1agdA b.1.1.2 20855 d.19.1.1 38319 1ig8A 486 1.51e-01 2yhx c.55.1.3 64746 c.55.1.3 64747 1gjwA 637 2.04e-01 b.71.1.1 60582 c.1.8.1 60583 2hft 218 2.20e-01 1boy b.1.2.1 21951 b.1.2.1 21952 1gjuA 637 2.23e-01 b.71.1.1 60580 c.1.8.1 60581 1boy 219 2.68e-01 1boy b.1.2.1 21955 b.1.2.1 21956 1knyA 253 5.16e-01 1knyA e.9.1.3 43232 2btvA 901 9.23e-01 2btvA e.28.1.1 43376 1qhaA 917 9.43e-01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1kanA 253 9.46e-01 1knyA e.9.1.3 43234 1dcjA 81 1.21e+00 1dcjA d.68.3.1 59115 1qcsA 211 1.28e+00 1qcsA b.52.2.3 26927 d.31.1.1 38461 3cla 213 1.28e+00 3cla c.43.1.1 32610 1he1A 135 1.33e+00 1he1A a.24.11.1 16641 1f2tB 148 1.52e+00 1f2tB 1hkcA 917 1.56e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1iktA 120 1.56e+00 d.106.1.1 66188 1gcyA 527 1.66e+00 1jdc b.71.1.1 27788 c.1.8.1 28775 1rboC 123 1.82e+00 1rboC d.73.1.1 39634 8rucI 123 1.95e+00 1rboC d.73.1.1 39629 1eyqA 222 1.99e+00 1eypA d.36.1.1 38534 1lplA 95 2.05e+00 1fzoA 274 2.06e+00 1agdA b.1.1.2 60155 d.19.1.1 60156 1czaN 917 2.08e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1dfx 125 2.23e+00 1dfx b.1.13.1 22367 g.41.5.2 45255 1jepA 222 2.50e+00 d.36.1.1 66612 1qu0A 191 2.54e+00 1dykA b.29.1.4 24225 1hkbA 917 2.69e+00 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1eypA 222 3.12e+00 1eypA d.36.1.1 38536 1clqA 903 3.20e+00 1clqA c.55.3.5 33717 e.8.1.1 43006 1g5yA 238 3.39e+00 1lbd a.123.1.1 60294 1m4vA 204 3.66e+00 1jdc 429 3.74e+00 1jdc b.71.1.1 27789 c.1.8.1 28776 1e3mA 800 4.16e+00 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1vid 221 4.20e+00 1vid c.66.1.1 34178 1f8eA 388 4.21e+00 2qwc b.68.1.1 59694 2qwc 388 4.23e+00 2qwc b.68.1.1 27547 1danT 80 4.24e+00 1boy b.1.2.1 21953 3nn9 388 4.30e+00 2qwc b.68.1.1 27566 1go4A 205 4.41e+00 1dykA 394 4.48e+00 1dykA b.29.1.4 24223 b.29.1.4 24224 5nn9 388 4.57e+00 2qwc b.68.1.1 27563 1qf6A 642 4.59e+00 1qf6A c.51.1.1 33210 d.66.1.1 39551 d.67.1.1 39562 d.104.1.1 40759 1jeiA 53 4.60e+00 1jeiA a.140.1.1 62918 1g9uA 454 4.60e+00 c.10.2.6 65172 1lis 136 4.69e+00 1lis a.19.1.1 16406 1qd9A 124 4.77e+00 1qu9A d.79.1.1 39758 2lisA 136 4.84e+00 1lis a.19.1.1 16405 1apyB 141 4.89e+00 1apyB 1cd1A 315 5.01e+00 1cd1A b.1.1.2 21579 d.19.1.1 38155 1rypA 243 5.15e+00 1pmaA d.153.1.4 41932 1fx3B 169 5.24e+00 1fx3B d.33.1.1 38525 1f1sA 814 5.61e+00 a.102.3.2 64928 