# List of top-scoring protein chains for t2k-100-30-alpha-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.soe.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 3huiA 126 6.05e-01 1sayA 361 1.85e+00 1sayA c.2.1.4,c.23.12.2 30102,31362 2ko6A 89 1.85e+00 1qpbA 563 1.86e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 3cqcB 227 1.98e+00 1pjcA 361 2.05e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 2vk8A 563 2.24e+00 1mo2A 294 2.46e+00 c.69.1.22 79331 1fr2B 134 2.62e+00 d.4.1.1 83257 1pydA 556 2.72e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1pjaA 302 2.73e+00 c.69.1.13 94758 1pvdA 537 2.91e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1qwtA 255 3.50e+00 b.26.1.3 96501 3lfkA 129 3.72e+00 1itwA 741 3.74e+00 c.77.1.2 76793 3bhwA 209 4.19e+00 1emvB 134 4.27e+00 1bxiB d.4.1.1 37135 2gykB 134 4.62e+00 d.4.1.1 135857 1dfoA 417 4.67e+00 1bj4A c.67.1.4 34480 2peqA 134 5.20e+00 a.280.1.1 149443 3dm8A 143 5.21e+00 d.17.4.20 157804 3gbxA 420 5.94e+00 3c1qA 123 5.98e+00 2vlqB 134 6.19e+00 1fzdA 201 6.78e+00 3fib d.171.1.1 42484 3d5lA 221 7.89e+00 3kdqA 154 8.17e+00 2rfrA 155 8.69e+00 d.17.4.28 152000 1oalA 151 8.82e+00 b.1.8.1 86739 3dxqA 301 9.04e+00 3fncA 163 9.34e+00 2dtxA 264 9.90e+00 2jhmF 218 1.01e+01 1dx4A 586 1.02e+01 2bce c.69.1.1 34622 2rinA 298 1.04e+01 1hxvA 113 1.08e+01 d.26.1.1 71089 3loyA 633 1.10e+01 2wnpF 217 1.11e+01 1b4fA 82 1.13e+01 1b4fA a.60.1.2 17934 1yaiA 151 1.14e+01 1yaiA b.1.8.1 22289 1zetA 388 1.16e+01 d.240.1.1,e.8.1.7 124997,124998 2gf4A 100 1.21e+01 a.8.10.1 135074 3i04A 673 1.24e+01 1m70A 190 1.28e+01 a.3.1.4,a.3.1.4 91200,91201 2j5zA 221 1.33e+01 2qsfX 171 1.34e+01 3hinA 275 1.42e+01 1ru3A 732 1.42e+01 e.26.1.3 97835 2aplA 157 1.45e+01 a.258.1.1 127132 1uddA 226 1.45e+01 a.132.1.3 107776 2qzqA 152 1.51e+01 2alzA 390 1.51e+01 d.240.1.1,e.8.1.7 126994,126995 3h40A 389 1.53e+01 3g6xA 420 1.55e+01 2jexA 209 1.57e+01 2i4lA 458 1.60e+01 2dpiA 420 1.61e+01 d.240.1.1,e.8.1.7 131612,131613 3gv5B 420 1.65e+01 1r5mA 425 1.70e+01 3h4dA 390 1.76e+01 2g5dA 422 1.76e+01 b.52.1.4 147083 1l8rA 101 1.79e+01 a.6.1.4 73700 2hi2A 158 1.79e+01 1oaoA 674 1.80e+01 e.26.1.2 86744 3k2yA 109 1.85e+01 2d39A 237 1.87e+01 3f8mA 248 1.89e+01 1keaA 221 1.92e+01 a.96.1.2 68491 1f0yA 302 1.98e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 3e0jB 144 2.02e+01 2z7eA 157 2.16e+01 3ct7A 231 2.18e+01 2hdhA 293 2.21e+01 2hdhA a.100.1.3,c.2.1.6 18795,30199 3fc7A 125 2.21e+01 1zx2A 147 2.22e+01 d.17.4.2 146033 2regA 298 2.30e+01 1rhs 296 2.31e+01 