# 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 1srvA 145 4.17e-02 1derA c.8.5.1 30817 4gr1 478 3.97e-01 3grs c.3.1.5 30461 c.3.1.5 30462 d.87.1.1 40162 1bzyA 217 4.08e-01 1qk3A c.61.1.1 34071 3grs 478 4.12e-01 3grs c.3.1.5 30441 c.3.1.5 30442 d.87.1.1 40152 1kid 203 5.22e-01 1derA c.8.5.1 30771 1bif 469 5.47e-01 1bif c.37.1.7 31961 c.60.1.4 34003 1jztA 246 5.67e-01 c.104.1.1 63319 1chmA 401 7.84e-01 1chmA c.55.2.1 33545 d.127.1.1 41142 1bfd 528 8.70e-01 1bfd c.31.1.3 31745 c.36.1.1 31801 c.36.1.1 31802 1gajA 257 9.05e-01 1gajA c.37.1.12 60416 1g6hA 257 1.15e+00 1gajA c.37.1.12 60318 2nacA 393 1.30e+00 2nadA c.2.1.4 30088 c.23.12.1 31348 1lucA 355 1.57e+00 1lucA c.1.16.1 29547 2mbr 340 1.60e+00 2mbr d.145.1.2 41749 d.146.1.1 41762 1uxy 340 1.60e+00 2mbr d.145.1.2 41748 d.146.1.1 41761 1hskA 326 1.65e+00 2mbr d.145.1.2 61241 d.146.1.1 61242 1ex2A 189 1.68e+00 1ex2A c.51.4.2 33225 1nsyA 271 1.79e+00 2nsyA c.26.2.1 31614 2nsyA 271 1.79e+00 2nsyA c.26.2.1 31612 1kqpA 271 1.79e+00 1ih8A 271 1.89e+00 2nsyA c.26.2.1 62377 1ig0A 319 1.92e+00 1ig0A b.82.6.1 62354 c.100.1.1 62355 1brlA 355 2.00e+00 1lucA c.1.16.1 29553 1aa8A 347 2.18e+00 1an9A c.4.1.2 30619 d.16.1.3 37906 1pytA 94 2.29e+00 1pytA d.58.3.1 39064 1f5sA 211 2.55e+00 1f5sA c.108.1.4 59656 1j97A 211 2.55e+00 1f5sA c.108.1.4 62753 2nadA 393 2.63e+00 2nadA c.2.1.4 30090 c.23.12.1 31350 1id1A 153 2.65e+00 1id1A c.2.1.9 62286 1cjsA 219 2.71e+00 1cjsA e.24.1.1 43354 1an9A 340 2.87e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 2tmdA 729 3.21e+00 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1djnA 729 3.35e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1whsB 153 3.42e+00 1whtB 1akr 147 3.62e+00 1rcf c.23.5.1 31152 1whtB 153 3.72e+00 1whtB 1dbqA 289 3.75e+00 1qpzA c.93.1.1 35666 1chuA 540 3.79e+00 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1qpzA 340 3.80e+00 1qpzA a.35.1.5 17097 c.93.1.1 35673 1i7qB 193 4.15e+00 1qdlB c.23.16.1 61902 1dhy 292 4.16e+00 1han d.32.1.3 38504 d.32.1.3 38505 1hmpA 217 4.32e+00 1qk3A c.61.1.1 34075 1ec7A 446 4.38e+00 1bqg c.1.11.2 29218 d.54.1.1 38862 1nhs 447 4.56e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1jdfA 447 4.67e+00 c.1.11.2 62897 d.54.1.1 62898 1ipaA 274 4.77e+00 1l7mA 211 4.80e+00 1d1gA 168 4.81e+00 1d1gA c.71.1.1 34889 1cf9A 753 5.08e+00 1cf9A c.23.16.3 31441 e.5.1.1 42815 1jgtA 513 5.20e+00 c.26.2.1 66684 d.153.1.1 66685 1i58A 189 5.28e+00 1b3qA d.122.1.3 61773 1fhuA 320 5.31e+00 1fhuA c.1.11.2 29234 d.54.1.1 38878 1jmxA 494 5.52e+00 a.3.1.7 66901 a.3.1.7 66902 b.1.1.6 66903 b.1.1.6 66904 b.61.4.1 