# 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 1psuA 140 2.49e-17 d.38.1.5 88285 2fs2A 151 2.64e-17 1wluA 136 9.78e-15 1j1yA 136 1.10e-14 d.38.1.5 90776 1zkiA 133 2.39e-14 2b6eA 146 8.86e-13 1o0iA 138 2.10e-12 d.38.1.5 86532 1vh5A 148 8.00e-12 d.38.1.5 100642 1yliA 153 1.93e-11 1q4uA 151 5.37e-11 d.38.1.5 95828 1ixlA 131 2.63e-10 d.38.1.5 90717 1vpmA 169 3.11e-09 2gvhA 288 4.44e-09 1yocA 147 8.15e-07 2cyeA 133 3.65e-06 1sh8A 154 5.75e-06 d.38.1.5 105549 1s5uA 138 1.11e-05 d.38.1.1 98573 1njkA 156 1.15e-05 d.38.1.1 85818 2av9A 147 4.98e-05 1t82A 155 5.40e-05 d.38.1.5 106639 1z54A 132 1.08e-04 1u1zA 168 1.35e-04 d.38.1.6 107602 2b3nA 159 1.56e-04 1c8uA 285 4.94e-04 1c8uA d.38.1.3,d.38.1.3 38547,38548 2cwzA 141 1.09e-03 1z6bA 154 1.31e-03 1iq6A 134 3.21e-03 d.38.1.4 76755 2gf6A 135 6.90e-03 1lo7A 141 3.24e-02 d.38.1.1 74144 2essA 248 3.84e-02 1tbuA 118 3.99e-02 2bi0A 337 5.00e-02 1bvqA 141 5.35e-02 1bvqA d.38.1.1 38542 1mkaA 171 6.01e-02 1mkaA d.38.1.2 38543 2aliA 158 1.09e-01 1yycA 174 6.52e-01 2b59A 187 8.42e-01 2bm3A 166 9.92e-01 1l0wA 580 1.06e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 3proC 166 1.95e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1zo2A 129 1.96e+00 1n9pA 207 2.43e+00 b.1.18.16 80343 1y9qA 192 2.47e+00 3proD 166 2.59e+00 3proC d.52.1.1,d.52.1.1 38814,38815 2f57A 317 2.88e+00 1w9hA 427 3.15e+00 1pn2A 280 3.79e+00 d.38.1.4,d.38.1.4 94930,94931 1w6nA 134 4.73e+00 1q7lA 198 4.81e+00 c.56.5.4 96044 1rbp 182 5.41e+00 1aqb b.60.1.1 27085 1c0aA 585 5.51e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1sltB 134 6.19e+00 1c1lA b.29.1.3 24187 1slaA 134 6.21e+00 1c1lA b.29.1.3 24196 1mdc 133 7.03e+00 1hmt b.60.1.2 27198 1sltA 134 7.25e+00 1c1lA b.29.1.3 24186 2c30A 321 7.48e+00 1xnkA 196 8.06e+00 1u94A 356 9.18e+00 c.37.1.11,d.48.1.1 107743,107744 1tf4A 605 9.40e+00 1tf4A a.102.1.2,b.2.2.2 18827,22393 1sdjA 310 9.46e+00 d.21.1.2,d.21.1.2 98807,98808 1se8A 301 9.54e+00 b.40.4.3 105448 1h1aA 191 9.59e+00 b.29.1.11 83450 1i78A 297 9.83e+00 f.4.4.1 66046 2gr8A 99 1.01e+01 1nox 205 1.11e+01 1nox d.90.1.1 40242 2f86B 143 1.29e+01 2hgsA 474 1.33e+01 2hgsA c.30.1.4,d.142.1.6 31722,75997 1jjyA 636 1.35e+01 1jjyA 1su8A 636 1.35e+01 e.26.1.2 98999 1icxA 155 1.42e+01 d.129.3.1 71191 2fg1A 158 1.42e+01 1f5mB 180 1.46e+01 1f5mB d.110.2.1 40896 1f5mA 180 1.48e+01 1f5mB d.110.2.1 40895 1g87A 614 1.57e+01 a.102.1.2,b.2.2.2 83275,83276 1vrbA 342 1.59e+01 2fauA 341 1.59e+01 1eqkA 102 1.60e+01 1eqkA d.17.1.2 37998 1gzwA 134 1.63e+01 b.29.1.3 90535 2cu6A 103 1.76e+01 2fibA 269 1.80e+01 3fib d.171.1.1 42457 1eysH 259 1.81e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 2afcA 168 1.84e+01 1xypA 190 1.85e+01 1axkA b.29.1.11 24327 3fib 249 1.95e+01 3fib d.171.1.1 42455 1kzfA 230 1.96e+01 d.108.1.3 73354 1aqb 183 1.97e+01 1aqb b.60.1.1 27084 1fib 269 1.98e+01 3fib d.171.1.1 42456 1vehA 92 2.06e+01 2fyxA 143 2.08e+01 1xkpC 143 2.12e+01 1ygaA 342 2.12e+01 1g0dA 695 