# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1z2uA 150 8.43e-33 1x23A 155 4.54e-32 2ayvA 166 9.50e-32 1y6lA 149 1.67e-31 2bepA 159 3.32e-30 2e2c 156 2.66e-29 1u9aA d.20.1.1 38336 1jatA 155 4.03e-29 1u9aA d.20.1.1 62818 1jbbA 153 4.75e-29 1u9aA d.20.1.1 62842 1yh2A 175 5.64e-29 2ucz 165 1.22e-28 1u9aA d.20.1.1 38330 1fzyA 149 1.33e-28 d.20.1.1 65072 1u9aA 160 2.00e-28 1u9aA d.20.1.1 38333 1i7kA 179 2.76e-28 1u9aA d.20.1.1 61889 1fxtA 149 8.05e-27 d.20.1.1 65055 1zdnA 158 1.39e-26 1yrvA 169 4.20e-25 1yh6A 179 5.97e-25 1yf9A 171 1.72e-24 1wzvA 155 6.60e-24 2awfA 172 2.85e-23 2a4dA 160 2.14e-21 1j7dA 145 1.54e-20 1jatB d.20.1.1 62680 1jatB 138 2.37e-20 1jatB d.20.1.1 62819 1zuoA 186 1.86e-14 1s1qA 145 7.67e-05 d.20.1.2 98351 1uzxA 169 2.08e-03 d.20.1.2 100238 1kppA 145 4.56e-03 d.20.1.2 72846 2es9A 115 7.12e-02 1ois 223 6.62e-01 1a36A e.15.1.1 43267 1k3eA 156 8.61e-01 d.198.1.1 68103 1qhtA 775 1.19e+00 1tgoA c.55.3.5 33722 e.8.1.1 43011 1dvpA 220 1.27e+00 1dvpA a.118.9.2 19216 g.50.1.1 45358 1qqcA 773 1.43e+00 1tgoA c.55.3.5 33724 e.8.1.1 43013 1j7iA 264 2.06e+00 1j7iA d.144.1.6 62694 1ukxA 137 2.13e+00 d.20.1.3 107919 2c1dA 264 2.65e+00 1us7B 265 2.67e+00 a.205.1.1 99858 1vj7A 393 2.88e+00 a.211.1.1 100801 d.218.1.8 100802 1ai7A 209 3.09e+00 1ajqA d.153.1.2 41845 1nzyA 269 3.53e+00 1nzyA c.14.1.3 30903 1fx3A 169 3.80e+00 1fx3B d.33.1.1 38524 1ajqA 209 4.34e+00 1ajqA d.153.1.2 41840 1usuA 260 4.53e+00 d.14.1.8 99885 1h6hA 143 4.76e+00 d.189.1.1 65681 1jbkA 195 5.05e+00 c.37.1.20 71631 1jpzA 473 5.48e+00 a.104.1.1 67069 1gk9A 260 5.53e+00 d.153.1.2 65246 1fc3A 120 5.66e+00 1fc3A a.4.6.3 16237 1fx3B 169 6.20e+00 1fx3B d.33.1.1 38525 1srqA 341 6.38e+00 e.55.1.1 105967 1on2A 142 6.66e+00 a.4.5.24 87103 a.76.1.1 87104 1umkA 275 6.72e+00 1p32C 209 6.88e+00 1p32A d.25.1.1 38381 1qv9A 283 6.90e+00 c.127.1.1 96356 1upkA 341 7.60e+00 a.118.1.15 99758 1vf7A 369 7.77e+00 f.46.1.1 108557 1alu 186 8.33e+00 1alu a.26.1.1 16826 1q16B 512 8.85e+00 d.58.1.5 95548 1y5iB 512 9.01e+00 1ut1A 148 9.26e+00 b.2.3.6 108014 1ks8A 433 1.01e+01 a.102.1.2 77519 1hs6A 611 1.02e+01 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1vctA 205 1.06e+01 1wlmA 151 1.06e+01 1t5eA 360 1.07e+01 f.46.1.1 106436 1v9sA 208 1.07e+01 1m1eB 81 1.08e+01 a.161.1.1 78400 1su0B 159 1.16e+01 d.224.1.2 106015 1iynA 295 1.26e+01 a.93.1.1 90722 1pszA 303 1.26e+01 1toaA c.92.2.2 35600 1m9sA 605 1.34e+01 b.1.18.15 78874 b.34.11.1 78875 b.34.11.1 78876 b.34.11.1 78877 c.10.2.1 78878 2ae6A 166 1.37e+01 1qu1A 155 1.39e+01 1qu1A h.3.1.1 45670 1gakA 141 1.40e+01 1gakA a.19.1.1 16415 1poiA 317 1.48e+01 1poiA c.124.1.2 34153 1winA 143 1.53e+01 1ryc 294 1.54e+01 1ryc a.93.1.1 18601 2ac3A 316 1.55e+01 1p0yA 444 1.63e+01 a.166.1.1 87654 b.85.7.3 87655 1mlvA 444 1.65e+01 a.166.1.1 79283 b.85.7.3 79284 1qs0A 407 1.67e+01 1qs0A c.36.1.11 31829 1lj9A 144 1.73e+01 a.4.5.28 78035 1hg5A 289 1.75e+01 1hg5A a.7.8.2 90360 a.118.9.3 90361 1o5oA 221 1.77e+01 c.61.1.1 92509 1qhhA 167 1.79e+01 1pjr c.37.1.19 32393 1h3fA 432 1.84e+01 c.26.1.1 76631 d.66.1.4 76632 2bkkA 264 