# 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 1exmA 405 7.16e-26 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ha3A 405 7.23e-26 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1aipE 405 9.72e-26 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1efcA 393 5.03e-25 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1jnyA 435 5.25e-25 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1f60A 458 1.15e-23 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1d2eA 397 1.50e-23 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1kk1A 410 1.01e-11 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1s0uA 408 1.87e-09 1n0uA 842 4.19e-06 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1g7sA 594 5.34e-06 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1g7rA 594 7.69e-06 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1g7tA 594 3.48e-05 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1d1nA 99 9.13e-05 1d1nA b.43.3.1 25718 1dar 691 1.63e-02 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1fnmA 691 2.15e-02 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1qfgA 725 3.04e-02 1by5A f.4.3.3 43803 1pkoA 139 3.55e-02 b.1.1.1 88147 1oi1A 221 8.05e-02 b.34.9.3 87037 b.34.9.3 87038 2eifA 136 8.10e-02 1bkb b.34.5.2 24607 b.40.4.5 25339 1mq7A 154 9.46e-02 b.85.4.1 79404 1by5A 714 9.84e-02 1by5A f.4.3.3 43800 1by3A 714 1.02e-01 1by5A f.4.3.3 43801 1sixA 174 1.44e-01 2fcpA 723 1.49e-01 1by5A f.4.3.3 43802 1kn9A 249 1.91e-01 b.87.1.2 68699 1b12A 248 1.97e-01 1b12A b.87.1.2 28388 1pm4A 119 3.07e-01 1pmy 123 3.37e-01 1bqk b.6.1.1 22888 1po0A 751 5.04e-01 1kmoA 774 5.06e-01 f.4.3.3 72753 1bkb 136 5.76e-01 1bkb b.34.5.2 24609 b.40.4.5 25341 1fiwA 290 9.25e-01 5ptp 1etu 394 1.09e+00 1efcA c.37.1.8 64737 1gvhA 396 1.18e+00 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1vjnA 220 1.29e+00 1dupA 152 1.45e+00 1dupA b.85.4.1 28351 1euwA 152 1.45e+00 1dupA b.85.4.1 28349 1b7yB 785 1.52e+00 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1n7eA 97 1.66e+00 1khiA 176 1.75e+00 b.34.5.2 77408 b.40.4.5 77409 1sro 76 1.86e+00 1sro b.40.4.5 25327 1bmfA 510 2.01e+00 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1kzlA 208 2.15e+00 b.43.4.3 77635 b.43.4.3 77636 1ah6 220 2.43e+00 1yer d.122.1.1 41094 1gttA 429 2.54e+00 d.177.1.1 70529 d.177.1.1 70530 1g3p 217 2.61e+00 1g3p b.37.1.1 24788 b.37.1.1 24789 1h8eA 510 3.01e+00 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 3pmgA 561 3.07e+00 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1ten 90 3.21e+00 1ten b.1.2.1 21990 1irp 153 3.23e+00 1irp b.42.1.2 25559 1mgtA 174 3.29e+00 1mgtA a.4.2.1 16078 c.55.7.1 33753 1qhoA 686 3.35e+00 1cxlA b.1.18.2 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1pysB 785 3.44e+00 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1m56B 264 3.54e+00 b.6.1.2 74472 f.17.2.1 74473 1nb9A 147 3.62e+00 