2.13e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 1lurA 339 2.13e+01 b.30.5.4 84717 1v7rA 186 2.20e+01 c.51.4.1 100482 1b65A 375 2.21e+01 1b65A d.154.1.1 42020 2b20A 403 2.31e+01 1fqtA 112 2.44e+01 1fqtA b.33.1.1 24441 1f1sA 814 2.49e+01 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 2fm8A 135 2.49e+01 1kt6A 183 2.50e+01 b.60.1.1 84466 1k3eA 156 2.51e+01 d.198.1.1 68103 1hbp 183 2.52e+01 1aqb b.60.1.1 27079 1tyjA 170 2.62e+01 1pqzA 238 2.63e+01 b.1.1.2,d.19.1.1 104297,104298 1hbq 183 2.66e+01 1aqb b.60.1.1 27078 1n6zA 105 2.76e+01 d.263.1.1 85369 1o9yA 84 2.80e+01 b.139.1.1 92692 1jr7A 311 2.88e+01 b.82.2.3 63255 1aqdB 198 2.88e+01 1iakB b.1.1.2,d.19.1.1 21586,38160 1kwkA 645 2.88e+01 b.71.1.1,c.1.8.1,c.23.16.5 77565,77566,77567 1b8aA 438 2.90e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1kwgA 645 2.95e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1q7fA 286 3.11e+01 b.68.9.1 96036 1o94A 729 3.20e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1s7iA 124 3.21e+01 d.58.4.9 105353 1qyaA 307 3.24e+01 d.21.1.2,d.21.1.2 104653,104654 1vqwA 457 3.24e+01 2reb 352 3.26e+01 2reb c.37.1.11,d.48.1.1 32282,38767 2ac5A 316 3.28e+01 1ibvB 229 3.32e+01 2pelA 236 3.34e+01 1led b.29.1.1 24082 1m2rA 327 3.38e+01 d.144.1.7 84760 2ac3A 316 3.49e+01 1lpuA 332 3.56e+01 d.144.1.7 74177 1vhsA 175 3.66e+01 d.108.1.1 100698 1djnA 729 3.69e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1vr5A 547 3.71e+01 1q3lA 69 3.73e+01 1nnxA 109 3.73e+01 b.40.10.1 92013 1vcaA 202 3.76e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1o20A 427 3.77e+01 c.82.1.1 86556 1io1A 398 3.78e+01 1io1A e.32.1.1 62611 1djqA 729 3.79e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1pyaB 228 3.88e+01 1pyaB 1ltlA 279 3.93e+01 b.40.4.11 84701 1lwjA 441 3.96e+01 b.71.1.1,c.1.8.1 74303,74304 1uwvA 433 4.00e+01 b.40.4.12,c.66.1.40 100128,100129 1enxA 190 4.03e+01 1axkA b.29.1.11 24325 2oneA 436 4.08e+01 4enl c.1.11.1,d.54.1.1 29203,38847 1rpyA 114 4.10e+01 d.93.1.1 97718 1umhA 184 4.15e+01 b.18.1.21 99605 1hdr 244 4.16e+01 1dhr c.2.1.2 29837 1rz2A 254 4.17e+01 b.100.1.1 105130 1xdfA 157 4.19e+01 1oneA 436 4.23e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1ww7A 160 4.25e+01 7taa 478 4.31e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1zglB 192 4.34e+01 1knaA 69 4.35e+01 b.34.13.2 72771 1hgeA 328 4.46e+01 1hgeA b.19.1.2 23816 2al1A 436 4.48e+01 4enl 436 4.49e+01 4enl c.1.11.1,d.54.1.1 29202,38846 2al2A 436 4.50e+01 1a6o 332 4.62e+01 1a6o 2fmmA 74 4.65e+01 2viuA 328 4.69e+01 1hgeA b.19.1.2 23797 1jotA 133 4.75e+01 1jotA 1p6pA 125 4.90e+01 b.60.1.2 87839 1rz1A 161 4.99e+01 b.45.1.2 98124 2fxqA 264 5.05e+01 1aol 228 5.09e+01 1aol b.20.1.1 23840 1yezA 68 5.18e+01 1lp4A 332 5.25e+01 d.144.1.7 74170 1om1A 332 5.53e+01 d.144.1.7 93347 2tmdA 729 5.61e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1uasA 362 5.78e+01 b.71.1.1,c.1.8.1 88388,88389 1mzyA 333 5.82e+01 b.6.1.3,b.6.1.3 103848,103849 1iq4A 179 5.87e+01 1iq4A d.77.1.1 62641 