# List of top-scoring protein chains for t2k-100-30-str2-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 1dyqA 234 2.42e-01 3seb b.40.2.2,d.15.6.1 59140,59141 1esfA 233 3.71e-01 3seb b.40.2.2,d.15.6.1 25146,37735 1m93A 55 9.32e-01 e.1.1.1 91235 1hyuA 521 1.09e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1sqsA 242 1.20e+00 c.23.5.5 98968 1zynA 202 1.20e+00 1ge8A 249 1.44e+00 1plq d.131.1.2,d.131.1.2 41398,41399 1repC 251 1.62e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1agnA 373 1.63e+00 2ohxA b.35.1.2,c.2.1.1 24737,29753 1y96B 85 1.66e+00 2fclA 169 2.06e+00 2ewrA 170 2.08e+00 1gdtA 183 2.27e+00 2rslA a.4.1.2,c.53.1.1 16021,33348 2myr 501 2.66e+00 2afbA 351 3.06e+00 1iz5A 249 3.09e+00 d.131.1.2,d.131.1.2 83834,83835 1ockA 412 3.19e+00 c.117.1.1 86802 1hqz9 141 3.27e+00 1xewY 172 3.41e+00 1ycyA 71 3.42e+00 2bg5A 324 3.92e+00 1c52 131 4.18e+00 1c52 a.3.1.1 15810 2rslA 140 4.82e+00 2rslA c.53.1.1 33345 1d2pA 373 4.97e+00 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1j5vA 351 4.97e+00 c.72.1.1 71585 1k38A 254 5.20e+00 e.3.1.1 84303 2ifeA 100 5.69e+00 1tig d.68.1.1 39567 5gcnA 166 6.36e+00 1yghA d.108.1.1 40807 1yiyA 429 6.44e+00 1xn5A 146 6.57e+00 1a0rP 245 6.63e+00 1b9yC c.47.1.6 33054 1e70M 501 6.87e+00 1e70M c.1.8.4 28926 1e4mM 501 6.94e+00 1e70M c.1.8.4 59226 2pil 159 7.06e+00 2pil d.24.1.1 38376 1ay2 159 7.10e+00 2pil d.24.1.1 38377 1hqz1 141 7.11e+00 1vr7A 142 7.14e+00 1e6qM 501 7.17e+00 1e70M c.1.8.4 28920 1tluA 130 7.35e+00 d.156.1.2 107139 1hfbA 370 7.76e+00 c.1.10.4 76706 1of8A 370 7.92e+00 c.1.10.4 92819 2cxcA 144 8.44e+00 1sr4B 261 9.27e+00 d.151.1.1 105949 2fgtA 417 9.91e+00 1lwjA 441 9.95e+00 b.71.1.1,c.1.8.1 74303,74304 1fl2A 310 9.95e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 1qi9A 556 9.96e+00 1qhbA a.111.1.2 19053 1pnsC 206 9.98e+00 i.1.1.1 88170 1urnA 97 1.11e+01 1urnA d.58.7.1 39153 1fhgA 154 1.14e+01 1tlk b.1.1.4 21706 1fht 116 1.16e+01 1urnA d.58.7.1 39157 1cx0A 95 1.26e+01 1urnA d.58.7.1 39158 1j5eC 239 1.27e+01 d.52.3.1,d.53.1.1 71544,71545 2fkcA 247 1.31e+01 1d2oA 187 1.32e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1wmhB 86 1.34e+01 1o0pA 104 1.37e+01 d.58.7.1 86535 1m5oC 100 1.40e+01 d.58.7.1 78654 2g9iA 249 1.43e+01 1e9rA 437 1.44e+01 c.37.1.11 64827 1tlk 154 1.47e+01 1tlk b.1.1.4 21707 2amhA 207 1.53e+01 1rfeA 162 1.53e+01 2gmqA 118 1.57e+01 1bib 321 1.57e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1quqB 121 1.60e+01 1quqB b.40.4.3 25305 1iqaA 160 1.68e+01 b.22.1.1 71274 2wsyB 396 1.74e+01 2tysB c.79.1.1 35288 1wcdJ 441 1.77e+01 1s55A 156 1.77e+01 1uekA 275 1.77e+01 d.14.1.5,d.58.26.5 88483,88484 1bia 321 1.79e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1oiaA 95 1.84e+01 d.58.7.1 87051 1fw9A 164 1.84e+01 1fw9A d.190.1.1 60059 1tt8A 164 1.84e+01 1gnf 46 1.94e+01 1gatA g.39.1.1 45107 1c7qA 445 1.99e+01 2pgi c.80.1.2 35307 1ft5A 211 2.01e+01 1bvb a.138.1.3 19681 1m4jA 142 2.03e+01 d.109.1.2 78602 1f13A 731 2.04e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 