# List of top-scoring protein chains for t2k-100-30-str2 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 2cblA 305 7.28e-02 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1b47A 304 1.28e-01 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1g1eB 89 2.88e-01 1g1eB a.59.1.1 17931 1ei9A 279 9.90e-01 1ei9A c.69.1.13 34713 1k75A 434 1.01e+00 c.82.1.2 68253 2occJ 59 1.08e+00 2occJ f.23.4.1 43524 1lvwA 295 1.16e+00 c.68.1.6 84723 1v54J 59 1.23e+00 f.23.4.1 -12112 1mun 225 1.35e+00 1mun a.96.1.2 18744 1kaeA 434 1.40e+00 c.82.1.2 72247 1s9aA 257 1.67e+00 1aisB 200 1.67e+00 1aisB a.74.1.2 18384 a.74.1.2 18385 1ehkC 33 1.71e+00 1ehkC f.23.9.1 43626 1muyA 225 1.85e+00 1mun a.96.1.2 18745 1jggA 60 2.06e+00 2hddA a.4.1.1 62950 1top 162 2.18e+00 1ncx a.39.1.5 17223 1k5nA 276 2.30e+00 b.1.1.2 77266 d.19.1.1 77267 1keyA 235 2.37e+00 a.118.16.1 72389 1tkaA 678 2.67e+00 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 1gpuA 680 2.71e+00 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1ca1 370 2.73e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1p7gA 222 2.98e+00 a.2.11.1 -108 d.44.1.1 -9742 1trkA 680 3.11e+00 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1ncx 162 3.21e+00 1ncx a.39.1.5 17222 1cx4A 305 3.24e+00 b.82.3.2 59099 b.82.3.2 59100 1nozA 388 3.31e+00 1clqA c.55.3.5 33715 1pufA 77 3.58e+00 a.4.1.1 -191 1thg 544 3.63e+00 1thg c.69.1.17 34763 1ekeA 230 3.66e+00 1ekeA c.55.3.1 33572 1g4yR 148 3.67e+00 1cll a.39.1.5 60252 1hkhA 279 3.77e+00 c.69.1.12 -8342 1fzkA 274 3.85e+00 1agdA b.1.1.2 60149 d.19.1.1 60150 1ucpA 91 4.05e+00 unknown_sccs -1193 1nubA 229 4.22e+00 1sra a.39.1.3 17191 g.3.11.3 44330 unknown_sccs 44715 1ehyA 294 4.44e+00 1ehyA c.69.1.11 34693 1b72B 87 5.00e+00 1akhA a.4.1.1 16001 1gs5A 258 5.01e+00 c.73.1.2 70395 1bxlA 181 5.18e+00 1maz f.1.4.1 43396 1od2A 805 5.21e+00 c.14.1.4 86821 c.14.1.4 86822 1j03A 102 5.32e+00 unknown_sccs -10954 1e5eA 404 5.72e+00 1ibjA c.67.1.3 59265 1j1jA 240 5.83e+00 a.118.16.1 -1637 1dd3A 128 6.22e+00 1dd3C a.108.1.1 19031 d.45.1.1 38760 1pufB 73 6.27e+00 a.4.1.1 -192 1jdqA 98 6.29e+00 d.68.3.3 66559 1lk2A 274 6.31e+00 b.1.1.2 -2610 d.19.1.1 -9365 1kpuA 274 6.56e+00 b.1.1.2 84456 d.19.1.1 84457 1agdA 276 6.59e+00 1agdA b.1.1.2 20741 d.19.1.1 38260 1bgf 124 6.66e+00 1bgf a.90.1.1 18537 1foeA 377 6.78e+00 1foeA