# List of top-scoring protein chains for t2k-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 2gkeA 274 1.26e-02 1gqzA 274 1.85e-02 d.21.1.1,d.21.1.1 83311,83312 1bwzA 274 2.73e-02 1bwzA d.21.1.1,d.21.1.1 38337,38338 1w61A 414 6.29e-02 1usyA 275 1.23e-01 1sdjA 310 8.03e-01 d.21.1.2,d.21.1.2 98807,98808 2g6yA 217 9.27e-01 1qyaA 307 1.91e+00 d.21.1.2,d.21.1.2 104653,104654 1s7jA 262 2.09e+00 d.21.1.2 98647 1ci3M 249 2.69e+00 1hcz b.2.6.1,b.84.2.2 22480,28266 1lj5A 379 4.39e+00 e.1.1.1 73928 1wgoA 123 6.15e+00 1b0tA 106 6.41e+00 1a6l d.58.1.2 38965 1viwB 198 6.56e+00 1led b.29.1.1 24170 1a6l 106 7.23e+00 1a6l d.58.1.2 38966 2pcfB 250 7.69e+00 1hcz i.4.1.1 45911 1n26A 325 8.40e+00 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1x6zA 123 9.08e+00 1eft 405 9.37e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1tg7A 971 9.55e+00 1ds6B 180 1.00e+01 1rhoA b.1.18.8 21898 1diwA 441 1.06e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 2cxkA 95 1.08e+01 1lm4A 194 1.12e+01 d.167.1.1 84626 1bihA 395 1.33e+01 1bihA b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21752,21753,21754,21755 1xubA 298 1.33e+01 1tm0A 350 1.33e+01 d.21.1.3 107147 1qupA 222 1.42e+01 1qupA b.1.8.1,d.58.17.1 22301,39352 7fd1A 106 1.43e+01 1a6l d.58.1.2 38953 1q47A 495 1.50e+01 b.69.12.1 104532 1ioaA 240 1.53e+01 1led b.29.1.1 24168 1mqoA 227 1.55e+01 d.157.1.1 103846 1led 243 1.57e+01 1led b.29.1.1 24039 2fggA 101 1.58e+01 1mkeA 152 1.66e+01 b.55.1.4 79231 1lmhA 184 1.66e+01 d.167.1.1 74036 1d2sA 170 1.68e+01 1d2sA b.29.1.4 24221 1rec 201 1.71e+01 1rec a.39.1.5 17326 1eysH 259 1.78e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 1t6kA 278 1.78e+01 1dzoA 123 1.80e+01 1dzoA d.24.1.1 38378 2c34A 116 1.84e+01 1kiuB 279 1.85e+01 b.2.3.2,b.2.3.2 72525,72526 1omrA 201 1.86e+01 a.39.1.5 93349 1xqbA 247 1.86e+01 1g86A 142 1.88e+01 b.29.1.3 70161 1lcl 142 1.88e+01 1lcl b.29.1.3 24216 1a8d 452 1.89e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1ca1 370 1.89e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1d0hA 469 1.92e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 1gyvA 120 1.94e+01 b.1.10.2 70790 1ym5A 300 1.97e+01 1iqsA 88 1.98e+01 d.214.1.1 71278 2amhA 207 1.99e+01 1egxA 115 1.99e+01 1evhA b.55.1.4 27000 1iqoA 88 1.99e+01 d.214.1.1 71277 1ap8 213 2.01e+01 1ap8 d.86.1.1 40151 1e2wA 251 2.02e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1fdd 106 2.02e+01 1a6l d.58.1.2 38960 2a7bA 120 2.05e+01 1u1wA 298 2.05e+01 1dhkB 223 2.05e+01 1led b.29.1.1 24157 1klfB 279 2.07e+01 b.2.3.2,b.2.3.2 72684,72685 1kk1A 410 2.11e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1fd2 106 2.12e+01 1a6l