# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1xngA 268 8.87e-03 1eiyB 785 9.05e-02 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16305,16306,25314,39313,40782,41458 1pysB 785 9.51e-02 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16299,16300,25311,39310,40779,41455 1b7yB 785 1.08e-01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 2cokA 113 3.66e-01 1d2eA 397 4.04e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1zczA 464 4.45e-01 2a2pA 129 6.34e-01 1wh0A 134 1.05e+00 1po5A 476 1.69e+00 a.104.1.1 94963 1eal 127 1.82e+00 1hmt b.60.1.2 27227 1tif 78 2.22e+00 1tif d.15.8.1 37836 1pydA 556 2.47e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1gpmA 525 2.69e+00 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1f5aA 513 2.84e+00 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1gof 639 3.14e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 1b3mA 389 3.30e+00 1b3mA 1fkf 107 3.33e+00 1fkj d.26.1.1 38386 1k3iA 656 3.43e+00 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1goh 639 3.60e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21809,23711,27633 1fkj 107 3.84e+00 1fkj d.26.1.1 38384 1snnA 227 3.85e+00 d.115.1.2 105821 1fkd 107 4.02e+00 1fkj d.26.1.1 38383 1yhfA 115 4.09e+00 1pvyA 227 4.36e+00 d.115.1.2 95195 1pvdA 537 4.38e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1eft 405 4.39e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1cxqA 162 4.43e+00 1cxqA c.55.3.2 33621 1l9fA 389 4.48e+00 c.3.1.2,d.16.1.3 73716,73717 1g5cA 170 4.55e+00 1g5cA c.53.2.1 60264 1q79A 514 4.73e+00 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1asu 162 4.76e+00 1cxqA c.55.3.2 33626 1bkf 107 4.82e+00 1fkj d.26.1.1 38382 1zn8A 180 4.96e+00 1csbB 205 5.05e+00 1theB 1m2xA 223 5.16e+00 d.157.1.1 84764 1theB 260 5.35e+00 1theB d.3.1.1 37057 1p5hA 428 5.38e+00 c.123.1.1 87802 1exmA 405 5.47e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1a5v 162 5.76e+00 1cxqA c.55.3.2 33629 2aamA 309 5.80e+00 2azqA 311 5.80e+00 1el5A 389 5.93e+00 1b3mA c.3.1.2,d.16.1.3 30369,37937 1wlfA 179 6.30e+00 b.52.2.3,d.31.1.1 109396,109397 1theA 260 6.84e+00 1theB d.3.1.1 37056 1dd6A 228 7.18e+00 1a7tA d.157.1.1 42054 1efcA 393 7.19e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1jjeA 222 7.30e+00 1a7tA d.157.1.1 63117 1at3A 247 7.82e+00 1at3A b.57.1.1 27021 1v6fA 151 7.83e+00 d.109.1.2 108395 1dq3A 454 8.00e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1cjsA 219 8.04e+00 1cjsA e.24.1.1 43354 1vckA 115 8.16e+00 1gm6A 175 8.22e+00 b.60.1.1 70272 1x8hA 228 8.28e+00 1j83A 180 8.33e+00 b.18.1.12 66430 1kk1A 410 8.64e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1i2aA 219 8.96e+00 e.24.1.1 90660 1qpbA 563 9.26e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 1ha3A 405 9.55e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1jjtA 228 9.59e+00 1a7tA d.157.1.1 63139 1iq4A 179 9.63e+00 1iq4A d.77.1.1 62641 2aop 497 9.69e+00 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 1vlmA 219 1.04e+01 c.66.1.41 108836 2c78A 405 1.07e+01 1m6yA 301 1.12e+01 a.60.13.1,c.66.1.23 78716,78717 1hlvA 131 1.15e+01 a.4.1.7,a.4.1.7 65854,65855 1mvwB 145 1.16e+01 i.15.1.1 79524 1aop 497 1.21e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1j8yF 