a.87.1.1 18517 b.55.1.1 26969 1g7pA 274 6.80e+00 b.1.1.2 70153 d.19.1.1 70154 1il6 185 7.08e+00 1alu a.26.1.1 16827 1fzoA 274 7.18e+00 1agdA b.1.1.2 60155 d.19.1.1 60156 1dat 174 7.69e+00 2fha a.25.1.1 16677 1noyA 388 7.79e+00 1clqA c.55.3.5 33713 1alu 186 8.20e+00 1alu a.26.1.1 16826 1aew 174 8.45e+00 2fha a.25.1.1 16676 1v54C 261 8.49e+00 f.25.1.1 -12239 2lhb 149 8.51e+00 2fal a.1.1.2 15597 1ad6 185 8.53e+00 1guxA a.74.1.3 18390 1aj8A 371 8.58e+00 1aj8A a.103.1.1 18900 1gpb 842 8.72e+00 1a8i c.87.1.4 35478 1f46A 140 8.81e+00 1f46A d.129.4.1 59643 1dioB 224 8.83e+00 1dioB c.51.3.1 33219 1c8kA 842 8.84e+00 1a8i c.87.1.4 35491 1eexB 224 9.15e+00 1dioB c.51.3.1 33213 1h5uA 842 9.38e+00 1a8i c.87.1.4 60655 1q8iA 783 9.49e+00 c.55.3.5 -7635 e.8.1.1 -11885 1f7wA 144 9.49e+00 1f46A d.129.4.1 59679 1l0oC 243 9.73e+00 a.4.13.2 73405 1ocrC 261 1.01e+01 1ocrC f.25.1.1 43540 1ac5 483 1.01e+01 1ac5 c.69.1.5 34653 1ggwA 140 1.01e+01 1ggwA a.39.1.5 60490 2occC 261 1.02e+01 1ocrC f.25.1.1 43520 1g8iA 190 1.06e+01 1rec a.39.1.5 60363 1a8i 842 1.06e+01 1a8i c.87.1.4 35490 1jkw 323 1.07e+01 1jkw a.74.1.1 18356 a.74.1.1 18357 1kv9A 668 1.08e+01 a.3.1.6 73056 b.70.1.1 73057 1afwA 393 1.08e+01 1afwA c.95.1.1 35900 c.95.1.1 35901 1pprM 312 1.11e+01 1pprM a.131.1.1 19502 a.131.1.1 19503 1f47B 144 1.11e+01 1f46A d.129.4.1 59645 1dguA 183 1.12e+01 1dguA a.39.1.5 17333 1dtoA 221 1.13e+01 1dtoA b.91.1.1 28405 1pq1B 33 1.13e+01 1ithA 141 1.14e+01 1ithA a.1.1.2 15623 1sra 151 1.17e+01 1sra a.39.1.3 17190 1g7oA 215 1.19e+01 1g7oA a.45.1.1 60332 c.47.1.5 60333 1i4fA 275 1.20e+01 1agdA b.1.1.2 61687 d.19.1.1 61688 1b25A 619 1.23e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1sv7A 109 1.27e+01 1p65A 73 1.30e+01 unknown_sccs -10331 1duzA 275 1.30e+01 1agdA b.1.1.2 20670 d.19.1.1 38224 1b7eA 420 1.33e+01 1b7eA c.55.3.4 33680 2fha 183 1.34e+01 2fha a.25.1.1 16674 1exrA 148 1.35e+01 1cll a.39.1.5 17299 1e9lA 377 1.36e+01 1e9lA c.1.8.5 59395 d.26.3.1 59396 1aye 401 1.39e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1rgs 288 1.39e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1lvfA 110 1.41e+01 a.47.2.1 74280 1b72A 97 1.43e+01 2hddA a.4.1.1 16000 1jf2A 195 1.46e+01 1ej3A a.39.1.5 62930 1t0gA 109 1.46e+01 unknown_sccs -10955 1ibvB 229 1.54e+01 1broA 277 1.55e+01 1brt c.69.1.12 34700 1e0cA 271 