1.85e+01 1k94A 165 1.87e+01 a.39.1.8 68333 1yqcA 170 1.89e+01 1dseA 292 1.89e+01 1ryc a.93.1.1 59130 8prkA 287 1.89e+01 1wgjA b.40.5.1 25395 1htrB 329 1.94e+01 1smrA 1wteA 272 1.94e+01 1tf4A 605 2.01e+01 1tf4A a.102.1.2 18827 b.2.2.2 22393 1hg2A 289 2.01e+01 1hg5A a.7.8.2 90358 a.118.9.3 90359 1w94A 156 2.02e+01 1wgjA 286 2.05e+01 1wgjA b.40.5.1 25397 1ej8A 140 2.08e+01 1qupA b.1.8.1 22300 2pgd 482 2.15e+01 2pgd a.100.1.1 18778 c.2.1.6 30190 1e9gA 286 2.17e+01 1wgjA b.40.5.1 59393 2ac5A 316 2.19e+01 1b0pA 1231 2.28e+01 c.36.1.8 31831 c.36.1.12 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1qc7A 101 2.31e+01 1qc7A a.118.14.1 18456 1jenA 267 2.33e+01 1jenA 1gm7A 209 2.35e+01 d.153.1.2 65302 1ywmA 200 2.43e+01 1nnxA 109 2.52e+01 b.40.10.1 92013 1j7lA 264 2.54e+01 d.144.1.6 62697 1cpt 412 2.55e+01 1cpt a.104.1.1 18968 1fjgM 126 2.55e+01 1fjfM a.156.1.1 16293 1ufhA 180 2.55e+01 d.108.1.1 88485 1il6 185 2.56e+01 1alu a.26.1.1 16827 1hf8A 289 2.58e+01 1hg5A a.7.8.2 90354 a.118.9.3 90355 1kekA 1231 2.59e+01 c.36.1.8 68524 c.36.1.12 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1e9gB 286 2.69e+01 1wgjA b.40.5.1 59394 1lnwA 147 2.77e+01 a.4.5.28 78104 1q52A 314 2.77e+01 c.14.1.3 95846 1i7pA 274 2.80e+01 b.43.4.2 66048 c.25.1.1 66049 1zbyA 294 2.84e+01 1br0A 120 2.84e+01 a.47.2.1 17772 1pyiA 96 2.86e+01 1pyiA g.38.1.1 45079 h.1.3.1 45512 1y60A 169 2.88e+01 2arhA 203 2.95e+01 1kqwA 134 2.96e+01 b.60.1.2 72887 1crzA 403 2.98e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 2bzuA 181 2.99e+01 1f5nA 592 3.00e+01 1dg3A a.114.1.1 19077 c.37.1.8 32152 1wer 334 3.02e+01 1wer a.116.1.2 19108 1ds4A 292 3.05e+01 1ryc a.93.1.1 59129 1dlyA 164 3.07e+01 1dlyA a.1.1.1 14983 1nd4A 264 3.16e+01 d.144.1.6 91815 1jdrA 294 3.18e+01 1ryc a.93.1.1 62908 1dlc 584 3.19e+01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1se7A 83 3.20e+01 1on0A 158 3.21e+01 d.108.1.1 87095 1fm2A 169 3.24e+01 1fm2A d.153.1.2 59877 1jk0A 419 3.26e+01 a.25.1.2 63142 1ku2A 241 3.27e+01 a.4.13.1 83096 a.177.1.1 83097 1jvr 137 3.30e+01 1jvr a.61.1.2 18132 1ijtA 128 3.31e+01 1bfg b.42.1.1 62510 1z53A 294 3.34e+01 1jyhA 157 3.35e+01 d.60.1.3 71956 1ccg 291 3.36e+01 1ryc a.93.1.1 18627 1dg3A 592 3.45e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1w33A 181 3.45e+01 2tmkA 216 3.49e+01 3tmkA c.37.1.1 31928 1jb0F 164 3.50e+01 1jb0F f.23.16.1 62825 1fjgI 128 3.51e+01 1fjfI d.14.1.1 37559 1senA 164 3.52e+01 c.47.1.1 105465 1cp3A 277 3.52e+01 1pauA c.17.1.1 30992 1lokA 291 3.57e+01 c.56.5.4 78122 1molA 94 3.58e+01 1molA d.17.1.1 37988 1fqvJ 149 3.59e+01 1fqvD a.157.1.1 19266 d.42.1.1 38670 1or7A 194 3.62e+01 a.4.13.2 87332 a.177.1.1 87333 1ej5A 107 3.69e+01 1ej5A a.68.1.1 18268 7atjA 308 3.72e+01 1bgp a.93.1.1 18673 1stfI 98 3.74e+01 1stfI d.17.1.2 38006 1zeeA 403 3.76e+01 1dqeA 137 3.84e+01 1dqeA a.39.2.1 17388 1h7wD 1025 3.87e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1fa3A 96 3.89e+01 1molA d.17.1.1 37996 1bu7A 455 3.90e+01 1bu7A a.104.1.1 18937 1gt8C 1025 3.93e+01 a.1.2.2 70428 c.1.4.1 70429 c.3.1.1 70430 c.4.1.1 70431 d.58.1.5 70432