# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1b47A 304 7.54e-02 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 2cblA 305 1.87e-01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 2occJ 59 7.18e-01 2occJ f.23.4.1 43524 1d3uB 201 7.40e-01 1aisB a.74.1.2 18386 a.74.1.2 18387 1g1eB 89 7.95e-01 1g1eB a.59.1.1 17931 1ei9A 279 8.14e-01 1ei9A c.69.1.13 34713 1s9aA 257 1.03e+00 1v54J 59 1.07e+00 f.23.4.1 -12112 1nozA 388 1.18e+00 1clqA c.55.3.5 33715 1trkA 680 1.30e+00 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1gpuA 680 1.36e+00 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1kaeA 434 1.43e+00 c.82.1.2 72247 1ehkC 33 1.48e+00 1ehkC f.23.9.1 43626 1ibvB 229 1.61e+00 1tkaA 678 1.68e+00 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 1k75A 434 1.78e+00 c.82.1.2 68253 1noyA 388 2.25e+00 1clqA c.55.3.5 33713 1pyaB 228 2.29e+00 1pyaB 1aisB 200 2.32e+00 1aisB a.74.1.2 18384 a.74.1.2 18385 1muyA 225 2.38e+00 1mun a.96.1.2 18745 1ehyA 294 2.66e+00 1ehyA c.69.1.11 34693 1mun 225 2.70e+00 1mun a.96.1.2 18744 1jggA 60 2.72e+00 2hddA a.4.1.1 62950 1ekeA 230 2.84e+00 1ekeA c.55.3.1 33572 1dk8A 147 2.95e+00 1agrE a.91.1.1 18548 1i50A 1733 3.60e+00 e.29.1.2 61754 1top 162 4.04e+00 1ncx a.39.1.5 17223 1jdqA 98 4.15e+00 d.68.3.3 66559 1e3dB 542 4.37e+00 1h2rL e.18.1.1 59189 1dioB 224 4.52e+00 1dioB c.51.3.1 33219 1eexB 224 4.53e+00 1dioB c.51.3.1 33213 1ucpA 91 4.85e+00 unknown_sccs -1193 1nubA 229 4.94e+00 1sra a.39.1.3 17191 g.3.11.3 44330 unknown_sccs 44715 1aew 174 5.23e+00 2fha a.25.1.1 16676 1lvwA 295 5.42e+00 c.68.1.6 84723 1ncx 162 5.43e+00 1ncx a.39.1.5 17222 1ggwA 140 5.46e+00 1ggwA a.39.1.5 60490 1dat 174 5.56e+00 2fha a.25.1.1 16677 1b25A 619 5.84e+00 1b25A a.110.1.1 19044 d.152.1.1 41796 1cx4A 305 6.16e+00 b.82.3.2 59099 b.82.3.2 59100 1c8kA 842 6.25e+00 1a8i c.87.1.4 35491 1dd3A 128 6.41e+00 1dd3C a.108.1.1 19031 d.45.1.1 38760 1h5uA 842 6.79e+00 1a8i c.87.1.4 60655 1hkhA 279 6.98e+00 c.69.1.12 -8342 1e5eA 404 7.22e+00 1ibjA c.67.1.3 59265 1thg 544 7.37e+00 1thg c.69.1.17 34763 1g8iA 190 7.48e+00 1rec a.39.1.5 60363 1pufB 73 7.61e+00 a.4.1.1 -192 1q18A 332 7.64e+00 1kv9A 668 7.76e+00 a.3.1.6 73056 b.70.1.1 73057 1gpb 842 8.51e+00 1a8i c.87.1.4 35478 1ci9A 392 8.55e+00 e.3.1.1 64767 1ac5 483 8.59e+00 1ac5 c.69.1.5 34653 1iw8A 231 8.74e+00 a.111.1.1 76866 1e9lA 377 8.88e+00 1e9lA c.1.8.5 59395 d.26.3.1 59396 1ijyA 130 9.45e+00 1ijxA a.141.1.1 62517 1e0cA 271 9.72e+00 1e0cA c.46.1.2 32717 c.46.1.2 32718 1od2A 805 9.84e+00 c.14.1.4 86821 c.14.1.4 86822 1j03A 102 1.04e+01 unknown_sccs -10954 1sv7A 109 1.07e+01 1a8i 842 1.13e+01 1a8i c.87.1.4 35490 1pufA 77 1.14e+01 a.4.1.1 -191 1fha 183 1.15e+01 2fha a.25.1.1 16675 2fha 183 1.15e+01 2fha a.25.1.1 16674 1jf2A 195 1.15e+01 1ej3A a.39.1.5 62930 2occM 46 1.16e+01 2occM f.23.7.1 