1.56e+01 1e0cA c.46.1.2 32717 c.46.1.2 32718 1chuA 540 1.57e+01 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1b7bA 310 1.58e+01 1b7bA c.73.1.1 34963 1rl4A 188 1.58e+01 d.167.1.1 -11593 2spo 154 1.58e+01 1a6m a.1.1.2 15053 1a6m 151 1.58e+01 1a6m a.1.1.2 15018 1d3uB 201 1.65e+01 1aisB a.74.1.2 18386 a.74.1.2 18387 1oc2A 348 1.65e+01 c.2.1.2 -5753 1v54M 46 1.67e+01 f.23.7.1 -12124 1b79A 119 1.67e+01 1b79A a.81.1.1 18451 1ne6A 283 1.71e+01 b.82.3.2 -4918 b.82.3.2 -4919 1i50A 1733 1.72e+01 e.29.1.2 61754 1pyaB 228 1.73e+01 1pyaB 1ax4A 467 1.74e+01 1ax4A c.67.1.2 34391 1ee8A 266 1.74e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1kepA 348 1.75e+01 c.2.1.2 68536 1fpoA 171 1.75e+01 1fpoA a.2.3.1 15693 a.23.1.1 16487 1ftt 68 1.76e+01 2hddA a.4.1.1 15997 1iw8A 231 1.76e+01 a.111.1.1 76866 1aje 194 1.77e+01 1ctqA c.37.1.8 32071 1fha 183 1.78e+01 2fha a.25.1.1 16675 1r12A 258 1.78e+01 e.4.1.1 -11807 1brt 277 1.80e+01 1brt c.69.1.12 34699 1pxtB 390 1.81e+01 1afwA c.95.1.1 35906 c.95.1.1 35907 1h96A 182 1.84e+01 2fha a.25.1.1 60811 1lb3A 182 1.84e+01 a.25.1.1 77873 1ggzA 148 1.86e+01 a.39.1.5 70176 1osa 148 1.87e+01 1cll a.39.1.5 17300 1ysc 421 1.92e+01 1ivyA c.69.1.5 34652 1crl 534 1.92e+01 1thg c.69.1.17 34765 1rprA 63 1.94e+01 1nkd a.30.1.1 16989 1m1eB 81 1.96e+01 a.161.1.1 78400 1h6pA 203 1.98e+01 a.146.1.1 60690 1r4pA 297 2.03e+01 d.165.1.2 -11560 2occM 46 2.04e+01 2occM f.23.7.1 43527 1e3dB 542 2.06e+01 1h2rL e.18.1.1 59189 1hsbA 270 2.06e+01 1agdA b.1.1.2 20736 d.19.1.1 38257 1rxqA 178 2.10e+01 1enh 54 2.12e+01 2hddA a.4.1.1 15973 1neyA 247 2.17e+01 c.1.1.1 80449 1dk8A 147 2.18e+01 1agrE a.91.1.1 18548 1b22A 114 2.19e+01 1b22A a.60.4.1 17969 1ll7A 392 2.20e+01 c.1.8.5 78085 d.26.3.1 78086 1jraA 117 2.20e+01 a.24.15.1 67117 1bvp1 349 2.23e+01 1bvp1 1ji1A 637 2.24e+01 b.1.18.2 71666 b.71.1.1 71667 c.1.8.1 71668 1gc0A 398 2.26e+01 c.67.1.3 70168 1bzpA 153 2.26e+01 1a6m a.1.1.2 15020 1pzlA 237 2.26e+01 1gr8A 412 2.29e+01 1ockA 412 2.29e+01 c.117.1.1 86802 1jo0A 98 2.30e+01 d.68.4.1 77140 1ohuA 175 2.31e+01 f.1.4.1 -12058 1cll 148 2.37e+01 1cll a.39.1.5 17263 1i45A 248 2.37e+01 1amk c.1.1.1 61665 3ygsP 97 2.41e+01 3ygsP a.77.1.3 18435 1fx4A 231 2.42e+01 1fx2A d.58.29.1 39431 3cln 148 2.42e+01 1cll a.39.1.5 17286 1a88A 275 2.43e+01 1brt c.69.1.12 34707 1mbd 153 2.43e+01 1a6m