# List of top-scoring protein chains for t04-100-30-dssp-ehl2-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 2fh7A 595 1.23e-55 1larA 575 2.51e-54 1larA c.45.1.2,c.45.1.2 32693,32694 2shpA 525 5.89e-49 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 2f71A 298 2.13e-48 1g7fA 298 2.47e-48 1pty c.45.1.2 60330 1p15A 253 4.54e-48 c.45.1.2 93894 1pa1A 310 4.73e-48 c.45.1.2 94404 1ptvA 321 5.22e-48 1pty c.45.1.2 32665 2b3oA 532 1.17e-47 2b49A 287 1.31e-47 1wchA 315 8.04e-46 2bzlA 325 1.05e-44 1jlnA 297 7.63e-44 1pty c.45.1.2 63172 2bv5A 282 5.15e-43 2bijA 305 9.13e-43 1ytw 306 7.26e-20 1ytw c.45.1.2 32689 1lyvA 306 2.72e-19 c.45.1.2 74348 1g4wR 383 1.68e-16 1g4uS a.24.11.1,c.45.1.2 16644,32692 1oheA 348 1.50e-14 c.45.1.1,c.45.1.1 87013,87014 1x24A 180 5.89e-13 1zclA 180 2.41e-12 1zckA 154 4.42e-12 1rxdA 159 5.29e-12 1fpzA 212 1.78e-08 1fpzA c.45.1.1 59976 1d5rA 324 2.56e-06 1d5rA b.7.1.1,c.45.1.1 23181,32697 1vhrA 184 1.22e-05 1vhrA c.45.1.1 32651 1yn9A 169 1.50e-05 1wrmA 165 2.01e-05 1yz4A 160 5.27e-05 1i9sA 210 2.61e-04 1i9sA c.45.1.1 62099 2c46A 241 2.89e-04 1mkp 144 1.51e-03 1vhrA c.45.1.1 32654 1u24A 337 2.73e-03 1ywfA 296 2.13e-02 1lw3A 657 3.46e-02 b.55.1.8,c.45.1.3 91152,91153 1zsqA 528 4.43e-02 1xriA 151 7.43e-02 1w6sA 599 9.70e-02 1wkbA 810 3.92e-01 1k47A 337 4.25e-01 d.14.1.5,d.58.26.4 72040,72041 2d5cA 263 8.76e-01 1wxdA 263 8.83e-01 1npyA 271 9.01e-01 c.2.1.7,c.58.1.5 85995,85996 2cy0A 263 9.66e-01 1gvhA 396 1.56e+00 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 2a6hA 315 2.08e+00 1usyA 275 2.10e+00 1pg4A 652 2.20e+00 e.23.1.1 88067 1g60A 260 2.39e+00 c.66.1.11 70151 1ojrA 274 2.68e+00 c.74.1.1 93147 1h2wA 710 2.83e+00 b.69.7.1,c.69.1.4 76596,76597 1qfmA 710 2.83e+00 1qfmA b.69.7.1,c.69.1.4 27673,34641 1aqb 183 3.44e+00 1aqb b.60.1.1 27084 1xg4A 295 3.66e+00 2akaA 776 3.70e+00 1mumA 295 3.73e+00 c.1.12.7 85108 1jhdA 396 3.86e+00 b.122.1.3,c.26.1.5 66712,66713 1nx8A 273 4.06e+00 b.82.2.8 86374 1lrwA 600 4.36e+00 b.70.1.1 91111 1zoiA 276 4.45e+00 1x9pA 523 4.89e+00 1d0yA 761 5.80e+00 1lvk b.34.3.1,c.37.1.9 24581,32178 1rj9A 304 6.07e+00 a.24.13.1,c.37.1.10 97553,97554 1j8mF 297 6.20e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1zboA 210 6.37e+00 1a88A 275 6.50e+00 1brt c.69.1.12 34707 1e5mA 416 6.53e+00 1dd8A c.95.1.1,c.95.1.1 58973,58974 1ujqA 305 6.79e+00 c.1.12.7 99463 1ihuA 589 6.98e+00 c.37.1.10,c.37.1.10 62394,62395 1yqyA 523 7.06e+00 1vimA 200 7.58e+00 c.80.1.3 100758 1m1zA 513 7.77e+00 c.26.2.1,d.153.1.1 78457,78458 1vom 762 7.81e+00 1lvk b.34.3.1,c.37.1.9 24577,32174 1j8yF 297 7.96e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 1kt6A 183 8.44e+00 b.60.1.1 84466 1f2tA 149 8.46e+00 1f2tA c.37.1.12 32373 1w9iA 770 8.56e+00 