b.1.1.5 64929 b.24.1.1 64930 b.30.3.1 64931 1b37B 472 5.80e+00 1b37B c.3.1.2 30390 d.16.1.5 37954 1cr5A 189 5.80e+00 1cr5A b.52.2.3 26931 d.31.1.1 38465 1fsu 492 6.03e+00 1auk c.76.1.2 35032 1fx3A 169 6.06e+00 1fx3B d.33.1.1 38524 3lynA 136 6.23e+00 1lis a.19.1.1 16413 1dgkN 917 6.31e+00 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1eduA 149 6.50e+00 1eduA a.118.9.1 19215 1e2o 233 6.70e+00 1eaf c.43.1.1 32631 1pgtA 210 6.90e+00 1pgtA a.45.1.1 17515 c.47.1.5 32809 1pprM 312 6.91e+00 1pprM a.131.1.1 19502 a.131.1.1 19503 1egpA 45 6.95e+00 1egpA d.40.1.1 38561 1jbbA 153 7.11e+00 1u9aA d.20.1.1 62842 1jl5A 454 7.11e+00 c.10.2.6 66830 1rec 201 7.14e+00 1rec a.39.1.5 17326 1vcaA 202 7.16e+00 1vcaA b.1.1.3 21649 b.1.1.4 21685 1jtgB 165 7.49e+00 d.98.1.1 67267 1e0cA 271 7.87e+00 1e0cA c.46.1.2 32717 c.46.1.2 32718 1larA 575 8.31e+00 1larA c.45.1.2 32693 c.45.1.2 32694 1eyhA 144 8.76e+00 1eduA a.118.9.1 19214 2ucz 165 9.16e+00 1u9aA d.20.1.1 38330 1l0oA 150 9.36e+00 1ceqA 316 9.36e+00 1ceqA c.2.1.5 30163 d.162.1.1 42130 1cczA 171 9.54e+00 1cczA b.1.1.1 19758 b.1.1.3 21683 1d5mC 239 9.54e+00 3seb b.40.2.2 25185 d.15.6.1 37774 1b5qA 472 9.67e+00 1b37B c.3.1.2 30404 d.16.1.5 37968 1agdA 276 9.68e+00 1agdA b.1.1.2 20741 d.19.1.1 38260 2ts1 419 1.01e+01 2ts1 c.26.1.1 31564 1ji8A 111 1.02e+01 d.203.1.1 66733 1fzkA 274 1.02e+01 1agdA b.1.1.2 60149 d.19.1.1 60150 1ib2A 349 1.03e+01 1ib2A a.118.1.8 62141 1ib3A 349 1.05e+01 1ib2A a.118.1.8 62142 1dqsA 393 1.07e+01 1dqsA e.22.1.1 43347 1vdrA 162 1.17e+01 1vdrA c.71.1.1 34893 1jpmA 366 1.20e+01 c.1.11.2 67031 d.54.1.1 67032 1ba1 386 1.26e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1jilA 420 1.27e+01 c.26.1.1 66745 3rubS 123 1.28e+01 1rboC d.73.1.1 39616 1cewI 108 1.28e+01 1cewI d.17.1.2 37999 1fjgM 126 1.29e+01 1fjfM a.5.5.1 16293 1acx 108 1.29e+01 2mcm b.1.7.1 22211 1k6wA 426 1.32e+01 b.92.1.2 68236 c.1.9.5 68237 1jq5A 370 1.32e+01 e.22.1.2 67084 1pmd 675 1.32e+01 1pmd d.11.1.1 37491 d.11.1.1 37492 d.175.1.1 42562 e.3.1.1 42771 1cseI 71 1.36e+01 1egpA d.40.1.1 38559 2bidA 197 1.38e+01 2bidA f.1.4.1 43398 1kpsB 171 1.38e+01 a.118.12.1 68787 1g7pA 274 1.40e+01 1hskA 326 1.41e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1kezA 300 1.44e+01 c.69.1.22 68546 1d2kA 392 1.45e+01 1d2kA c.1.8.5 29008 d.26.3.1 38442 1g8iA 190 1.48e+01 1rec a.39.1.5 60363 1gs5A 