297 1.27e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1vsd 152 1.33e+01 1cxqA c.55.3.2 33625 1gmyA 261 1.36e+01 d.3.1.1 76236 1xhbA 472 1.42e+01 1mszA 86 1.43e+01 d.68.7.1 79428 1k4mA 213 1.44e+01 c.26.1.3 77258 1tzyD 103 1.55e+01 a.22.1.1 107533 2ait 74 1.60e+01 1hoe b.5.1.1 22837 1lbvA 252 1.61e+01 e.7.1.1 73813 2f9lA 199 1.63e+01 1qg6A 261 1.64e+01 1eny c.2.1.2 29919 1hoe 74 1.70e+01 1hoe b.5.1.1 22833 1r7lA 110 1.75e+01 d.277.1.1 104837 3ait 74 1.81e+01 1hoe b.5.1.1 22835 1j3mA 129 1.83e+01 d.129.7.1 103836 1nezG 128 1.84e+01 b.1.1.1 85592 1usuA 260 1.86e+01 d.14.1.8 99885 1id3B 102 1.89e+01 a.22.1.1 66113 2fhxA 246 2.00e+01 1ars 396 2.07e+01 1ajsA c.67.1.1 34287 1a6vL 110 2.08e+01 1mfa b.1.1.1 20256 1qsgA 265 2.10e+01 1eny c.2.1.2 29935 1zmaA 118 2.12e+01 1ok0A 74 2.12e+01 b.5.1.1 93191 1ao5A 237 2.14e+01 5ptp b.47.1.2 26334 1j8mF 297 2.23e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1qmeA 702 2.25e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1sg0A 230 2.28e+01 1a6wL 109 2.29e+01 1mfa b.1.1.1 20252 1a6uL 108 2.33e+01 1mfa b.1.1.1 20254 1kx5B 102 2.36e+01 a.22.1.1 77594 1spa 396 2.37e+01 1ajsA c.67.1.1 34291 1cj3A 392 2.47e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1hq3D 103 2.47e+01 1aoiB a.22.1.1 16464 1oaqL 120 2.50e+01 b.1.1.1 92708 1bgj 394 2.58e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 2bzsA 236 2.58e+01 1sh0A 510 2.60e+01 e.8.1.4 98876 1zx1A 231 2.61e+01 1bqhG 129 2.61e+01 1cd8 b.1.1.1 19715 2bl0B 145 2.62e+01 1aoiB 87 2.63e+01 1aoiB a.22.1.1 16470 1ps1A 337 2.64e+01 1ps1A a.128.1.4 19450 2a1vA 144 2.69e+01 1mkeA 152 2.69e+01 b.55.1.4 79231 1fsgA 233 2.76e+01 1qk3A c.61.1.1 34029 1l6rA 227 2.83e+01 c.108.1.10 77768 1cqqA 180 2.86e+01 1cqqA b.47.1.4 26422 1dbrA 231 3.09e+01 1qk3A c.61.1.1 34041 1aoiF 87 3.09e+01 1aoiB a.22.1.1 16471 1ykjA 394 3.11e+01 2d13A 227 3.13e+01 1h97A 147 3.15e+01 1h97A a.1.1.2 60812 1h6kZ 98 3.18e+01 d.58.7.1 60686 1odkA 235 3.20e+01 c.56.2.1 86863 1lb2B 84 3.23e+01 a.60.3.1 77871 1z3eB 73 3.25e+01 1efuA 385 3.29e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1s1hC 192 3.36e+01 i.1.1.1 105156 2sas 185 3.37e+01 2sas a.39.1.5 17258 1i6uA 130 3.38e+01 d.140.1.1 61850 1aipE 405 3.48e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1c14A 262 3.52e+01 1eny c.2.1.2 29927 1mioA 534 3.55e+01 1qguA c.92.2.3 35601 2b43A 526 3.61e+01 1k0iA 394 3.63e+01 c.3.1.2,d.16.1.2 67942,67943 1dceB 331 3.66e+01 1dceB a.102.4.3 18872 1ew3A 159 3.73e+01 1mup b.60.1.1 27114 1j3gA 187 3.82e+01 d.118.1.1 77075 1rzfL 213 3.99e+01 b.1.1.1,b.1.1.2 98152,98153 1ariA 396 4.01e+01 1ajsA c.67.1.1 34331 2phh 394 4.02e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1nw3A 416 4.07e+01 c.66.1.31 86288 1s6cA 183 4.08e+01 a.39.1.5 98594 1v52A 133 4.16e+01 1bn7A 294 4.18e+01 1bn6A c.69.1.8 34677 1aipA 405 4.24e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1wi6A 88 4.32e+01 1suh 146 4.38e+01 1edhA b.1.6.1 22206 1cc1L 498 4.39e+01 1h2rL e.18.1.1 43301 1tul 108 4.47e+01 1tul b.85.5.1 28373 1tiu 98 4.48e+01 1tit b.1.1.4 21715 1vkyA 347 4.51e+01 e.53.1.1 108696 1bn6A 294 4.60e+01 1bn6A c.69.1.8 34678 1q4mA 221 4.61e+01 a.132.1.3 95805 1tocR 120 4.62e+01 1tocR g.8.1.2,g.8.1.2 44558,44559 1fa0B 537 