1b0zA 445 2.06e+01 2pgi c.80.1.2 35309 2pgi 445 2.06e+01 2pgi c.80.1.2 35308 2g5dA 422 2.07e+01 1h72C 296 2.10e+01 d.14.1.5,d.58.26.1 60712,60713 1qhlA 227 2.12e+01 1qhlA c.37.1.12 32382 1ynmA 247 2.14e+01 2tysB 397 2.18e+01 2tysB c.79.1.1 35272 1kqpA 271 2.18e+01 c.26.2.1 72883 1nsyA 271 2.18e+01 2nsyA c.26.2.1 31614 1wouA 123 2.18e+01 c.47.1.16 109471 1audA 101 2.23e+01 1urnA d.58.7.1 39156 1bvb 211 2.24e+01 1bvb a.138.1.3 19683 1kvs 338 2.25e+01 1xel c.2.1.2 29799 1b25A 619 2.29e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1vjpA 394 2.34e+01 c.2.1.3,d.81.1.3 100828,100829 2b7eA 59 2.34e+01 1bksB 397 2.35e+01 2tysB c.79.1.1 35285 2gh1A 301 2.39e+01 1fsz 372 2.39e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1nf3C 128 2.41e+01 b.36.1.1 85596 1jfbA 404 2.45e+01 a.104.1.1 66624 1f24A 402 2.46e+01 1rom a.104.1.1 18953 1evuA 731 2.50e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1ve0A 134 2.52e+01 1a50B 396 2.53e+01 2tysB c.79.1.1 35280 2aefA 234 2.56e+01 1fwkA 296 2.58e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1pbgA 468 2.60e+01 1e70M c.1.8.4 28946 1w2iA 91 2.63e+01 d.58.10.1 109127 1k8yB 396 2.67e+01 c.79.1.1 72184 1zhrA 238 2.73e+01 1ih8A 271 2.76e+01 2nsyA c.26.2.1 62377 1wrjA 156 2.79e+01 1v0lA 313 2.81e+01 c.1.8.3 108207 2nsyA 271 2.82e+01 2nsyA c.26.2.1 31612 1yizA 429 2.82e+01 1od8A 313 2.83e+01 c.1.8.3 86838 3pbgA 468 2.84e+01 1e70M c.1.8.4 28951 1ex0A 731 2.84e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1fjgC 239 2.84e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1luzA 88 2.86e+01 b.40.4.5 74271 1o1zA 234 2.90e+01 c.1.18.3 86555 1zhmA 238 2.94e+01 1wspA 84 2.94e+01 2culA 232 2.95e+01 1ee2A 373 2.96e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1no5A 114 2.97e+01 d.218.1.5 92014 1te7A 103 3.05e+01 1juvA 193 3.09e+01 c.71.1.1 90912 1id0A 152 3.10e+01 d.122.1.3 66111 1focA 132 3.16e+01 1c52 a.3.1.1 15812 1e0wA 313 3.19e+01 1taxA c.1.8.3 59150 1ghtA 105 3.19e+01 2rslA c.53.1.1 60526 1o9gA 250 3.20e+01 c.66.1.29 86692 1qlmA 316 3.25e+01 1qlmA d.147.1.1 41765 1gguA 731 3.30e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21885,22179,22180,37115 1n99A 166 3.33e+01 b.36.1.1,b.36.1.1 85459,85460 1zhpA 238 3.35e+01 1cojA 212 3.37e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1ep3B 262 3.37e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1nu4A 97 3.39e+01 d.58.7.1 80731 1wmhA 89 3.41e+01 1qopB 396 3.43e+01 2tysB c.79.1.1 35270 2dfkA 402 3.45e+01 1gd1O 334 3.48e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2adoA 196 3.61e+01 1vcvA 226 3.62e+01 1n8kA 374 3.69e+01 b.35.1.2,c.2.1.1 80298,80299 1gh6A 114 3.69e+01 a.2.3.1 65191 1hetA 374 3.69e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 8adh 374 3.71e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1a71A 374 3.76e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1heuA 374 3.77e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 2d9rA 104 3.77e+01 1jhsA 188 3.77e+01 d.107.1.1 84172 1eceA 358 3.77e+01 1eceA c.1.8.3 28813 