# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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.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 1esfA 233 3.91e-01 3seb b.40.2.2,d.15.6.1 25146,37735 1dyqA 234 5.62e-01 3seb b.40.2.2,d.15.6.1 59140,59141 1zynA 202 1.33e+00 1gdtA 183 1.42e+00 2rslA a.4.1.2,c.53.1.1 16021,33348 1hyuA 521 1.76e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 2rslA 140 1.91e+00 2rslA c.53.1.1 33345 1repC 251 2.11e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1iz5A 249 2.23e+00 d.131.1.2,d.131.1.2 83834,83835 1agnA 373 2.26e+00 2ohxA b.35.1.2,c.2.1.1 24737,29753 1ge8A 249 2.58e+00 1plq d.131.1.2,d.131.1.2 41398,41399 2fclA 169 2.73e+00 2ewrA 170 2.74e+00 1hqz9 141 3.21e+00 1sqsA 242 3.46e+00 c.23.5.5 98968 1y96B 85 3.60e+00 1a0rP 245 3.64e+00 1b9yC c.47.1.6 33054 1m93A 55 3.66e+00 e.1.1.1 91235 1hqz1 141 5.52e+00 1c52 131 5.99e+00 1c52 a.3.1.1 15810 2bg5A 324 6.42e+00 2afbA 351 6.50e+00 1j5vA 351 6.81e+00 c.72.1.1 71585 1wspA 84 6.98e+00 1pnsC 206 7.54e+00 i.1.1.1 88170 1ockA 412 7.89e+00 c.117.1.1 86802 1xn5A 146 8.63e+00 2ifeA 100 9.84e+00 1tig d.68.1.1 39567 1hfbA 370 1.01e+01 c.1.10.4 76706 1of8A 370 1.01e+01 c.1.10.4 92819 1jfbA 404 1.03e+01 a.104.1.1 66624 1f24A 402 1.03e+01 1rom a.104.1.1 18953 5gcnA 166 1.11e+01 1yghA d.108.1.1 40807 1j5eC 239 1.12e+01 d.52.3.1,d.53.1.1 71544,71545 1p8kZ 254 1.24e+01 d.95.2.1,d.95.2.1 94361,94362 1qlmA 316 1.27e+01 1qlmA d.147.1.1 41765 1xewY 172 1.28e+01 1ghtA 105 1.30e+01 2rslA c.53.1.1 60526 1ycyA 71 1.33e+01 2wsyB 396 1.42e+01 2tysB c.79.1.1 35288 1vcvA 226 1.44e+01 1c0dA 358 1.44e+01 1eceA c.1.8.3 28815 1eceA 358 1.44e+01 1eceA c.1.8.3 28813 2gfgA 193 1.46e+01 1ur1A 378 1.50e+01 c.1.8.3 99804 1tf1A 198 1.61e+01 d.110.2.2 106826 1qhlA 227 1.61e+01 1qhlA c.37.1.12 32382 1k38A 254 1.66e+01 e.3.1.1 84303 1fjgC 239 1.80e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1lwjA 441 1.81e+01 b.71.1.1,c.1.8.1 74303,74304 1bksB 397 1.82e+01 2tysB c.79.1.1 35285 1a50B 396 1.86e+01 2tysB c.79.1.1 35280 1f13A 731 1.89e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 2tysB 397 1.93e+01 2tysB c.79.1.1 35272 1vddA 228 1.98e+01 e.49.1.1 108519 1mo9A 523 1.99e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1zp4A 304 2.07e+01 1a3wA 500 2.09e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27060,29288,33142 1sr4B 261 2.10e+01 d.151.1.1 105949 1vjpA 394 2.12e+01 c.2.1.3,d.81.1.3 100828,100829 1evuA 731 2.12e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1vr7A 142 2.14e+01 1tluA 130 2.22e+01 d.156.1.2 107139 1k8yB 396 2.23e+01 c.79.1.1 72184 1ex0A 731 2.30e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 2b33A 140 2.32e+01 1gyxA 76 2.34e+01 d.80.1.1 76387 1o58A 303 2.34e+01 c.79.1.1 92491 1gguA 731 2.44e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21885,22179,22180,37115 1c7sA 858 2.47e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1qavA 90 2.51e+01 1qauA b.36.1.1 24777 2g6tA 306 2.63e+01 1e0tA 470 2.72e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1e9rA 437 2.72e+01 c.37.1.11 64827 1tiqA 180 2.75e+01 d.108.1.1 107010 1ygs 234 2.80e+01 1ygs b.26.1.1 23907 1qba 858 2.82e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21810,22406,29009,40408 1pnsB 234 2.84e+01 i.1.1.1 88169 1x8dA 104 2.87e+01 1qopB 396 2.95e+01 2tysB c.79.1.1 35270 1j5eB 256 2.96e+01 c.23.15.1 71543 1gm6A 175 3.05e+01 