66905 1b3qA 379 5.59e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1brlB 324 5.82e+00 1lucA c.1.16.1 29554 1bmtA 246 5.95e+00 1bmtA a.46.1.1 17757 c.23.6.1 31235 1f8rA 498 5.98e+00 1f8rA c.3.1.2 30410 d.16.1.5 37974 1aye 401 6.23e+00 1aye c.56.5.1 33824 d.58.3.1 39065 1ofgA 381 6.35e+00 1ofgA c.2.1.3 30064 d.81.1.5 39979 1bu5A 147 6.45e+00 5nul c.23.5.1 31155 1wetA 340 6.92e+00 1qpzA a.35.1.5 17093 c.93.1.1 35670 1kyqA 274 7.06e+00 1qguB 519 7.08e+00 1qguB c.92.2.3 35626 1dguA 183 7.15e+00 1dguA a.39.1.5 17333 1eulA 994 7.42e+00 1eulA f.2.1.10 43726 1f32A 149 8.39e+00 1f32A d.62.1.1 39539 1qk4A 233 8.62e+00 1qk3A c.61.1.1 34037 1f93A 104 8.65e+00 1dcpA d.74.1.1 39688 2cb5A 453 8.83e+00 3gcb d.3.1.1 37035 1jq3A 296 8.87e+00 c.66.1.17 67079 1ktbA 405 8.96e+00 1lucB 324 8.97e+00 1lucA c.1.16.1 29548 1eudA 311 9.05e+00 2scuA c.2.1.8 30312 c.23.4.1 31140 1i1qB 192 9.06e+00 1qdlB c.23.16.1 61544 1dcpA 104 9.07e+00 1dcpA d.74.1.1 39672 1kczA 413 9.12e+00 c.1.11.2 68451 d.54.1.1 68452 1qdlB 195 9.22e+00 1qdlB c.23.16.1 31437 1dcoA 104 9.23e+00 1dcpA d.74.1.1 39680 1gesA 450 9.24e+00 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1inlA 296 9.28e+00 c.66.1.17 66220 1dxeA 256 9.32e+00 1dxeA c.1.12.5 29310 1bykA 255 9.51e+00 1bykA c.93.1.1 35706 1nedA 183 1.06e+01 1nedA d.153.1.4 41974 2cevA 299 1.08e+01 1d3vA c.42.1.1 32576 1jm6A 407 1.08e+01 a.29.5.1 66876 d.122.1.4 66877 1nhp 447 1.09e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1krhA 338 1.11e+01 1je0A 236 1.12e+01 c.56.2.1 66581 1lx7A 253 1.15e+01 1irxA 523 1.16e+01 1aw5 326 1.24e+01 1b4kA c.1.10.3 29181 1poxA 585 1.26e+01 1poxA c.31.1.3 31731 c.36.1.1 31793 c.36.1.1 31794 1dbtA 239 1.27e+01 1dbtA c.1.2.3 28539 1evlA 401 1.29e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 3grx 82 1.30e+01 1aba c.47.1.1 32769 9ldtA 332 1.40e+01 3ldh c.2.1.5 30154 d.162.1.1 42121 1bt4A 362 1.43e+01 1bjnA c.67.1.4 34468 1g6sA 427 1.43e+01 1eps d.68.2.2 39584 1ylvA 342 1.48e+01 1b4kA c.1.10.3 29180 1fukA 165 1.48e+01 1fukA c.37.1.13 32409 1ig3A 263 1.49e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1ceqA 316 1.51e+01 1ceqA c.2.1.5 30163 d.162.1.1 42130 1dchA 104 1.51e+01 1dcpA d.74.1.1 39692 1dcfA 136 1.55e+01 1dcfA c.23.1.2 31124 1joa 447 1.55e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 2mjpA 193 1.60e+01 1b78A c.51.4.1 33223 1d1qA 161 1.60e+01 1dg9A c.44.1.1 32642 1b78A 193 1.60e+01 1b78A c.51.4.1 33221 1rgs 288 1.67e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1h7nA 342 1.70e+01 1b4kA c.1.10.3 60726 1mjhA 162 1.75e+01 1mjhA c.29.1.2 31639 1af7 274 