1bby 69 3.78e+01 2bby a.4.5.15 16149 1axgA 374 3.80e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 2gd1O 334 3.81e+01 1dssG c.2.1.3,d.81.1.1 29978,39893 1c0dA 358 3.85e+01 1eceA c.1.8.3 28815 2bby 69 3.86e+01 2bby a.4.5.15 16148 2ohxA 374 3.87e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1axeA 374 3.87e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 2aq4A 434 3.88e+01 1woqA 267 3.89e+01 c.55.1.10,c.55.1.10 109462,109463 2awpA 198 3.91e+01 2g6tA 306 3.92e+01 1xfcA 384 3.98e+01 1nijA 318 4.01e+01 c.37.1.10,d.237.1.1 85741,85742 1f0cA 305 4.03e+01 1c8oA e.1.1.1 42676 1vkuA 100 4.06e+01 a.28.1.1 108690 1ri7A 171 4.10e+01 a.4.5.32,d.58.4.2 97504,97505 1mo9A 523 4.14e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 2etxA 209 4.15e+01 1bdfA 235 4.17e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1smlA 269 4.18e+01 1smlA d.157.1.1 42053 1ggtB 731 4.19e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21882,22173,22174,37112 1xx9A 238 4.25e+01 1cby 259 4.31e+01 1cby d.103.1.1 40705 1rh9A 373 4.36e+01 1xtoA 311 4.40e+01 2a15A 139 4.45e+01 1enwA 114 4.47e+01 1enwA a.5.4.1 16291 1vddA 228 4.47e+01 e.49.1.1 108519 1c8oA 300 4.52e+01 1c8oA e.1.1.1 42677 1sq9A 397 4.53e+01 b.69.4.1 105889 1d1gA 168 4.54e+01 1d1gA c.71.1.1 34889 1vicA 262 4.54e+01 c.68.1.13 100756 2gfgA 193 4.54e+01 1x74A 360 4.56e+01 1z6gA 218 4.57e+01 1pbjA 125 4.58e+01 d.37.1.1,d.37.1.1 94414,94415 1ma3A 253 4.61e+01 c.31.1.5 78883 1mu7A 485 4.65e+01 d.136.1.3,d.136.1.3 79475,79476 1hdoA 206 4.66e+01 1he2A c.2.1.2 60965 1b5tA 275 4.68e+01 1b5tA c.1.23.1 29676 1he2A 206 4.70e+01 1he2A c.2.1.2 60966 1vr4A 103 4.70e+01 1xttA 216 4.71e+01 1ifa 158 4.72e+01 1ifa a.26.1.3 16892 1h7zA 194 4.72e+01 1qhvA b.21.1.1 60733 1toaA 313 4.76e+01 1toaA c.92.2.2 35598 1r6jA 82 4.83e+01 b.36.1.1 97151 1tiqA 180 4.85e+01 d.108.1.1 107010 2aioA 269 4.90e+01 1r5jA 337 4.91e+01 c.77.1.5 97097 1xyfA 436 4.92e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 2udpA 338 4.99e+01 1xel c.2.1.2 29791 1vbvA 105 5.03e+01 1ny4A 82 5.06e+01 b.40.4.5 92316 1qx4A 274 5.08e+01 b.43.4.2,c.25.1.1 104624,104625 1aogA 485 5.08e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1nteA 82 5.09e+01 b.36.1.1 86163 1wluA 136 5.10e+01 1ri5A 298 5.20e+01 c.66.1.34 97502 1o0yA 260 5.24e+01 c.1.10.1 80756 1cz3A 168 5.25e+01 1d1gA c.71.1.1 34891 1ve6A 582 5.28e+01 1wlyA 333 5.31e+01 1fzqA 181 5.33e+01 1hurA c.37.1.8 32060 1duvG 333 5.44e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1kjwA 295 5.45e+01 b.34.2.1,c.37.1.1 68643,68644 1a9y 338 5.53e+01 1xel c.2.1.2 29789 1xel 338 5.55e+01 1xel c.2.1.2 29786 1tbrR 103 5.55e+01 1tbrR g.68.1.1,g.68.1.1 44707,44708 1jxmA 301 5.55e+01 b.34.2.1,c.37.1.1 67420,67421 1udb 338 5.55e+01 1xel c.2.1.2 29787 1a9z 338 5.56e+01 1xel c.2.1.2 29795 1udc 338 5.62e+01 1xel c.2.1.2 29785 2b4rO 345 5.67e+01 2gw6A 123 5.72e+01 1o58A 303 5.75e+01 c.79.1.1 92491 1sn4A 64 5.78e+01 1aho g.3.7.1 44136 1d0sA 356 5.80e+01 1d0vA c.39.1.1 32477 2hvm 273 5.80e+01 1cnv c.1.8.5 28985 2bo4A 