b.43.5.1 85515 1e79A 510 3.90e+00 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1skyB 502 4.05e+00 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1i7oA 429 4.36e+00 1i7oA d.177.1.1 61893 d.177.1.1 61894 2sfa 191 4.53e+00 1qq4A b.47.1.1 25815 1f1gA 154 4.62e+00 b.1.8.1 76153 1jcv 153 4.73e+00 1mfmA b.1.8.1 22279 1eiyB 785 4.75e+00 1pysB a.6.1.1 16305 a.6.1.1 16306 b.40.4.4 25314 d.58.13.1 39313 d.104.1.1 40782 d.138.1.1 41458 1bb9 115 4.81e+00 1bb9 b.34.2.1 24554 1qtfA 246 4.90e+00 1agjA b.47.1.1 25830 1o54A 277 5.05e+00 1umwA 237 5.12e+00 1hh2P 344 5.43e+00 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1n7fA 97 6.37e+00 1g8lA 411 6.48e+00 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1im3D 95 6.78e+00 1im3D b.1.18.5 62568 1rtfB 252 7.06e+00 5ptp 1pgs 314 7.10e+00 1pgs b.121.1.1 23653 b.121.1.1 23654 1uz5A 402 7.13e+00 1hxmA 229 7.15e+00 1hxmA b.1.1.1 61367 b.1.1.2 61368 1e0tA 470 7.20e+00 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1jhfA 202 7.21e+00 a.4.5.2 63057 b.87.1.1 63058 1jj2A 239 7.21e+00 1rl2A b.34.5.3 63084 b.40.4.5 63085 1paz 123 7.24e+00 1bqk b.6.1.1 22878 1h0jA 60 7.33e+00 g.7.1.1 83432 1ui0A 205 7.68e+00 1gg6B 131 7.71e+00 5ptp 1fr3A 67 7.81e+00 1fr3A b.40.6.1 25436 1j7lA 264 7.87e+00 d.144.1.6 62697 1earA 147 7.93e+00 b.107.1.1 64875 d.58.38.1 64876 1miuA 738 8.03e+00 a.170.1.1 79153 a.171.1.1 79154 b.40.4.3 79155 b.40.4.3 79156 b.40.4.3 79157 1h6yA 170 8.28e+00 b.18.1.7 70904 1gc1H 229 8.29e+00 1gc1H b.1.1.1 20265 b.1.1.2 21265 1cdtA 60 8.65e+00 1tgxA g.7.1.1 44415 1j5qA 437 8.67e+00 b.121.2.3 77084 b.121.2.3 77085 1fa4A 105 9.01e+00 1plc b.6.1.1 22867 1vpsA 289 9.46e+00 1vpsA b.121.6.1 23336 1ejeA 192 9.48e+00 1ejeA b.45.1.2 25757 1hcxA 127 9.62e+00 b.109.1.1 65800 1oxsC 353 1.02e+01 b.40.6.3 87519 c.37.1.12 87520 1eylA 186 1.02e+01 1wba b.42.4.1 25593 1v74A 107 1.04e+01 1g2lA 235 1.06e+01 b.47.1.2 65112 1oxxK 353 1.06e+01 1nfiC 301 1.09e+01 b.1.18.1 21943 b.2.5.3 22456 1h9mA 145 1.14e+01 1h9jA b.40.6.2 60833 b.40.6.2 60834 1lxtA 561 1.21e+01 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1t5eA 360 1.21e+01 1d5mB 192 1.22e+01 1iakB b.1.1.2 21618 d.19.1.1 38192 1gj7B 253 1.22e+01 1ordA 730 1.24e+01 1ordA c.23.1.4 31274 c.67.1.5 34503 d.125.1.1 41124 1ospH 218 1.25e+01 1igtB b.1.1.1 20117 b.1.1.2 21147 1ff4A 65 1.26e+01 g.7.1.1 83251 1gmmA 133 1.26e+01 b.18.1.10 65314 1bdo 80 1.26e+01 1bdo b.84.1.1 28214 1mhnA 59 1.27e+01 b.34.9.1 84964 1eysH 259 1.28e+01 6prcH b.41.1.1 25484 f.23.10.1 43517 1gztA 115 1.29e+01 b.115.1.1 76428 1sva1 361 1.31e+01 1vpsA 1k2i1 245 1.32e+01 1h9jA 145 1.32e+01 1h9jA b.40.6.2 60829 b.40.6.2 60830 2sga 181 1.35e+01 1qq4A b.47.1.1 25808 1jroA 462 1.35e+01 a.56.1.1 67137 d.15.4.2 67138 d.87.2.1 67139 d.145.1.3 67140 1c5yB 253 1.38e+01 5ptp 1uxxX 133 1.38e+01 1hfuA 503 1.41e+01 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1i16 130 