258 1.48e+01 1i4fA 275 1.50e+01 1agdA b.1.1.2 61687 d.19.1.1 61688 1c8bA 371 1.51e+01 1c8bA c.56.1.2 59082 1uteA 313 1.51e+01 1uteA d.159.1.1 42078 1sesA 421 1.52e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1kshB 152 1.54e+01 1l3lA 234 1.56e+01 1gpl 432 1.62e+01 1gpl b.12.1.2 23645 c.69.1.19 34793 1nkd 65 1.65e+01 1nkd a.30.1.1 16974 3seb 238 1.67e+01 3seb b.40.2.2 25184 d.15.6.1 37773 1a5t 334 1.68e+01 1a5t a.80.1.1 18450 c.37.1.13 32423 6paxA 133 1.72e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1g2qA 187 1.74e+01 c.61.1.1 65117 1bn8A 420 1.74e+01 1pcl b.80.1.1 28022 1hi9A 274 1.75e+01 1hi9A c.99.1.1 61063 1yghA 164 1.78e+01 1yghA d.108.1.1 40802 1u9aA 160 1.83e+01 1u9aA d.20.1.1 38333 1eo6A 117 1.84e+01 1eo6A d.15.1.3 37609 1hfc 169 1.88e+01 1hfc d.92.1.11 40335 1f15A 218 1.88e+01 1f15B b.10.1.2 23320 1fs0E 138 1.88e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1rpo 65 1.90e+01 1nkd a.30.1.1 16975 1gmeA 151 1.96e+01 b.15.1.1 65305 1kay 381 1.97e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1a2vA 655 2.02e+01 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 1ap6A 198 2.02e+01 1avmA a.2.11.1 15746 d.44.1.1 38705 1l5jA 865 2.03e+01 2dln 306 2.05e+01 1iow c.30.1.2 31715 d.142.1.1 41483 1scuA 288 2.10e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1bupA 386 2.12e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1qmuA 380 2.12e+01 1qmuA b.3.2.1 22534 c.56.5.1 33827 2gar 212 2.14e+01 2gar c.65.1.1 34161 1rlw 126 2.16e+01 1rlw b.7.1.1 23177 1lbd 282 2.18e+01 1lbd a.123.1.1 19279 2act 220 2.18e+01 1cs8A d.3.1.1 37002 1ks9A 291 2.18e+01 a.100.1.7 68857 c.2.1.6 68858 2scuA 288 2.18e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1kcvH 217 2.20e+01 1g40A 244 2.22e+01 1e5gA g.18.1.1 44823 g.18.1.1 44824 g.18.1.1 44825 g.18.1.1 44826 1jr3E 334 2.23e+01 a.80.1.1 63253 c.37.1.13 63254 1duzA 275 2.24e+01 1agdA b.1.1.2 20670 d.19.1.1 38224 1b77A 228 2.30e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1hsbA 270 2.31e+01 1agdA b.1.1.2 20736 d.19.1.1 38257 2azaA 129 2.41e+01 1nwpA b.6.1.1 22901 1f9vA 347 2.41e+01 1bg2 c.37.1.9 59745 1hxxA 340 2.42e+01 2omf f.4.3.1 61385 1ldg 316 2.42e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1g2oA 268 2.48e+01 1b8oA c.56.2.1 60228 1k77A 260 2.49e+01 1b87A 181 2.51e+01 1b87A d.108.1.1 40797 1l8bA 190 2.54e+01 2omf 340 