4.62e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 1pmzA 86 4.63e+01 a.39.1.10 104195 2g76A 335 4.71e+01 1art 396 4.76e+01 1ajsA c.67.1.1 34285 1h6kX 97 4.76e+01 d.58.7.1 60684 1yovA 537 4.79e+01 1q1vA 70 4.87e+01 a.159.4.1 104479 2a7oA 112 4.89e+01 1rsy 152 4.99e+01 1rsy b.7.1.2 23192 1qzzA 374 5.04e+01 a.4.5.29,c.66.1.12 96719,96720 1fa0A 537 5.08e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1zljA 78 5.09e+01 1ru8A 232 5.39e+01 c.26.2.1 97849 1qk3A 233 5.52e+01 1qk3A c.61.1.1 34031 1rypI 222 5.56e+01 d.153.1.4 41877 1q2yA 140 5.58e+01 d.108.1.1 95655 1g0xA 197 5.62e+01 1nkr b.1.1.4,b.1.1.4 21805,21806 1gv9A 260 5.68e+01 b.29.1.13 70596 2fyxA 143 5.69e+01 1gzsB 165 5.89e+01 a.168.1.1 76425 1pbe 394 5.90e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1a4pA 96 5.98e+01 1b4cA a.39.1.2 17176 2a7yA 83 6.38e+01 1m45A 148 6.40e+01 a.39.1.5 78598 2gn5 87 6.40e+01 1gvp b.40.4.7 25386 1qk4A 233 6.46e+01 1qk3A c.61.1.1 34037 2f5gA 133 6.48e+01 1pil 112 6.48e+01 2pii d.58.5.1 39072 1y7rA 133 6.48e+01 2f2gA 221 6.56e+01 1b43A 340 6.61e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 2pii 112 6.62e+01 2pii d.58.5.1 39071 1oixA 191 6.71e+01 1zvnA 99 6.74e+01 1ae2 87 6.74e+01 1gvp b.40.4.7 25382 1bymA 97 6.75e+01 1bi0 b.34.1.2 24458 2fp3A 316 6.78e+01 1m07A 111 6.80e+01 d.5.1.1 78328 1h6yA 170 6.82e+01 b.18.1.7 70904 1d06A 130 6.82e+01 1drmA d.110.3.2 40906 1oivA 191 6.83e+01 c.37.1.8 93076 1kb9D 246 6.85e+01 a.3.1.3,f.23.11.1 77317,77318 1c0aA 585 6.86e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1v6tA 255 6.94e+01 1aroL 151 6.96e+01 1lba d.118.1.1 41063 1js8A 394 6.99e+01 a.86.1.1,b.112.1.1 67219,67220 1cye 129 6.99e+01 3chy c.23.1.1 31077 1t5jA 313 7.10e+01 a.209.1.1 99125 1l1eA 287 7.10e+01 c.66.1.18 73454 1txb 73 7.22e+01 1txb g.7.1.1 44455 2fpoA 202 7.28e+01 1xj4A 119 7.28e+01 1ahxA 396 7.30e+01 1ajsA c.67.1.1 34293 1vqb 87 7.33e+01 1gvp b.40.4.7 25370 1s0uA 408 7.40e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1ezvD 245 7.42e+01 1be3D a.3.1.3,f.23.11.1 59546,59547 1pswA 348 7.46e+01 c.87.1.7 88287 1t0aA 159 7.50e+01 1b96A 244 7.51e+01 1rvaA c.52.1.2 33268 2gvaA 87 7.53e+01 1gvp b.40.4.7 25389 1ml9A 302 7.55e+01 b.85.7.1 79282 1vhqA 232 7.62e+01 c.23.16.2 100696 1zeeA 403 7.64e+01 1r5jA 337 7.68e+01 c.77.1.5 97097 1vqoE 178 7.68e+01 1jalA 363 7.69e+01 c.37.1.8,d.15.10.2 84138,84139 1kn0A 212 7.74e+01 d.50.1.3 77444 2rveA 244 7.81e+01 1rvaA c.52.1.2 33283 1wkvA 389 7.85e+01 1fl9A 161 7.94e+01 c.37.1.18 70137 1arhA 396 7.97e+01 1ajsA c.67.1.1 34321 1azzA 226 7.99e+01 5ptp b.47.1.2 26072 1e6mA 128 8.03e+01 3chy c.23.1.1 31039 1g13A 162 8.14e+01 1g13A b.95.1.1 60194 1o0wA 252 8.21e+01 a.149.1.1,d.50.1.1 80751,80752 1ybiA 288 8.33e+01 1gvp 87 8.34e+01 1gvp b.40.4.7 25369 1ugnA 198 8.37e+01 b.1.1.4,b.1.1.4 107828,107829 1bssA 244 8.39e+01 1rvaA c.52.1.2 33256 1xmxA 385 8.49e+01 1wdcC 156 8.49e+01 1wdcC a.39.1.5 17317 1uldA 150 8.60e+01 b.29.1.3 99545 3chy 128 8.63e+01 3chy c.23.1.1 31038 1qxoA 388 8.64e+01 d.258.1.1 96539 1cjbA 231 8.72e+01 1qk3A c.61.1.1 34079 1lckA 175 8.75e+01 1lckA b.34.2.1,d.93.1.1 24552,40421 1wy5A 317 8.78e+01 2cmd 312 8.96e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1oy1A 228 8.98e+01 c.23.16.2 87548