1.79e+01 1af7 a.58.1.1 17928 c.66.1.8 34203 1cd9C 175 1.80e+01 1bgc a.26.1.1 16816 1srrA 124 1.84e+01 1dz3A c.23.1.1 31110 2bosA 68 1.84e+01 2bosA b.40.2.1 25025 1d5yA 292 1.85e+01 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1ejjA 511 1.86e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1ijyA 130 1.87e+01 1ijxA a.141.1.1 62517 1f21A 155 1.89e+01 2rn2 c.55.3.1 33550 1ihvA 52 1.91e+01 1ihvA b.34.7.1 24629 1adjA 421 1.97e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1cjbA 231 1.98e+01 1qk3A c.61.1.1 34079 1asyA 490 2.02e+01 1b8aA b.40.4.1 25242 d.104.1.1 40763 3timA 250 2.02e+01 1amk c.1.1.1 28483 1fcbA 511 2.03e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1derA 547 2.03e+01 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1ihcA 188 2.03e+01 1di6A c.57.1.1 62379 1jljA 189 2.05e+01 c.57.1.1 63169 1ev0A 58 2.06e+01 1ev0A d.71.1.1 39594 1b9yC 246 2.07e+01 1b9yC c.47.1.6 33052 1tpfA 250 2.07e+01 1amk c.1.1.1 28467 1f4pA 147 2.07e+01 5nul c.23.5.1 59651 1qba 858 2.08e+01 1qba b.1.1.5 21810 b.2.2.3 22406 c.1.8.6 29009 d.92.2.1 40408 1j8mF 297 2.12e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1b24A 188 2.13e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 1ee9A 320 2.13e+01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1sesA 421 2.14e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1b63A 333 2.20e+01 1b63A d.14.1.3 37566 d.122.1.2 41107 1id0A 152 2.21e+01 d.122.1.3 66111 1bc5A 269 2.22e+01 1af7 a.58.1.1 17929 c.66.1.8 34204 1ct9A 553 2.25e+01 1ct9A c.26.2.1 31616 d.153.1.1 41834 1ep3B 262 2.25e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1kv5A 250 2.26e+01 1jmrA 249 2.28e+01 1i27A 73 2.30e+01 1i27A a.4.5.30 61555 1kq4A 232 2.37e+01 d.207.1.1 68791 1jl1A 155 2.41e+01 c.55.3.1 66821 1amk 251 2.43e+01 1amk c.1.1.1 28503 1kao 167 2.44e+01 1ctqA c.37.1.8 32014 2plc 274 2.45e+01 2plc c.1.18.2 29614 1pjcA 361 2.48e+01 1sayA c.2.1.4 30101 c.23.12.2 31361 2minB 522 2.50e+01 1qguB c.92.2.3 35610 1rpjA 288 2.50e+01 2dri c.93.1.1 35656 1fh0A 221 2.51e+01 1cs8A d.3.1.1 59832 1a8p 258 2.51e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 1qkkA 155 2.51e+01 1dbwA c.23.1.1 31104 1dn1B 267 2.52e+01 1dn1B a.47.2.1 17771 1e19A 314 2.52e+01 1b7bA c.73.1.1 34967 1eps 427 2.53e+01 1eps d.68.2.2 39586 1nfp 228 2.58e+01 1nfp c.1.16.2 29555 1sayA 361 2.62e+01 1sayA c.2.1.4 30102 c.23.12.2 31362 1j9eA 147 2.67e+01 c.23.5.1 62756 2rslA 140 2.68e+01 2rslA c.53.1.1 33345 1qhtA 775 2.69e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1mjhB 162 2.70e+01 1mjhA c.29.1.2 31640 1h6dA 433 2.71e+01 c.2.1.3 