1rhs 1rhsA 296 2.31e+01 c.46.1.2,c.46.1.2 32703,32704 2r7rA 1095 2.38e+01 3kraB 274 2.39e+01 2pil 159 2.40e+01 2pil 2fsjA 346 2.45e+01 c.55.1.12,c.55.1.12 134025,134026 1csyA 112 2.46e+01 1lckA d.93.1.1 40519 3hadA 308 2.50e+01 2hdhA a.100.1.3,c.2.1.6 18799,30203 1wudA 89 2.51e+01 a.60.8.1 121283 1tqyA 424 2.54e+01 c.95.1.1,c.95.1.1 107245,107246 1jcfA 344 2.58e+01 c.55.1.1,c.55.1.1 62878,62879 3e38A 343 2.64e+01 2wojA 354 2.64e+01 2pvpA 367 2.72e+01 3lnoA 108 2.74e+01 3bvsA 239 2.76e+01 2djkA 133 2.91e+01 c.47.1.2 131548 1ly7A 121 2.91e+01 d.82.2.1 74339 3k9iA 117 2.97e+01 1ekgA 127 3.01e+01 1dlxA d.82.2.1 40021 1jroA 462 3.03e+01 a.56.1.1,d.15.4.2,d.87.2.1,d.145.1.3 67137,67138,67139,67140 2ewfA 610 3.05e+01 3fo3A 525 3.06e+01 3ctdA 213 3.07e+01 a.80.1.2 156981 1ac1A 189 3.08e+01 1fvkA c.47.1.13 90326 1gtfA 74 3.10e+01 b.82.5.1 70460 1rqjA 299 3.16e+01 a.128.1.1 97744 3kusA 88 3.17e+01 1s4uX 407 3.28e+01 b.69.4.1 112027 2gmnA 274 3.35e+01 d.157.1.1 147132 2x49A 333 3.35e+01 3ctlA 231 3.36e+01 1pgjA 478 3.38e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1yqyA 523 3.45e+01 d.92.1.14,d.166.1.1 123903,123904 3eucA 367 3.51e+01 1fvkA 189 3.53e+01 1fvkA c.47.1.13 90351 2uuzA 99 3.61e+01 2rkqA 169 3.67e+01 2cvkA 110 3.70e+01 1irzA 64 3.70e+01 a.4.1.11 76772 2bjoA 136 3.73e+01 1moq 368 3.74e+01 1moq 1moqA 368 3.74e+01 c.80.1.1 35302 1zy4A 303 3.75e+01 1a81A 254 3.81e+01 1a81A d.93.1.1,d.93.1.1 40507,40508 1e12A 253 3.87e+01 1c3wA f.13.1.1 43428 1wyjA 125 3.88e+01 2yzuA 109 3.98e+01 2x04A 80 4.09e+01 1i5pA 633 4.12e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 2nn6B 249 4.14e+01 d.14.1.4,d.101.1.1 148297,148298 2qiyA 154 4.29e+01 d.17.4.2 150815 1fc4A 401 4.30e+01 1bs0A c.67.1.4 59760 2c5rA 67 4.32e+01 a.251.1.1 129944 2scpA 174 4.33e+01 2scpA a.39.1.5 17256 1ehwA 162 4.34e+01 1npk d.58.6.1 39088 3pmgA 561 4.36e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1kcqA 104 4.36e+01 d.109.1.1 68449 3g3lA 327 4.36e+01 2v7kA 361 4.36e+01 1iynA 295 4.40e+01 a.93.1.1 90722 1wkaA 147 4.44e+01 b.51.1.1 120978 1n62A 166 4.46e+01 a.56.1.1,d.15.4.2 80090,80091 2wff1 246 4.49e+01 3e4rA 324 4.57e+01 2pnfA 248 4.63e+01 1gdtA 183 4.63e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 2nnuA 205 4.65e+01 b.91.1.1 138401 2o9pA 454 4.72e+01 1kezA 300 4.76e+01 c.69.1.22 68546 1tp4A 97 4.77e+01 a.189.1.1 107183 3c7mA 195 4.78e+01 2zeqA 78 4.83e+01 d.15.1.1 154405 1uhnA 189 4.92e+01 a.39.1.5 99399 3c25A 383 4.97e+01 2tct 207 4.98e+01 2tct 2hxjA 144 4.99e+01 a.136.1.1 147432 3fxvA 