d.58.1.2 38962 1lqwA 183 2.18e+01 d.167.1.1 74210 1kn9A 249 2.19e+01 b.87.1.2 68699 1n9pA 207 2.25e+01 b.1.18.16 80343 1dykA 394 2.31e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1yqzA 438 2.39e+01 1hdkA 141 2.39e+01 b.29.1.3 65807 1hcz 252 2.42e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 2dddA 225 2.44e+01 1xssA 225 2.49e+01 2ch4A 320 2.52e+01 2wsyB 396 2.54e+01 2tysB c.79.1.1 35288 2fbeA 201 2.56e+01 1t0pB 86 2.58e+01 1l1nA 183 2.58e+01 b.47.1.4 73476 1b59A 370 2.59e+01 1bn5 a.4.5.25,d.127.1.1 16225,41162 1ax0 239 2.59e+01 1led b.29.1.1 24042 1bksB 397 2.62e+01 2tysB c.79.1.1 35285 1iq6A 134 2.66e+01 d.38.1.4 76755 1ov3A 138 2.70e+01 b.34.2.1,b.34.2.1 87451,87452 1lm8V 160 2.71e+01 b.3.3.1 74035 1vzyA 291 2.71e+01 1b0vA 106 2.75e+01 1a6l d.58.1.2 38982 1lqbC 162 2.76e+01 b.3.3.1 74186 1qi9A 556 2.83e+01 1qhbA a.111.1.2 19053 1ats 386 2.83e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1gjuA 637 2.87e+01 b.71.1.1,c.1.8.1 60580,60581 2c78A 405 2.88e+01 1c1bB 440 2.93e+01 1rthA e.8.1.2 43077 1gzcA 239 3.05e+01 b.29.1.1 70803 1exmA 405 3.05e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1mp9A 198 3.10e+01 d.129.1.1,d.129.1.1 91385,91386 1a50B 396 3.12e+01 2tysB c.79.1.1 35280 1wb9A 800 3.15e+01 1hpm 386 3.16e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1c76A 136 3.17e+01 2sak d.15.5.1 37718 1bupA 386 3.17e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1ba1 386 3.17e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 2aaiB 262 3.18e+01 1abrB b.42.2.1,b.42.2.1 25561,25562 1umzA 278 3.19e+01 b.29.1.2 99639 1a5kC 566 3.21e+01 1ubpC b.92.1.1,c.1.9.2 28425,29047 1ejxC 567 3.21e+01 b.92.1.1,c.1.9.2 83184,83185 1d3bA 75 3.23e+01 1d3bA b.38.1.1 24798 1js8A 394 3.25e+01 a.86.1.1,b.112.1.1 67219,67220 1a5lC 566 3.25e+01 1ubpC b.92.1.1,c.1.9.2 28426,29048 1qunB 279 3.28e+01 b.2.3.2,b.2.3.2 22411,22412 2tysB 397 3.28e+01 2tysB c.79.1.1 35272 1q1lA 401 3.30e+01 d.258.1.1 95591 1fkoB 440 3.31e+01 1rthA e.8.1.2 43095 1gywA 128 3.31e+01 b.1.10.2 70791 1bg1A 722 3.32e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17767,22461,40527 1avbA 226 3.32e+01 1led b.29.1.1 24158 1gjwA 637 3.34e+01 b.71.1.1,c.1.8.1 60582,60583 1a5mC 566 3.37e+01 1ubpC b.92.1.1,c.1.9.2 28423,29045 2sak 121 3.38e+01 2sak d.15.5.1 37711 2g1lA 104 3.40e+01 1prxA 224 3.41e+01 1prxA c.47.1.10 33076 1qmyA 167 3.45e+01 1qmyA d.3.1.2 37094 1kay 381 3.47e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1k8yB 396 3.48e+01 c.79.1.1 72184 1erjA 393 3.50e+01 1erjA b.69.4.1 27660 1r7lA 110 3.54e+01 d.277.1.1 104837 1igtB 444 3.57e+01 1igtB b.1.1.1,b.1.1.2,b.1.1.2,b.1.1.2 19765,20867,20868,20869 