1hbq 183 8.58e+00 1aqb b.60.1.1 27078 1vqvA 306 8.76e+00 1geqA 248 9.50e+00 2tysA c.1.2.4 28589 1vk3A 615 9.68e+00 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 2btoA 473 1.02e+01 1sotA 320 1.05e+01 b.36.1.4,b.47.1.1 105852,105853 1yub 245 1.09e+01 2ercA c.66.1.24 34219 1ako 268 1.12e+01 1ako d.151.1.1 41779 2fbmA 291 1.12e+01 1lvk 762 1.16e+01 1lvk b.34.3.1,c.37.1.9 24576,32173 1vjhA 122 1.17e+01 d.129.3.1 100811 1jrrA 382 1.18e+01 e.1.1.1 63256 1erjA 393 1.22e+01 1erjA b.69.4.1 27660 1pjr 724 1.29e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 1zz1A 369 1.33e+01 1pbgA 468 1.35e+01 1e70M c.1.8.4 28946 2gcuA 245 1.38e+01 1x6oA 174 1.39e+01 b.34.5.2,b.40.4.5 109493,109494 1nm8A 616 1.40e+01 c.43.1.3,c.43.1.3 85872,85873 1gmxA 108 1.41e+01 c.46.1.3 65355 1a8s 273 1.42e+01 1brt c.69.1.12 34710 2b2nA 344 1.45e+01 2d29A 387 1.47e+01 1ws9A 387 1.48e+01 1xzwA 426 1.49e+01 1oo4A 111 1.50e+01 d.93.1.1 87185 2cx9A 387 1.53e+01 1m1nB 522 1.54e+01 c.92.2.3 78418 1huxA 270 1.54e+01 1huxA c.55.1.5 61278 1dmuA 299 1.67e+01 1dmuA c.52.1.4 33294 1vkrA 125 1.69e+01 c.44.2.1 108689 1h65A 270 1.69e+01 c.37.1.8 65640 1dciA 275 1.72e+01 1dciA c.14.1.3 30918 1yb5A 351 1.77e+01 1cqxA 403 1.81e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1yt8A 539 1.85e+01 1ujpA 271 1.92e+01 c.1.2.4 99462 1zkpA 268 1.93e+01 1aa8A 347 1.94e+01 1an9A 1dbqA 289 2.01e+01 1qpzA c.93.1.1 35666 1quqB 121 2.01e+01 1quqB b.40.4.3 25305 1naqA 112 2.03e+01 d.58.5.2 91761 1iz0A 302 2.08e+01 b.35.1.2,c.2.1.1 83821,83822 1qqfA 277 2.10e+01 1c3d a.102.4.4 18875 1tj9A 121 2.12e+01 a.133.1.2 107015 1te5A 257 2.13e+01 d.153.1.1 106795 1us8A 147 2.17e+01 c.37.1.12 99859 2fw2A 260 2.19e+01 1lfwA 470 2.21e+01 c.56.5.4,d.58.19.1 77942,77943 1hp5A 512 2.25e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1czaN 917 2.26e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1sqzA 121 2.28e+01 a.133.1.2 98975 1tk4A 121 2.28e+01 a.133.1.2 107073 1w7jA 795 2.29e+01 1bg0 356 2.31e+01 1qh4A a.83.1.1,d.128.1.2 18476,41211 1oe9A 795 2.35e+01 b.34.3.1,c.37.1.9 92792,92793 1m15A 357 2.42e+01 a.83.1.1,d.128.1.2 78368,78369 1zwpA 121 2.45e+01 2g58A 121 2.45e+01 1p2fA 220 2.45e+01 a.4.6.1,c.23.1.1 87720,87721 1vg0A 650 2.58e+01 c.3.1.3,d.16.1.6 108596,108597 1wrrA 301 2.59e+01 1oqcA 125 2.62e+01 a.24.15.1 87264 1jltB 122 2.64e+01 a.133.1.2 66868 1l3aA 228 2.71e+01 d.18.1.2 73531 2atfA 200 2.71e+01 2cyeA 133 2.75e+01 1r12A 258 2.78e+01 e.4.1.1 96780 2f46A 156 2.90e+01 1f9vA 347 3.03e+01 1bg2 c.37.1.9 59745 1vlbA 907 3.03e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1r4uA 301 3.09e+01 d.96.1.4,d.96.1.4 97047,97048 1r6lA 239 3.16e+01 d.14.1.4,d.101.1.1 97153,97154 1uox 296 3.17e+01 1uox 1kpgA 287 3.21e+01 