233 5.05e+01 2vkeA 208 5.06e+01 a.4.1.9,a.121.1.1 153221,153222 2jafA 274 5.10e+01 1gxmA 332 5.14e+01 a.102.5.1 76371 1vyxA 60 5.15e+01 g.44.1.3 114033 1whsB 153 5.21e+01 1whtB 3d01A 165 5.22e+01 3k26A 366 5.23e+01 2a6mA 155 5.25e+01 d.58.57.1 126287 1dtoA 221 5.25e+01 1dtoA b.91.1.1 28405 1p3dA 475 5.36e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1r7lA 110 5.42e+01 d.277.1.1 104837 3iiwA 365 5.43e+01 2wp8A 305 5.44e+01 2b8nA 429 5.46e+01 c.118.1.1 128093 2p67A 341 5.47e+01 c.37.1.10 149269 1akyA 220 5.52e+01 c.37.1.1,g.41.2.1 31896,45197 1ta8A 332 5.56e+01 d.142.2.2 112375 2juyA 28 5.57e+01 1g9lA 144 5.62e+01 1g9lA a.144.1.1 60399 1whtB 153 5.67e+01 1whtB 2d0eA 407 5.70e+01 1l5aA 436 5.72e+01 c.43.1.2,c.43.1.2 75923,75924 3h0lB 478 5.73e+01 1qkrA 188 5.77e+01 1qkrA a.24.9.1 16628 3eetA 274 5.78e+01 3cjkB 75 5.86e+01 1bcsB 160 5.88e+01 1whtB 3ieyB 153 5.90e+01 3i4fA 264 5.91e+01 2qywA 102 5.99e+01 1w0mA 226 6.01e+01 c.1.1.1 109027 2w1vA 276 6.03e+01 2d09A 407 6.07e+01 1x93A 55 6.09e+01 a.43.1.3 145859 2vkjA 106 6.15e+01 1y8aA 332 6.17e+01 c.108.1.24 145913 1hgeB 175 6.17e+01 1hgeB h.3.1.1 45680 1gdeA 389 6.22e+01 c.67.1.1 60456 2ot4A 525 6.25e+01 3f27D 83 6.28e+01 1r03A 182 6.30e+01 a.25.1.1 104675 1mykA 53 6.35e+01 1bazA a.43.1.1 17425 1s1fA 406 6.37e+01 a.104.1.1 112008 3l6dA 306 6.46e+01 1vkeA 133 6.50e+01 a.152.1.2 108650 3c6fA 153 6.54e+01 2viuB 175 6.54e+01 1hgeB h.3.1.1 45676 2ivnA 330 6.56e+01 3ismC 359 6.57e+01 1zcjA 463 6.57e+01 1kpfA 125 6.63e+01 d.13.1.1 37507 2extA 77 6.63e+01 b.82.5.1 132563 2z1eA 342 6.65e+01 d.79.4.1,d.139.1.1 153932,153933 1kpf 126 6.73e+01 1kpf 1b97A 244 6.74e+01 1rvaA c.52.1.2 33252 3lwsA 357 6.78e+01 1q0uA 219 6.78e+01 c.37.1.19 95512 2x75A 431 6.79e+01 1bdtA 53 6.80e+01 1bazA a.43.1.1 17433 3h35A 185 6.84e+01 2vjvA 159 6.96e+01 d.58.57.1 153201 1rm6C 161 7.11e+01 a.56.1.1,d.15.4.2 111876,111877 2w87A 139 7.11e+01 1rhxA 87 7.17e+01 c.114.1.2 111805 1wh8A 111 7.26e+01 a.35.1.7 114636 3ei9A 432 7.29e+01 1j7nA 776 7.38e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 3hh1A 117 7.38e+01 1r0dA 206 7.43e+01 a.216.1.1 104715 1bazA 53 7.43e+01 1bazA a.43.1.1 17421 2p19A 149 7.45e+01 d.190.1.2 149156 1u3aA 189 7.50e+01 c.47.1.13 119504 1f8xA 157 7.56e+01 1f8xA c.23.14.1 31397 1bgf 124 7.67e+01 1bgf 1bgfA 124 7.67e+01 a.90.1.1 18537 1rv3A 483 7.71e+01 c.67.1.4 105101 1im5A 180 7.80e+01 c.33.1.3 66211 1ha0A 494 7.85e+01 1hgeA b.19.1.2,h.3.1.1 23824,45697 2ekpA 239 7.86e+01 2p71A 132 7.98e+01 a.39.2.1 139516 3kxeA 110 7.99e+01