1ciy 590 3.62e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1wucA 250 3.62e+01 1ju3A 583 3.64e+01 b.18.1.13,c.69.1.21 67300,67301 1s6lA 212 3.66e+01 1fwcC 567 3.67e+01 1ubpC b.92.1.1,c.1.9.2 28410,29032 1xiwA 105 3.67e+01 1ejrC 567 3.71e+01 1ubpC b.92.1.1,c.1.9.2 28420,29042 1v54F 98 3.74e+01 g.41.5.3 100327 1xfjA 261 3.76e+01 d.194.1.2 109585 1kdgA 546 3.77e+01 c.3.1.2,d.16.1.1 77337,77338 1p4uA 153 3.80e+01 b.1.10.2 87780 1m2xA 223 3.81e+01 d.157.1.1 84764 1iu1A 146 3.85e+01 b.1.10.2 71428 1h4aX 173 3.87e+01 b.11.1.1,b.11.1.1 83479,83480 1yua 122 3.95e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1e42A 258 4.04e+01 1e42A b.1.10.1,d.105.1.1 22316,40792 1hka 158 4.11e+01 1hka d.58.30.1 39433 1n3gA 113 4.14e+01 d.204.1.1 79962 1v5tA 90 4.30e+01 d.15.1.1 108385 1c4rA 182 4.32e+01 1c4rA b.29.1.4 24229 1bjwA 382 4.36e+01 1bjwA c.67.1.1 34349 4sli 679 4.41e+01 2sli b.29.1.9,b.68.1.1 24275,27612 2sli 679 4.42e+01 2sli b.29.1.9,b.68.1.1 24274,27611 2bvlA 543 4.44e+01 2bjqA 345 4.49e+01 1dk4A 252 4.51e+01 1dk4A e.7.1.1 42970 1g8iA 190 4.56e+01 1rec a.39.1.5 60363 1rtu 114 4.69e+01 9rnt d.1.1.4 36139 1db2A 377 4.77e+01 1sek e.1.1.1 42672 1hyvA 166 4.79e+01 1b9dA c.55.3.2 61424 1f76A 336 4.79e+01 c.1.4.1 76160 1w97L 246 4.82e+01 1qopB 396 4.84e+01 2tysB c.79.1.1 35270 1yqfA 203 4.86e+01 1uisA 231 4.87e+01 d.22.1.1 99431 1fx7A 230 4.89e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1ukvY 206 4.91e+01 c.37.1.8 107918 1b3qA 379 4.91e+01 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 3ait 74 4.96e+01 1hoe b.5.1.1 22835 1f5fA 205 4.97e+01 1d2sA b.29.1.4 24222 1ncwH 222 4.97e+01 b.1.1.1,b.1.1.2 85555,85556 1e66A 543 5.10e+01 c.69.1.1 59291 1vcbC 160 5.10e+01 1vcbC b.3.3.1 22535 1qidA 537 5.13e+01 2bce c.69.1.1 34593 1ha3A 405 5.14e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1rthA 560 5.16e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1q48A 134 5.18e+01 d.224.1.2 95783 1azdA 237 5.18e+01 1nls b.29.1.1 24020 1b9dA 163 5.22e+01 1b9dA c.55.3.2 33649 1gr3A 160 5.28e+01 b.22.1.1 65476 1suwA 249 5.33e+01 e.52.1.1 106027 1bs4A 168 5.35e+01 1bs4A d.167.1.1 42287 1atr 386 5.35e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1dttA 560 5.39e+01 1rthA c.55.3.1,e.8.1.2 33611,43088 1smxA 96 5.43e+01 b.40.4.5 105772 1vrtA 560 5.52e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1bn5 478 5.62e+01 1bn5 a.4.5.25,d.127.1.1 16224,41161 1b5pA 385 5.63e+01 c.67.1.1 90403 1yfqA 342 5.65e+01 1at0 145 5.65e+01 1at0 b.86.1.1 28374 1ut9A 609 5.67e+01 a.102.1.2,b.1.18.2 99912,99913 1bl3A 160 5.70e+01 1b9dA c.55.3.2 33655 1e3mA 800 5.73e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 