c.66.1.18 68735 1uyrA 737 3.23e+01 c.14.1.4,c.14.1.4 100188,100189 1igwA 434 3.26e+01 c.1.12.7 62370 2bjvA 265 3.26e+01 1b74A 254 3.29e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1euvA 221 3.35e+01 1euvA d.3.1.7 37133 1hlrA 907 3.39e+01 1jakA 512 3.40e+01 c.1.8.6,d.92.2.1 66472,66473 1aokB 122 3.42e+01 1poa a.133.1.2 19561 2g8yA 385 3.46e+01 1w2xA 758 3.48e+01 c.14.1.4,c.14.1.4 109134,109135 1xgsA 295 3.50e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1tqyB 415 3.50e+01 c.95.1.1,c.95.1.1 107247,107248 1ri6A 343 3.57e+01 b.69.11.1 97503 1mdl 359 3.59e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 2b5hA 200 3.66e+01 2aa4A 289 3.67e+01 1m2kA 249 3.69e+01 c.31.1.5 84754 1t3uA 104 3.76e+01 d.244.1.1 99120 1g9mG 321 3.76e+01 1gc1G d.172.1.1 42492 2awfA 172 3.79e+01 1f2dA 341 3.84e+01 1f2dA c.79.1.1 35298 1x54A 434 3.89e+01 1o63A 219 3.93e+01 c.94.1.1 92540 1tc5A 194 3.95e+01 c.110.1.1 106752 1tzjA 338 3.96e+01 1zpdA 568 3.98e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 1mk4A 157 4.00e+01 d.108.1.1 84979 1u0mA 382 4.09e+01 c.95.1.2,c.95.1.2 107557,107558 2b4gA 317 4.10e+01 2bhvA 246 4.19e+01 1z7dA 433 4.20e+01 2a6hC 1119 4.22e+01 1zczA 464 4.27e+01 2b06A 155 4.28e+01 1nf3C 128 4.39e+01 b.36.1.1 85596 1qdeA 224 4.39e+01 1qvaA c.37.1.19 32410 1rz2A 254 4.42e+01 b.100.1.1 105130 1x0rA 249 4.44e+01 1kvkA 395 4.46e+01 d.14.1.5,d.58.26.3 73060,73061 2fl7A 232 4.48e+01 1x9iA 302 4.58e+01 2mnr 357 4.65e+01 2mnr c.1.11.2,d.54.1.1 29245,38889 1htqA 477 4.71e+01 d.15.9.1,d.128.1.1 71035,71036 1ixh 321 4.75e+01 1ixh c.94.1.1 35761 1f8vA 355 4.79e+01 2bbvA b.121.4.4 23329 1z5vA 474 4.82e+01 1zr5A 214 4.85e+01 2a2cA 478 4.85e+01 1f75A 249 4.90e+01 1f75A c.101.1.1 59662 1e3pA 757 4.91e+01 1e3hA a.4.9.1,b.40.4.5,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16258,25328,37574,37575,38811,40697,40698 1wx1A 335 4.98e+01 1qlwA 328 4.99e+01 1qlwA c.69.1.15 34722 1kyqA 274 5.01e+01 c.2.1.11,e.37.1.1 73281,73282 1gsa 316 5.03e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 2b9wA 424 5.06e+01 1rzjG 321 5.06e+01 d.172.1.1 98200 1foeA 377 5.07e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1tzbA 302 5.15e+01 c.80.1.1 107470 1gr0A 367 5.15e+01 c.2.1.3,d.81.1.3 70379,70380 1pl8A 356 5.15e+01 b.35.1.2,c.2.1.1 94878,94879 1sazA 381 5.18e+01 1ywmA 200 5.24e+01 1fnc 314 5.45e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1xm7A 195 5.49e+01 1fnd 314 5.52e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1gveA 327 5.53e+01 c.1.7.1 70597 2a2dA 478 5.53e+01 2c27A 315 5.56e+01 1an9A 340 5.56e+01 1an9A c.4.1.2,d.16.1.3 30617,37904 1jffA 451 5.60e+01 c.32.1.1,d.79.2.1 62932,62933 1svdA 473 5.63e+01 1yjmA 110 5.65e+01 1yfsA 465 5.66e+01 1m4zA 238 5.69e+01 