1.41e+01 1i16 b.36.1.2 24787 1iknA 286 1.52e+01 1a3qA b.1.18.1 21936 b.2.5.3 22449 1qcsA 211 1.52e+01 1qcsA b.52.2.3 26927 d.31.1.1 38461 1vpsB 289 1.54e+01 1vpsA b.121.6.1 23337 1tuc 63 1.56e+01 1tuc b.34.2.1 24492 1fh0A 221 1.56e+01 1cs8A d.3.1.1 59832 1j7iA 264 1.57e+01 1j7iA d.144.1.6 62694 2gpr 154 1.58e+01 1gpr b.84.3.1 28269 1s3iA 310 1.59e+01 1sgc 181 1.60e+01 1qq4A b.47.1.1 25810 1gnhA 206 1.61e+01 1sacA b.29.1.5 24252 1wwcA 118 1.61e+01 1wwcA b.1.1.4 21778 1bv4A 118 1.62e+01 1rtm1 d.169.1.1 42380 1vi4A 174 1.64e+01 2hft 218 1.66e+01 1boy b.1.2.1 21951 b.1.2.1 21952 1cz4A 185 1.68e+01 1cz4A b.52.2.3 26934 d.31.1.1 38468 1bjt 793 1.68e+01 1bjt e.11.1.1 43249 1oj4A 283 1.72e+01 2cdx 60 1.73e+01 1tgxA g.7.1.1 44436 1ig0A 319 1.78e+01 1ig0A b.82.6.1 62354 c.100.1.1 62355 1jp4A 308 1.78e+01 1jp4A e.7.1.1 63223 1m4vA 204 1.80e+01 b.40.2.2 74459 d.15.6.1 74460 1mnnA 340 1.82e+01 b.2.5.7 79324 1pwt 61 1.83e+01 1tud b.34.2.1 24490 1b65A 375 1.84e+01 1b65A d.154.1.1 42020 1qwyA 291 1.85e+01 1jdw 423 1.87e+01 1jdw d.126.1.2 41129 1oruA 195 1.90e+01 1dlc 584 1.90e+01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1h9sA 140 1.90e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1rot 149 1.92e+01 1fkj d.26.1.1 38429 1nglA 179 1.93e+01 1nglA b.60.1.1 27146 1lnsA 763 1.93e+01 a.40.2.1 78101 b.18.1.13 78102 c.69.1.21 78103 1m6uA 272 1.94e+01 b.2.5.7 78706 1q7hA 153 1.98e+01 1scs 237 2.00e+01 1nls b.29.1.1 23930 1e96B 203 2.00e+01 1e96B a.118.8.1 19211 1ngzB 220 2.00e+01 b.1.1.1 80502 b.1.1.2 80503 2cgaA 245 2.01e+01 5ptp b.47.1.2 26028 1m3yA 413 2.04e+01 b.121.2.3 78579 b.121.2.3 78580 1c5mD 255 2.04e+01 5ptp b.47.1.2 26338 1qorA 327 2.04e+01 1qorA b.35.1.2 24766 c.2.1.1 29782 1qfxA 460 2.06e+01 1qfxA c.60.1.3 33994 1mtnC 97 2.07e+01 5ptp 1h0hA 977 2.07e+01 b.52.2.2 76435 c.81.1.1 76436 1tgxA 60 2.08e+01 1tgxA g.7.1.1 44398 1krhA 338 2.11e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1kobA 387 2.12e+01 1tkiA d.144.1.7 41640 1c3hA 137 2.14e+01 1aohA 147 2.15e+01 1aohA b.2.2.2 22401 1vpfA 102 2.25e+01 1vpfA g.17.1.1 44767 1fjxA 327 2.29e+01 6mhtA c.66.1.26 34228 1mkyA 439 2.30e+01 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1jjoC 261 2.32e+01 1vppV 102 2.32e+01 1vpfA g.17.1.1 44753 1hurA 180 2.39e+01 1hurA c.37.1.8 32052 1shg 62 2.40e+01 1ckaA b.34.2.1 24493 4blmA 265 2.43e+01 1btl e.3.1.1 42721 1ga1A 372 2.46e+01 1ga1A c.41.1.2 32557 1l1nA 183 2.47e+01 b.47.1.4 73476 1bw0A 416 2.47e+01 1bw0A c.67.1.1 34385 1fwcB 106 2.48e+01 1ubpB b.85.3.1 28324 2kauB 106 2.48e+01 1ubpB b.85.3.1 28328 1qpcA 279 2.52e+01 1fgkA d.144.1.7 41685 1bbzA 58 2.55e+01 1bbzA b.34.2.1 24477 1qpoA 284 2.55e+01 1qpoA c.1.17.1 29561 d.41.2.1 38597 1vjuA 309 2.55e+01 1bbzE 58 2.57e+01 1bbzA b.34.2.1 24479 1rds 105 2.59e+01 9rnt d.1.1.4 36236 1l5jA 865 2.62e+01 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1hmy 327 2.63e+01 6mhtA