1b6a 478 5.84e+01 1bn5 a.4.5.25,d.127.1.1 16223,41160 1v7wA 807 5.84e+01 a.102.1.4,b.30.5.3 108411,108412 3pchA 200 5.86e+01 3pchA b.3.6.1 22653 1a6pA 94 5.87e+01 1cdcA b.1.1.1 19748 1dceA 567 5.88e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1mpp 361 5.96e+01 2rmpA b.50.1.2 26856 1cojA 212 5.98e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1b12A 248 6.01e+01 1b12A b.87.1.2 28388 1e69B 322 6.03e+01 1e69B c.37.1.12 32377 1fkoA 543 6.03e+01 1rthA c.55.3.1,e.8.1.2 33612,43094 1j1tA 233 6.04e+01 b.29.1.18 90771 2a46A 238 6.10e+01 3pcgA 200 6.11e+01 3pchA b.3.6.1 22647 1bqnA 558 6.13e+01 1rthA c.55.3.1,e.8.1.2 33599,43064 1jjuA 489 6.15e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 2azpA 318 6.29e+01 1a02N 301 6.47e+01 1a02N b.1.18.1,b.2.5.3 21923,22440 2occF 98 6.55e+01 2occF g.41.5.3 45256 1o0xA 262 6.58e+01 d.127.1.1 80755 1kdkA 177 6.61e+01 b.29.1.4 72351 1wkbA 810 6.65e+01 1iq4A 179 6.72e+01 1iq4A d.77.1.1 62641 1xeoA 168 6.79e+01 1ng2A 193 6.83e+01 b.34.2.1,b.34.2.1 85660,85661 1mjuL 219 6.87e+01 b.1.1.1,b.1.1.2 91304,91305 1abrA 251 6.95e+01 1mrj d.165.1.1 42196 1itg 166 7.00e+01 1b9dA c.55.3.2 33661 1bsjA 168 7.19e+01 1bs4A d.167.1.1 42302 3sxlA 184 7.23e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1z0sA 278 7.35e+01 1cqxA 403 7.36e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 2ncm 99 7.38e+01 2ncm b.1.1.4 21703 1m7xA 617 7.38e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1c9uA 454 7.47e+01 1c9uA b.68.2.1 27623 2bcgY 206 7.51e+01 2fomB 185 7.53e+01 1ac5 483 7.62e+01 1ac5 c.69.1.5 34653 1ea5A 537 7.63e+01 2bce c.69.1.1 34592 1vk1A 242 7.73e+01 d.268.1.2 108634 1qqsA 174 7.73e+01 1nglA b.60.1.1 27143 1rz3A 201 7.81e+01 c.37.1.6 98132 1fk9A 543 7.81e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 1qa1A 554 7.91e+01 1tyv b.80.1.6 28047 2hmiA 558 7.95e+01 1rthA c.55.3.1,e.8.1.2 33604,43106 1qq1A 559 8.11e+01 1tyv b.80.1.6 28041 2pcdA 200 8.16e+01 3pchA b.3.6.1 22665 1t0qC 86 8.16e+01 d.15.12.1 106222 1k42A 168 8.19e+01 b.18.1.14 72032 1evhA 112 8.21e+01 1evhA b.55.1.4 26997 1tyu 543 8.21e+01 1tyv b.80.1.6 28037 1k12A 158 8.21e+01 b.18.1.15 71978 1cruA 454 8.28e+01 1c9uA b.68.2.1 27617 1zc3B 113 8.29e+01 1lr0A 129 8.36e+01 d.212.1.1 74213 1uyjA 296 8.38e+01 f.8.1.2 108143 1tyv 542 8.46e+01 1tyv b.80.1.6 28038 2cbf 234 8.49e+01 1cbf c.90.1.1 35588 1yqcA 170 8.50e+01 1a7cA 379 8.51e+01 1sek e.1.1.1 42660 2e2c 156 8.51e+01 1u9aA d.20.1.1 38336 1ok7A 366 8.63e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1y2tA 142 8.78e+01 1xbrA 184 8.83e+01 1xbrA b.2.5.4 22458 2bgiA 272 8.84e+01 2fnbA 95 8.86e+01 2fnbA b.1.2.1 21979 2f4lA 297 8.93e+01