65656 d.81.1.5 65657 1k3fA 253 2.71e+01 c.56.2.1 68105 1prxA 224 2.74e+01 1prxA c.47.1.10 33076 2fx2 147 2.77e+01 1rcf c.23.5.1 31158 4gatA 66 2.79e+01 1gatA g.39.1.1 45100 1jg1A 235 2.83e+01 c.66.1.7 66661 1h75A 81 2.86e+01 1h75A c.47.1.1 60716 1h4vB 421 2.86e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1jdqA 98 2.89e+01 d.68.3.2 66559 1djxB 624 2.90e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1im5A 180 2.91e+01 c.33.1.2 66211 1aszB 490 2.98e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1b43A 340 2.98e+01 1a76 a.60.7.1 18092 c.53.1.2 33362 1ep2B 261 3.03e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1pjbA 361 3.08e+01 1sayA c.2.1.4 30103 c.23.12.2 31363 3adk 195 3.10e+01 1zin c.37.1.1 31885 1fts 295 3.11e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1qcwA 410 3.14e+01 1gox c.1.4.1 28622 1g97A 459 3.16e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 2thiA 379 3.21e+01 2thiA c.94.1.1 35794 1i0hA 205 3.22e+01 1avmA a.2.11.1 15760 d.44.1.1 38685 2rn2 155 3.22e+01 2rn2 c.55.3.1 33551 1cx4A 305 3.24e+01 b.82.3.2 59099 b.82.3.2 59100 1jk7A 323 3.26e+01 1auiA d.159.1.3 63144 1kp9B 287 3.29e+01 c.66.1.18 68734 1dbuA 158 3.32e+01 1dbuA d.116.1.1 40930 1c7sA 858 3.35e+01 1qba b.1.1.5 21812 b.2.2.3 22408 c.1.8.6 29011 d.92.2.1 40410 1kgsA 225 3.37e+01 a.4.6.1 68596 c.23.1.1 68597 2af8 86 3.39e+01 2af8 a.28.1.1 16933 1jwhA 337 3.41e+01 1ii2A 524 3.44e+01 c.91.1.1 66146 c.109.1.1 66147 2scuA 288 3.44e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1b8gA 429 3.48e+01 1b8gA c.67.1.4 34499 1f0yA 302 3.56e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1fs5A 266 3.57e+01 c.35.1.1 65044 1b1cA 181 3.58e+01 1amoA c.23.5.2 31212 1ap8 213 3.59e+01 1ap8 d.86.1.1 40151 1fsfA 266 3.60e+01 c.35.1.1 65047 7timA 247 3.62e+01 1amk c.1.1.1 28457 1eqjA 511 3.62e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1af8 86 3.63e+01 2af8 a.28.1.1 16932 3minB 522 3.64e+01 1qguB c.92.2.3 35606 1cs8A 316 3.64e+01 1cs8A d.3.1.1 37065 1j4wA 174 3.64e+01 1deaA 266 3.67e+01 1deaA c.35.1.1 31760 1dppA 507 3.69e+01 1dpe c.94.1.1 35800 1gdtA 183 3.71e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1e2kA 331 3.72e+01 1qhiA c.37.1.1 31854 1hkcA 917 3.77e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1scuA 288 3.78e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1l0oA 150 3.84e+01 1bqg 451 3.85e+01 1bqg c.1.11.2 29217 d.54.1.1 38861 1c3pA 375 3.86e+01 1c3pA c.42.1.2 32606 1qc7A 101 3.89e+01 1qc7A a.82.1.1 18456 1i50B 1224 3.90e+01 e.29.1.2 61755 1j5pA 253 3.92e+01 1bdtA 53 3.96e+01 1bazA a.43.1.1 17433