43527 1rgs 288 1.17e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1k4mA 213 1.18e+01 c.26.1.3 77258 1p65A 73 1.19e+01 unknown_sccs -10331 1m1eB 81 1.23e+01 a.161.1.1 78400 1pq1B 33 1.26e+01 1ggzA 148 1.27e+01 a.39.1.5 70176 1fzkA 274 1.27e+01 1agdA b.1.1.2 60149 d.19.1.1 60150 1h6pA 203 1.27e+01 a.146.1.1 60690 2pvbA 107 1.31e+01 1a75A a.39.1.4 17205 1rl4A 188 1.31e+01 d.167.1.1 -11593 1ffyA 917 1.32e+01 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 1.32e+01 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1cfzA 162 1.33e+01 1cfzA c.56.1.1 33754 1ax4A 467 1.33e+01 1ax4A c.67.1.2 34391 1crl 534 1.37e+01 1thg c.69.1.17 34765 1j1bA 420 1.38e+01 d.144.1.7 -11312 1enh 54 1.39e+01 2hddA a.4.1.1 15973 1osa 148 1.40e+01 1cll a.39.1.5 17300 1n93X 375 1.41e+01 unknown_sccs -1540 1b79A 119 1.44e+01 1b79A a.81.1.1 18451 1sqgA 429 1.48e+01 1v54M 46 1.56e+01 f.23.7.1 -12124 1as4A 341 1.58e+01 1sek e.1.1.1 42623 1chuA 540 1.59e+01 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1o89A 345 1.63e+01 b.35.1.2 -3703 c.2.1.1 -5727 1exrA 148 1.63e+01 1cll a.39.1.5 17299 1lb3A 182 1.63e+01 a.25.1.1 77873 1g4yR 148 1.64e+01 1cll a.39.1.5 60252 1il6 185 1.64e+01 1alu a.26.1.1 16827 1h96A 182 1.67e+01 2fha a.25.1.1 60811 1b72B 87 1.68e+01 1akhA a.4.1.1 16001 1esmA 316 1.69e+01 1esmA c.37.1.6 31953 1aj8A 371 1.73e+01 1aj8A a.103.1.1 18900 1uouA 474 1.76e+01 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1mgn 154 1.78e+01 1a6m a.1.1.2 15097 1lit 144 1.79e+01 1qddA d.169.1.1 42325 1sra 151 1.80e+01 1sra a.39.1.3 17190 1agdA 276 1.86e+01 1agdA b.1.1.2 20741 d.19.1.1 38260 1n55A 251 1.89e+01 c.1.1.1 80007 1cll 148 1.89e+01 1cll a.39.1.5 17263 1fzoA 274 1.92e+01 1agdA b.1.1.2 60155 d.19.1.1 60156 1lk2A 274 1.92e+01 b.1.1.2 -2610 d.19.1.1 -9365 1jbaA 204 1.92e+01 1rec a.39.1.5 17330 1g7pA 274 1.93e+01 b.1.1.2 70153 d.19.1.1 70154 1kpuA 274 1.93e+01 b.1.1.2 84456 d.19.1.1 84457 1qddA 144 1.97e+01 1qddA d.169.1.1 42324 1otvA 259 1.98e+01 unknown_sccs -1915 1pal 108 2.00e+01 1a75A a.39.1.4 17209 1bxlA 181 2.01e+01 1maz f.1.4.1 43396 1k5dC 386 2.08e+01 c.10.1.2 68170 1brt 277 2.13e+01 1brt c.69.1.12 34699 1q8iA 783 2.15e+01 c.55.3.5 -7635 e.8.1.1 -11885 1k8kE 178 2.16e+01 a.148.1.1 68311 1ne6A 283 2.17e+01 b.82.3.2 -4918 b.82.3.2 -4919 1elkA 157 2.17e+01 1dvpA a.118.9.2 19217 1amk 251 2.17e+01 1amk c.1.1.1 28503 1jo0A 98 2.18e+01 d.68.4.1 77140 1b7eA 420 2.18e+01 1b7eA c.55.3.4 33680 1b0uA 262 2.20e+01 1b0uA c.37.1.12 32370 1ad6 185 2.20e+01 1guxA a.74.1.3 18390 1icrA 217 2.26e+01 1vfrA d.90.1.1 62274 1k5nA 276 2.31e+01 b.1.1.2 77266 d.19.1.1 77267 1l0oC 243 2.33e+01 a.4.13.2 73405 1fx4A 231 2.38e+01 1fx2A d.58.29.1 39431 1gd5A 130 2.38e+01 1gd5A d.189.1.1 60439 1i39A 225 2.42e+01 1ekeA c.55.3.1 61585 1k3lA 221 2.42e+01 a.45.1.1 77229 c.47.1.5 77230 1gseA 