b.60.1.1 70272 1ca1 370 3.13e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1vkuA 100 3.14e+01 a.28.1.1 108690 1fht 116 3.14e+01 1urnA d.58.7.1 39157 1o0yA 260 3.15e+01 c.1.10.1 80756 1qrkA 731 3.24e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1ee2A 373 3.25e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1ggtB 731 3.40e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21882,22173,22174,37112 1rom 403 3.41e+01 1rom a.104.1.1 18963 1pyfA 312 3.44e+01 c.1.7.1 95334 1exg 110 3.46e+01 1exg b.2.2.1 22387 1ri7A 171 3.47e+01 a.4.5.32,d.58.4.2 97504,97505 1cf7A 76 3.53e+01 1cf7B a.4.5.17 16151 1a99A 344 3.55e+01 1pot c.94.1.1 35812 1nijA 318 3.55e+01 c.37.1.10,d.237.1.1 85741,85742 1fjgB 256 3.55e+01 1fjfB c.23.15.1 31400 8adh 374 3.75e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1cx0A 95 3.75e+01 1urnA d.58.7.1 39158 1kfiA 572 3.77e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 2adoA 196 3.88e+01 1c7qA 445 3.89e+01 2pgi c.80.1.2 35307 1n8kA 374 3.91e+01 b.35.1.2,c.2.1.1 80298,80299 1bia 321 3.92e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1hetA 374 3.94e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1axeA 374 3.94e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 2ohxA 374 3.94e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1a71A 374 3.95e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 2g50A 530 3.96e+01 1nf3C 128 4.00e+01 b.36.1.1 85596 2aefA 234 4.01e+01 1ydmA 187 4.01e+01 1qg8A 255 4.03e+01 1qg8A c.68.1.1 34505 1s0pA 176 4.03e+01 a.192.1.1 98300 1bby 69 4.03e+01 2bby a.4.5.15 16149 1axgA 374 4.05e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1b25A 619 4.06e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1o0pA 104 4.06e+01 d.58.7.1 86535 1ta3B 303 4.09e+01 c.1.8.3 106732 1b0zA 445 4.15e+01 2pgi c.80.1.2 35309 2pgi 445 4.15e+01 2pgi c.80.1.2 35308 1heuA 374 4.15e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1d2oA 187 4.18e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1d2pA 373 4.22e+01 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1qdlB 195 4.29e+01 1qdlB c.23.16.1 31437 2pil 159 4.31e+01 2pil d.24.1.1 38376 1ay2 159 4.32e+01 2pil d.24.1.1 38377 1fzqA 181 4.34e+01 1hurA c.37.1.8 32060 1cby 259 4.38e+01 1cby d.103.1.1 40705 1u2xA 474 4.40e+01 c.72.1.3 107622 1urnA 97 4.42e+01 1urnA d.58.7.1 39153 1bib 321 4.57e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1rwzA 245 4.59e+01 d.131.1.2,d.131.1.2 98005,98006 1od8A 313 4.60e+01 c.1.8.3 86838 1m5oC 100 4.61e+01 d.58.7.1 78654 1pp0A 199 4.64e+01 d.103.1.1 104211 1xhfA 123 4.66e+01 1vbvA 105 4.74e+01 1vr4A 103 4.78e+01 1dkuA 317 4.78e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 2ab5A 269 4.82e+01 1focA 132 4.88e+01 1c52 a.3.1.1 15812 2etxA 209 4.92e+01 1ma3A 253 4.98e+01 c.31.1.5 78883 1wrjA 156 5.07e+01 1v0lA 313 5.09e+01 c.1.8.3 108207 2amhA 207 5.10e+01 1wmhB 86 5.11e+01 1no5A 114 5.19e+01 d.218.1.5 92014 1ri6A 343 5.21e+01 b.69.11.1 97503 1fieA 731 5.23e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21879,22167,22168,37109 1e0wA 313 5.25e+01 1taxA c.1.8.3 59150 1wu3I 161 5.25e+01 1h09A 338 5.46e+01 b.109.1.1,c.1.8.8 83420,83421 1rboC 123 5.46e+01 1rboC d.73.1.1 39634 1audA 101 5.49e+01 1urnA d.58.7.1 39156 8rucI 123 5.57e+01 1rboC d.73.1.1 39629 1larA 575 5.57e+01 1larA c.45.1.2,c.45.1.2 32693,32694 2u2fA 85 5.62e+01 2u2fA d.58.7.1 39167 1rmi 160 5.63e+01 1ifa