2bolA 314 5.91e+01 1ve4A 206 5.92e+01 3cox 507 5.94e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 2cwaA 263 5.95e+01 1ifc 132 6.00e+01 b.60.1.2 27173 1coy 507 6.00e+01 1b8sA c.3.1.2,d.16.1.1 30333,37864 1owfB 94 6.21e+01 a.55.1.1 87488 1sceA 112 6.27e+01 1puc d.97.1.1 40676 1qttA 117 6.31e+01 1a1x b.63.1.1 27516 3hmgA 328 6.43e+01 1hgeA b.19.1.2 23825 1wbpA 397 6.45e+01 1n9lA 109 6.46e+01 d.110.3.6 85468 1ihfB 94 6.50e+01 1huuA a.55.1.1 17894 1iyxA 432 6.61e+01 c.1.11.1,d.54.1.1 83815,83816 1w6tA 444 6.64e+01 1s1dA 331 6.67e+01 b.67.3.1 98344 1f2hA 169 6.67e+01 1f3vA d.58.22.1 59612 1ry9A 145 6.68e+01 d.198.1.1 98094 1yr0A 175 6.70e+01 2tpt 440 6.73e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1j1bA 420 6.77e+01 d.144.1.7 90758 2bw2A 140 6.79e+01 1obpA 159 6.80e+01 1obpA b.60.1.1 27092 1r0pA 312 6.81e+01 d.144.1.7 96734 1jssA 224 6.91e+01 d.129.3.2 71844 1msc 129 6.97e+01 1msc d.85.1.1 40039 2bklA 695 7.07e+01 1d5mB 192 7.12e+01 1iakB b.1.1.2,d.19.1.1 21618,38192 1blxA 326 7.13e+01 1hcl d.144.1.7 41596 1yal 218 7.20e+01 1cs8A d.3.1.1 37025 1ksiB 642 7.23e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24409,38045,38046 1b8sA 504 7.26e+01 1b8sA c.3.1.2,d.16.1.1 30335,37866 1te6A 439 7.28e+01 c.1.11.1,d.54.1.1 106797,106798 1sjyA 159 7.33e+01 d.113.1.1 98900 1zthA 258 7.35e+01 1mxtA 504 7.35e+01 c.3.1.2,d.16.1.1 79671,79672 1n1pA 504 7.37e+01 c.3.1.2,d.16.1.1 91546,91547 1n4wA 504 7.37e+01 c.3.1.2,d.16.1.1 91676,91677 2fytA 340 7.39e+01 1fmaE 150 7.48e+01 1fmaE d.41.5.1 38630 1mqoA 227 7.50e+01 d.157.1.1 103846 1b4vA 504 7.52e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1ecfA 504 7.55e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ecfB 504 7.57e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1mmiA 366 7.62e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1o6vA 466 7.62e+01 b.1.18.15,c.10.2.1 81099,81100 1xezA 721 7.64e+01 1ijhA 504 7.64e+01 c.3.1.2,d.16.1.1 66161,66162 1s68A 249 7.66e+01 d.142.2.4 98591 1nbcA 155 7.74e+01 1nbcA b.2.2.2 22390 1e0tA 470 7.77e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2akzA 439 7.81e+01 1bjt 793 7.82e+01 1bjt e.11.1.1 43249 1od3A 168 7.88e+01 b.18.1.10 86825 1ksiA 642 7.95e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 2aalA 131 7.95e+01 1pfsA 78 8.00e+01 1pfsA b.40.4.7 25391 1e2tA 284 8.11e+01 1e2tA d.3.1.5 37121 1snzA 344 8.30e+01 b.30.5.4 98930 1cr5A 189 8.30e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1h6tA 291 8.31e+01 b.1.18.15,c.10.2.1 65686,65687 1vp2A 208 8.33e+01 2bwqA 129 8.39e+01 1gypA 358 8.42e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1yroB 286 8.44e+01 2agdA 287 8.49e+01 1vkwA 218 8.49e+01 d.90.1.2 108695 1kskA 234 8.55e+01 d.66.1.5,d.265.1.3 72920,90389 1buhB 79 8.57e+01 1puc d.97.1.1 40686 1o6sA 466 8.67e+01 b.1.18.15,c.10.2.1 81094,81095 1ay2 159 8.77e+01 2pil d.24.1.1 38377 1m0wA 491 8.78e+01 c.30.1.4,d.142.1.6 78363,78364 2pil 159 8.79e+01 2pil d.24.1.1 38376 1wlyA 333 8.91e+01