a.1.1.2 15033 1ffyA 917 2.44e+01 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 2.44e+01 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1ps9A 671 2.48e+01 c.1.4.1 -5206 1bxsA 501 2.51e+01 1bpwA c.82.1.1 35357 1us7B 265 2.53e+01 unknown_sccs -1518 2pvbA 107 2.55e+01 1a75A a.39.1.4 17205 1n55A 251 2.58e+01 c.1.1.1 80007 1jr8A 117 2.59e+01 a.24.15.1 67115 1mgn 154 2.61e+01 1a6m a.1.1.2 15097 2hddA 61 2.61e+01 2hddA a.4.1.1 15971 1va4A 279 2.70e+01 1ln4A 104 2.72e+01 d.68.4.1 74043 1d2kA 392 2.72e+01 1d2kA c.1.8.5 29008 d.26.3.1 38442 2cro 71 2.73e+01 1r69 a.35.1.2 17038 7timA 247 2.73e+01 1amk c.1.1.1 28457 1k5dC 386 2.82e+01 c.10.1.2 68170 1rh5A 436 2.83e+01 unknown_sccs -12298 1q2wA 308 2.84e+01 b.47.1.4 88355 1amk 251 2.88e+01 1amk c.1.1.1 28503 1m55A 197 2.90e+01 d.89.1.3 74469 1pioA 257 2.96e+01 1btl e.3.1.1 42719 1kxu 333 2.97e+01 1jkw a.74.1.1 18358 a.74.1.1 18359 1jssA 224 2.99e+01 d.129.3.2 71844 1zug 71 3.05e+01 1r69 a.35.1.2 17041 1jlnA 297 3.08e+01 1pty c.45.1.2 63172 1oivA 191 3.10e+01 c.37.1.8 -7074 1h8aC 128 3.16e+01 a.4.1.3 65731 a.4.1.3 65732 1qddA 144 3.18e+01 1qddA d.169.1.1 42324 1izmA 184 3.22e+01 unknown_sccs -1233 2admA 421 3.22e+01 2admA c.66.1.27 34238 1icrA 217 3.25e+01 1vfrA d.90.1.1 62274 2sxl 88 3.27e+01 1b7fA d.58.7.1 39179 1bupA 386 3.27e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1f5xA 208 3.28e+01 1f5xA a.87.1.1 18516 1c9qA 117 3.34e+01 1c9qA g.52.1.1 45377 1odoA 408 3.41e+01 a.104.1.1 -1463 1lit 144 3.46e+01 1qddA d.169.1.1 42325 1acf 125 3.49e+01 3nul d.110.1.1 40882 1i39A 225 3.58e+01 1ekeA c.55.3.1 61585 1o08A 221 3.60e+01 c.108.1.6 86525 1a8s 273 3.68e+01 1brt c.69.1.12 34710 1jpnA 296 3.71e+01 a.24.13.1 67039 c.37.1.10 67040 1esmA 316 3.71e+01 1esmA c.37.1.6 31953 1svsA 353 3.71e+01 1hqcA 324 3.72e+01 1hqcA a.4.5.11 16127 c.37.1.20 32424 1irqA 71 3.75e+01 unknown_sccs 66297 1ub4C 85 3.76e+01 b.129.1.1 88401 1jjoC 261 3.79e+01 3blm 257 3.82e+01 1btl e.3.1.1 42709 1sqgA 429 3.84e+01 1fx2A 235 3.85e+01 1fx2A d.58.29.1 39430 1alq 266 3.86e+01 1btl e.3.1.1 42707 1ctf 74 3.88e+01 1ctf d.45.1.1 38759 1rylA 167 3.92e+01 1ba1 386 3.94e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1ls1A 295 3.94e+01 a.24.13.1 78170 c.37.1.10 78171 1dw0A 112 3.94e+01 1dw0A a.3.1.1 15911 1hl8A 449 3.99e+01 unknown_sccs -4690 unknown_sccs -5361