b.34.12.1 78630 1zo0A 126 5.73e+01 1udh 244 5.80e+01 3eugA c.18.1.1 31015 1wcgA 464 5.82e+01 1a8d 452 5.89e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 2f5xA 312 5.91e+01 1p3dA 475 5.96e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1rqbA 539 5.96e+01 a.5.7.2,c.1.10.5 105057,105058 1f28A 297 5.96e+01 1bkpA d.117.1.1 59608 1y13A 181 6.01e+01 1ve9A 347 6.02e+01 c.4.1.2,d.16.1.3 100571,100572 1z6aA 500 6.03e+01 1ab4 477 6.09e+01 1ab4 e.11.1.1 43251 1n2zA 245 6.11e+01 c.92.2.2 79865 2av4A 162 6.13e+01 1mgpA 313 6.14e+01 c.119.1.1 79098 1yzgA 179 6.19e+01 1uekA 275 6.23e+01 d.14.1.5,d.58.26.5 88483,88484 1vqoQ 96 6.31e+01 1ysrA 150 6.43e+01 1t9kA 347 6.43e+01 c.124.1.5 106721 1r45A 204 6.48e+01 1j33A 335 6.48e+01 c.39.1.1 77069 1tvjA 166 6.49e+01 2ex4A 241 6.60e+01 1pyfA 312 6.61e+01 c.1.7.1 95334 2brfA 110 6.61e+01 1jkmB 361 6.69e+01 1jkmA c.69.1.2 34634 1d3yA 301 6.85e+01 1d3yA e.12.1.1 43252 1ujxA 119 6.92e+01 b.26.1.2 99473 1t0iA 191 6.98e+01 c.23.5.4 106209 1mr3F 181 7.00e+01 c.37.1.8 79422 1qwzA 235 7.01e+01 b.100.1.1 96510 1s72Q 96 7.03e+01 b.34.5.1 105336 2aq6A 147 7.05e+01 1fm0E 150 7.11e+01 1fmaE d.41.5.1 38629 1rvgA 305 7.12e+01 c.1.10.2 97920 1ve6A 582 7.23e+01 1tph1 247 7.35e+01 1amk 1qgoA 264 7.36e+01 1qgoA c.92.1.2 35596 1lvwA 295 7.40e+01 c.68.1.6 84723 1isiA 265 7.40e+01 e.4.1.1 71394 1o6yA 299 7.41e+01 d.144.1.7 81106 1j0dA 341 7.46e+01 c.79.1.1 83902 2ahxA 617 7.53e+01 2aaa 484 7.53e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1jj2P 95 7.58e+01 1ffkN b.34.5.1 63101 1di6A 195 7.61e+01 1di6A c.57.1.1 33863 1ryiA 382 7.73e+01 1i1dA 161 7.76e+01 1i21A d.108.1.1 61526 2c34A 116 7.84e+01 1iw7C 1119 7.84e+01 e.29.1.1 71474 1j7nA 776 7.85e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1luaA 287 7.87e+01 c.2.1.7,c.58.1.4 78216,78217 1f8eA 388 7.88e+01 2qwc b.68.1.1 59694 1wtjA 343 7.90e+01 1r0wA 286 7.93e+01 c.37.1.12 96754 1iybA 208 7.97e+01 d.124.1.1 90720 1qopB 396 8.01e+01 2tysB c.79.1.1 35270 1umwA 237 8.02e+01 d.223.1.2,d.223.1.2 99631,99632 3cla 213 8.22e+01 3cla c.43.1.1 32610 2ddrA 306 8.26e+01 1riqA 465 8.42e+01 a.203.1.1,d.104.1.1 97516,97517 1kcfA 258 8.47e+01 a.140.2.1,c.55.3.7 68434,68435 1q52A 314 8.51e+01 c.14.1.3 95846 1jftA 340 8.56e+01 a.35.1.5,c.93.1.1 66652,66653 2fsxA 148 8.61e+01 1kaeA 434 8.66e+01 c.82.1.2 72247 1spvA 184 8.67e+01 c.50.1.2 98957 2bmoA 447 8.70e+01 1yixA 265 8.75e+01 1z63A 500 8.76e+01 1jvbA 347 8.79e+01 b.35.1.2,c.2.1.1 77181,77182 1fadA 99 8.80e+01 1fadA a.77.1.2 18428 2f2fC 186 8.86e+01 1ogsA 497 8.92e+01 b.71.1.2,c.1.8.3 86997,86998 1wouA 123 8.92e+01 c.47.1.16 109471 1j58A 385 8.93e+01 b.82.1.2 71531 2as0A 396 8.95e+01 1m2xA 223 8.98e+01 d.157.1.1 84764 1mtzA 293 9.00e+01 c.69.1.7 79467