397 5.86e+01 1i8fA 81 5.89e+01 1i8fA b.38.1.1 61959 1exg 110 5.90e+01 1exg b.2.2.1 22387 1wu3I 161 5.97e+01 1ml8A 134 5.97e+01 d.227.1.2 85013 1f2tB 148 6.04e+01 1f2tB 1j1yA 136 6.04e+01 d.38.1.5 90776 1jy1A 464 6.09e+01 d.136.1.3,d.136.1.3 67438,67439 1ri6A 343 6.09e+01 b.69.11.1 97503 1dkuA 317 6.14e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1wyxA 69 6.17e+01 2dldA 337 6.24e+01 1dxy c.2.1.4,c.23.12.1 30099,31359 1s0pA 176 6.32e+01 a.192.1.1 98300 1hm9A 468 6.36e+01 b.81.1.4,c.68.1.5 65866,65867 1qg8A 255 6.41e+01 1qg8A c.68.1.1 34505 1z52A 470 6.47e+01 1icxA 155 6.54e+01 d.129.3.1 71191 1pyfA 312 6.58e+01 c.1.7.1 95334 1vi1A 345 6.60e+01 c.77.1.4 100724 1t0hA 132 6.60e+01 b.34.2.1 106207 1wkqA 164 6.64e+01 c.97.1.2 109393 1rboC 123 6.67e+01 1rboC d.73.1.1 39634 8rucI 123 6.68e+01 1rboC d.73.1.1 39629 1qdlB 195 6.70e+01 1qdlB c.23.16.1 31437 1ydmA 187 6.70e+01 1w9zA 283 6.74e+01 1ydyA 356 6.76e+01 1s50A 259 6.78e+01 1ej6D 418 6.84e+01 i.7.1.1 45970 1rmi 160 6.88e+01 1ifa a.26.1.3 16891 1eq6A 189 6.97e+01 1eq6A d.107.1.1 40796 1larA 575 6.98e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1ip9A 85 6.99e+01 1ip9A d.15.2.2 62638 1e0tA 470 7.04e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1es6A 296 7.04e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1xcbA 211 7.09e+01 a.4.5.38,c.2.1.12 109552,109553 1ep2B 261 7.21e+01 1ep2B b.43.4.2,c.25.1.3 25666,31556 1t8qA 336 7.21e+01 c.1.18.3 106669 1f9vA 347 7.27e+01 1bg2 c.37.1.9 59745 1ur1A 378 7.31e+01 c.1.8.3 99804 1vqoI 162 7.36e+01 1fjgB 256 7.42e+01 1fjfB c.23.15.1 31400 1uwzA 136 7.45e+01 c.97.1.1 108081 1zc1A 208 7.48e+01 1bg6 359 7.52e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1ylqA 96 7.54e+01 1jtkA 136 7.55e+01 c.97.1.1 71862 1b33N 67 7.56e+01 1b33N d.30.1.1 38459 1u46A 291 7.66e+01 d.144.1.7 107656 1k0fA 277 7.67e+01 c.92.2.2 71974 1ll2A 333 7.76e+01 c.68.1.14 74005 1uurA 473 7.80e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1ltlA 279 7.82e+01 b.40.4.11 84701 1qayA 428 7.84e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 1xvqA 175 7.84e+01 2amyA 246 7.90e+01 1g291 372 8.10e+01 1g291 1vhxA 150 8.12e+01 c.55.3.8 100712 2fh7A 595 8.14e+01 1vphA 149 8.18e+01 1ck9A 104 8.25e+01 1ck9A d.79.3.1 39806 1g97A 459 8.28e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1zpvA 91 8.48e+01 1xdpA 687 8.49e+01 1z4rA 168 8.53e+01 1kqzA 273 8.62e+01 c.1.8.5 68844 1ejjA 511 8.66e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1wjcA 47 8.66e+01 1wjcA a.4.10.1 16261 3seb 238 8.67e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1pk9A 237 8.67e+01 c.56.2.1 94823 1cf7A 76 8.72e+01 1cf7B a.4.5.17 16151 1preB 470 8.79e+01 1preA d.169.1.2,f.8.1.1 42438,43825 1qrkA 731 8.81e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1kqyA 273 8.85e+01 c.1.8.5 68843 2akoA 251 8.87e+01 1vfsA 386 8.91e+01 b.49.2.2,c.1.6.1 108584,108585 1omzA 293 8.93e+01 c.68.1.15 87093 1ej0A 180 8.94e+01 1ej0A c.66.1.2 34179 1jjgA 102 8.95e+01 b.40.4.5 71696 1cfr 285 8.96e+01 1cfr c.52.1.7 33312