c.66.1.26 34229 1k5wA 152 2.63e+01 b.7.1.2 68212 1nls 237 2.63e+01 1nls b.29.1.1 23928 1m4zA 238 2.64e+01 b.34.12.1 78630 1iz6A 138 2.66e+01 b.34.5.2 76976 b.40.4.5 76977 1aboA 62 2.67e+01 1bbzA b.34.2.1 24474 1fjsA 234 2.71e+01 1ucyE b.47.1.2 26336 1apmE 350 2.72e+01 1cdkA d.144.1.7 41628 1l7lA 121 2.73e+01 b.18.1.16 77790 1eaxA 241 2.77e+01 b.47.1.2 64889 1pv9A 348 2.78e+01 1i8aA 189 2.78e+01 1i82A b.1.9.2 61951 1rdj1 113 2.79e+01 1rtm1 1gg6C 97 2.80e+01 5ptp 1ewkA 490 2.80e+01 1ewkA c.93.1.1 35712 1lox 662 2.81e+01 1lox a.119.1.2 19238 b.12.1.1 23638 1pk6A 133 2.84e+01 3ullA 132 2.84e+01 3ullA b.40.4.3 25282 1diwA 441 2.84e+01 1a8d b.29.1.6 24264 b.42.4.2 25609 1q5hA 147 2.88e+01 1dmhA 311 2.92e+01 1dmhA b.3.6.1 22633 1e6oL 212 2.95e+01 32c2A b.1.1.1 20494 b.1.1.2 21452 3mhtA 327 2.96e+01 6mhtA c.66.1.26 34234 1q0xH 221 3.02e+01 3lck 271 3.06e+01 1fmk d.144.1.7 41686 1kas 412 3.08e+01 1dd8A c.95.1.1 35964 c.95.1.1 35965 32c2A 217 3.10e+01 32c2A b.1.1.1 20438 b.1.1.2 21404 1erjA 393 3.12e+01 1erjA b.69.4.1 27660 1ijaA 148 3.12e+01 1ijaA b.100.1.1 62484 1iq6A 134 3.14e+01 d.38.1.4 76755 1qovH 260 3.14e+01 6prcH b.41.1.1 25464 f.23.10.1 43457 1vhzA 198 3.16e+01 12e8L 214 3.19e+01 8fabA b.1.1.1 20268 b.1.1.2 21268 1q8uA 350 3.21e+01 1a65A 504 3.24e+01 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1q9rA 219 3.24e+01 1lxyA 409 3.29e+01 1jb9A 316 3.30e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1h5bA 113 3.30e+01 1tvdA b.1.1.1 60638 1eb0A 147 3.31e+01 b.107.1.1 64890 d.58.38.1 64891 1fdr 248 3.37e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1lbvA 252 3.39e+01 e.7.1.1 73813 1oxcA 114 3.41e+01 1gqpA 221 3.43e+01 b.18.1.9 70372 1s9rA 410 3.43e+01 1iyu 79 3.48e+01 1iyu b.84.1.1 28227 1r0pA 312 3.54e+01 1aohB 147 3.54e+01 1aohA b.2.2.2 22402 1p8xA 344 3.56e+01 1ixlA 131 3.57e+01 1gc0A 398 3.58e+01 c.67.1.3 70168 1ejrB 101 3.58e+01 1ubpB b.85.3.1 28320 1flrL 219 3.58e+01 8fabA b.1.1.1 19904 b.1.1.2 20998 1awd 94 3.65e+01 1awd d.15.4.1 37673 1c28A 135 3.66e+01 1c28A b.22.1.1 23857 1c4kA 730 3.66e+01 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1gmeA 151 3.68e+01 b.15.1.1 65305 1qg0A 308 3.69e+01 1fnc b.43.4.2 25639 c.25.1.1 31529 1d5tA 433 3.70e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1mn4A 282 3.70e+01 b.2.5.7 79313 1ejxB 101 3.73e+01 b.85.3.1 83183 1rzhH 260 3.73e+01 1a8d 452 3.74e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 1i82A 189 3.74e+01 1i82A b.1.9.2 61937 1qhlA 227 3.76e+01 1qhlA c.37.1.12 32382 2phy 125 3.78e+01 3pyp d.110.3.1 40901 1oz2A 331 3.87e+01 1f20A 435 3.87e+01 b.43.4.1 64932 c.25.1.4 64933 1sh1 48 3.87e+01 1sh1 g.9.1.1 44597 1jj2S 119 3.89e+01 1ffkQ b.34.5.1 63104 1i3uA 127 3.90e+01 1gc1H b.1.1.1 61636 1bx2B 191 3.95e+01 1iakB b.1.1.2 21610 d.19.1.1 38184 1msk 331 3.95e+01 1msk d.173.1.1 42495 1rdo1 113 3.96e+01 1rtm1 1cdkA 350 3.98e+01 1cdkA d.144.1.7 41620