a.26.1.3 16891 2fh7A 595 5.64e+01 1woqA 267 5.67e+01 c.55.1.10,c.55.1.10 109462,109463 1szoA 257 5.85e+01 c.14.1.3 106164 1t0aA 159 5.87e+01 1xx4A 261 5.88e+01 1o8uA 257 5.90e+01 c.14.1.3 81194 2bby 69 5.90e+01 2bby a.4.5.15 16148 1i6lA 328 5.90e+01 c.26.1.1 66041 1i6kA 328 5.97e+01 c.26.1.1 66040 1aq0A 306 6.02e+01 1aq0A c.1.8.3 28842 1bvb 211 6.08e+01 1bvb a.138.1.3 19683 1ft5A 211 6.15e+01 1bvb a.138.1.3 19681 1reqB 637 6.32e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1wcdJ 441 6.32e+01 1i8fA 81 6.40e+01 1i8fA b.38.1.1 61959 1xyfA 436 6.45e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1u1hA 765 6.50e+01 c.1.22.2,c.1.22.2 107580,107581 1jhsA 188 6.50e+01 d.107.1.1 84172 1p9rA 418 6.50e+01 c.37.1.11 94399 1pkm 530 6.52e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27051,29254,33108 1cmnA 402 6.52e+01 1rom a.104.1.1 18958 1xubA 298 6.52e+01 1s50A 259 6.53e+01 1d2rB 326 6.53e+01 1d2rB c.26.1.1 31573 1aogA 485 6.54e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1cf7B 95 6.61e+01 1cf7B a.4.5.17 16152 2adbA 148 6.63e+01 1a8q 274 6.67e+01 1brt c.69.1.12 34702 1wkqA 164 6.69e+01 c.97.1.2 109393 1igs 248 6.70e+01 1a53 c.1.2.4 28565 1id0A 152 6.72e+01 d.122.1.3 66111 1o6dA 163 6.72e+01 c.116.1.3 92567 1yiyA 429 6.76e+01 2g9iA 249 6.86e+01 1ej0A 180 7.00e+01 1ej0A c.66.1.2 34179 1te7A 103 7.09e+01 2cxcA 144 7.11e+01 1a53 247 7.11e+01 1a53 c.1.2.4 28564 1ois 223 7.15e+01 1a36A e.15.1.1 43267 1ghr 306 7.16e+01 1aq0A c.1.8.3 28844 1hdoA 206 7.18e+01 1he2A c.2.1.2 60965 1enwA 114 7.19e+01 1enwA a.5.4.1 16291 1kqpA 271 7.22e+01 c.26.2.1 72883 1nsyA 271 7.23e+01 2nsyA c.26.2.1 31614 1he2A 206 7.24e+01 1he2A c.2.1.2 60966 1b5tA 275 7.30e+01 1b5tA c.1.23.1 29676 1o57A 291 7.30e+01 a.4.5.40,c.61.1.1 92483,92484 1juk 248 7.42e+01 1a53 c.1.2.4 28567 1xfcA 384 7.51e+01 1o1zA 234 7.55e+01 c.1.18.3 86555 1u1wA 298 7.56e+01 1fw9A 164 7.62e+01 1fw9A d.190.1.1 60059 1tt8A 164 7.62e+01 1ede 310 7.64e+01 1b6g c.69.1.8 34662 1ecfA 504 7.72e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ih8A 271 7.78e+01 2nsyA c.26.2.1 62377 2hvm 273 7.79e+01 1cnv c.1.8.5 28985 1b9yC 246 7.81e+01 1b9yC c.47.1.6 33052 2gh1A 301 7.83e+01 1ay9A 108 7.84e+01 1umuA b.87.1.1 28384 1z4rA 168 7.87e+01 1wouA 123 7.87e+01 c.47.1.16 109471 1qi9A 556 7.88e+01 1qhbA a.111.1.2 19053 1ydyA 356 7.89e+01 1u3wA 374 7.93e+01 2nsyA 271 8.00e+01 2nsyA c.26.2.1 31612 1oiaA 95 8.07e+01 d.58.7.1 87051 1tbrR 103 8.08e+01 1tbrR g.68.1.1,g.68.1.1 44707,44708 1umuB 116 8.13e+01 1umuA b.87.1.1 28383 2achA 360 8.14e+01 1c8oA e.1.1.1 42626 1qvaA 223 8.14e+01 1qvaA c.37.1.19 32411 1mk0A 97 8.15e+01 d.226.1.1 79216 1b9xC 246 8.17e+01 1b9yC c.47.1.6 33053 1umuA 116 8.20e+01 1umuA b.87.1.1 28382 1hbxA 92 8.21e+01 1mnmA d.88.1.1 60930 1t8qA 336 8.23e+01 c.1.18.3 106669 1h4vB 421 8.28e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1tljA 213 8.31e+01 d.282.1.1 107126 1g6gA 127 8.52e+01 1g6gA b.26.1.2 23916 1adjA 421 8.56e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1tlk 154 8.58e+01 1tlk b.1.1.4 21707 1d2rA 326 8.59e+01 1d2rB c.26.1.1 31572 1f2tB 148 8.65e+01 1f2tB 1yr2A 741 8.67e+01 1bc4 111 8.78e+01 1onc d.5.1.1 37279 1nu4A 97 8.80e+01 d.58.7.1 80731 2fkcA 247 8.90e+01 1ifa 158 8.91e+01 1ifa a.26.1.3 16892 1gewA 356 8.94e+01 1gewA c.67.1.1 60470 1r5jA 337 8.95e+01 c.77.1.5 97097 1quqB 121 8.96e+01 1quqB b.40.4.3 25305 1l9xA 315 8.98e+01 c.23.16.1 73762