221 2.42e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1mumA 295 2.47e+01 c.1.12.7 85108 1keyA 235 2.49e+01 a.118.16.1 72389 1o08A 221 2.49e+01 c.108.1.6 86525 1pprM 312 2.52e+01 1pprM a.131.1.1 19502 a.131.1.1 19503 1t0gA 109 2.52e+01 unknown_sccs -10955 1rxqA 178 2.55e+01 1aye 401 2.56e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1alu 186 2.58e+01 1alu a.26.1.1 16826 1fpoA 171 2.59e+01 1fpoA a.2.3.1 15693 a.23.1.1 16487 1b22A 114 2.62e+01 1b22A a.60.4.1 17969 1d3hA 367 2.63e+01 1d3gA c.1.4.1 28601 1a6m 151 2.73e+01 1a6m a.1.1.2 15018 1bvp1 349 2.73e+01 1bvp1 1q41A 424 2.75e+01 d.144.1.7 -11308 1sqnA 261 2.75e+01 1pzlA 237 2.75e+01 1hybA 181 2.77e+01 1f9aA c.26.1.3 61399 1a28A 256 2.78e+01 1a28A a.123.1.1 19290 1dguA 183 2.79e+01 1dguA a.39.1.5 17333 1ysc 421 2.80e+01 1ivyA c.69.1.5 34652 1rf8B 100 2.92e+01 unknown_sccs -2005 1sr7A 259 2.96e+01 1r12A 258 2.97e+01 e.4.1.1 -11807 1ln4A 104 3.01e+01 d.68.4.1 74043 1d3gA 367 3.03e+01 1d3gA c.1.4.1 28600 1ca1 370 3.03e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1ei5A 520 3.04e+01 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1ftt 68 3.05e+01 2hddA a.4.1.1 15997 1ll7A 392 3.06e+01 c.1.8.5 78085 d.26.3.1 78086 1c9qA 117 3.07e+01 1c9qA g.52.1.1 45377 2sxl 88 3.08e+01 1b7fA d.58.7.1 39179 1vjnA 220 3.10e+01 unknown_sccs -11458 2hddA 61 3.15e+01 2hddA a.4.1.1 15971 1ithA 141 3.15e+01 1ithA a.1.1.2 15623 1js3A 486 3.21e+01 c.67.1.6 67215 1lvfA 110 3.27e+01 a.47.2.1 74280 1bgf 124 3.27e+01 1bgf a.90.1.1 18537 1d2kA 392 3.35e+01 1d2kA c.1.8.5 29008 d.26.3.1 38442 1qcrF 103 3.39e+01 1be3F f.27.1.1 43676 1hmcA 148 3.42e+01 1hmcB a.26.1.2 16867 1ppjF 110 3.49e+01 2ccyA 128 3.50e+01 2ccyA a.24.3.2 16544 1q87A 221 3.50e+01 unknown_sccs -12028 1vduA 172 3.52e+01 unknown_sccs -1651 1jr3E 334 3.52e+01 a.80.1.1 63253 c.37.1.20 63254 1gc0A 398 3.53e+01 c.67.1.3 70168 1jraA 117 3.57e+01 a.24.15.1 67117 3ygsP 97 3.57e+01 3ygsP a.77.1.3 18435 1rprA 63 3.59e+01 1nkd a.30.1.1 16989 1tph1 247 3.60e+01 1amk 1nt4A 391 3.63e+01 c.60.1.2 -7942 1mmoD 512 3.71e+01 1mhyD a.25.1.2 16770 1b9mA 265 3.72e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1i4fA 275 3.72e+01 1agdA b.1.1.2 61687 d.19.1.1 61688 1mbd 153 3.73e+01 1a6m a.1.1.2 15033 1a5t 334 3.74e+01 1a5t a.80.1.1 18450 c.37.1.20 32423 1b9rA 105 3.76e+01 1ayfA d.15.4.1 37683 1hlvA 131 3.79e+01 a.4.1.7 65854 a.4.1.7 65855 1jkw 323 3.83e+01 1jkw a.74.1.1 18356 a.74.1.1 18357 1mplA 349 3.85e+01 e.3.1.1 79387 1pwgA 349 3.87e+01 1ej2A 181 3.87e+01 1f9aA c.26.1.3 59414 1hvbA 349 3.90e+01 3pte e.3.1.1 42686 3pte 349 3.90e+01 3pte e.3.1.1 42687 1gjjA 168 3.93e+01 a.140.1.1 83291 a.140.1.1 83292 1brwA 433 3.94e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1us7B 265 3.95e+01 unknown_sccs -1518 1duzA 275 3.96e+01 1agdA b.1.1.2 20670 d.19.1.1 38224