2.54e+01 2omf f.4.3.1 43749 1mldA 314 2.54e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1jatA 155 2.57e+01 1u9aA d.20.1.1 62818 1pex 207 2.59e+01 1gen b.66.1.1 27540 1fn9A 365 2.59e+01 1fn9A d.196.1.1 59894 1h6zA 913 2.60e+01 1hg5A 289 2.62e+01 1hg5A a.118.10.1 19221 1mwpA 96 2.64e+01 1mwpA d.170.2.1 42453 1repC 251 2.64e+01 1repC a.4.5.10 16125 a.4.5.10 16126 1jrrA 382 2.71e+01 e.1.1.1 63256 1qfcA 306 2.72e+01 1uteA d.159.1.1 42077 1qoiA 177 2.80e+01 2cpl b.62.1.1 27490 1jrkA 156 2.89e+01 1vhh 162 2.89e+01 1vhh d.65.1.2 39550 1hf8A 289 2.91e+01 1hg5A a.118.10.1 19219 1k20A 310 2.91e+01 c.107.1.1 68027 2ak3A 226 2.95e+01 1zin c.37.1.1 31892 g.41.2.1 45193 1dq3A 454 2.96e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 6prcH 258 3.04e+01 6prcH b.41.1.1 25457 f.2.1.2 43436 1byrA 155 3.04e+01 1byrA d.136.1.1 41450 1ede 310 3.06e+01 1b6g c.69.1.8 34662 1etpA 190 3.06e+01 1etpA a.3.1.4 15962 a.3.1.4 15963 1qmeA 702 3.14e+01 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1dlhB 188 3.14e+01 1iakB b.1.1.2 21598 d.19.1.1 38172 1hi0P 664 3.16e+01 1hi0P e.8.1.6 61051 1ew0A 130 3.17e+01 1drmA d.110.3.2 40905 1goh 639 3.20e+01 1gof b.1.1.5 21809 b.18.1.1 23711 b.69.1.1 27633 1cr0A 296 3.22e+01 1cr1A c.37.1.11 32287 1tlk 154 3.25e+01 1tlk b.1.1.4 21707 1jenA 267 3.32e+01 1jenA 1fmaE 150 3.33e+01 1fmaE d.41.5.1 38630 1ordA 730 3.35e+01 1ordA c.23.7.1 31274 c.67.1.5 34503 d.125.1.1 41124 1f15B 218 3.36e+01 1f15B b.10.1.2 23321 1ib8A 164 3.38e+01 1ejhA 190 3.38e+01 1ejhA d.86.1.1 40147 3mefA 69 3.40e+01 1mjc b.40.4.5 25320 1jeqA 609 3.41e+01 1jeqA a.140.2.1 64748 e.31.1.1 64749 1ef8A 261 3.46e+01 1ef8A c.14.1.3 30921 1hz4A 373 3.51e+01 a.118.8.2 65960 1gt7A 274 3.53e+01 1c53 79 3.53e+01 1c53 a.3.1.1 15801 1d06A 130 3.53e+01 1drmA d.110.3.2 40906 1bg1A 722 3.55e+01 1bg1A a.47.1.1 17767 b.2.5.1 22461 d.93.1.1 40527 1g6oA 330 3.55e+01 1g6oA c.37.1.13 32430 1hsq 71 3.58e+01 1ckaA b.34.2.1 24551 1ac5 483 3.76e+01 1ac5 c.69.1.5 34653 1aizA 129 3.80e+01 1nwpA b.6.1.1 22903 1pauA 147 3.82e+01 1pauA c.17.1.1 30994 1aroP 883 3.87e+01 1cezA e.8.1.3 43112 1euoA 180 3.90e+01 1np1A b.60.1.1 27163 1oya 400 3.90e+01 1oyc c.1.4.1 28604 1dxrH 258 3.92e+01 6prcH b.41.1.1 25456 f.2.1.2 43433 1faeA 629 3.95e+01 1fce a.102.1.2 18837 1foeA 377 3.98e+01 1foeA a.87.1.1 18517 b.55.1.1 26969 1hgxA 183 4.00e+01 1tc1A c.61.1.1 34027