# List of top-scoring protein chains for t2k-100-30-str 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 1jj2S 119 1.16e-15 1ffkQ b.34.5.1 63104 1ffkQ 119 4.03e-14 1ffkQ b.34.5.1 24605 1az9 457 1.59e-01 1az9 c.55.2.1 33547 d.127.1.1 41164 1a16 440 1.59e-01 1az9 c.55.2.1 33548 d.127.1.1 41165 1qa7B 217 4.45e-01 1havA b.47.1.4 26426 1bmfA 510 6.21e-01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1ejfA 125 8.66e-01 1ejfA b.15.1.2 23683 1qmyA 167 9.68e-01 1qmyA d.3.1.2 37094 1e79A 510 1.27e+00 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1havA 217 1.31e+00 1havA b.47.1.4 26423 1bbzA 58 1.50e+00 1bbzA b.34.2.1 24477 1bbzE 58 1.52e+00 1bbzA b.34.2.1 24479 1aboA 62 1.69e+00 1bbzA b.34.2.1 24474 1qa7A 217 1.70e+00 1havA b.47.1.4 26425 1nhp 447 1.92e+00 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1g2oA 268 2.08e+00 1b8oA c.56.2.1 60228 1axiB 236 2.25e+00 1axiB b.1.2.1 21997 b.1.2.1 21998 1jj2A 239 2.27e+00 1rl2A b.34.5.3 63084 b.40.4.5 63085 1hlcA 129 2.36e+00 1c1lA b.29.1.3 24208 1g291 372 2.43e+00 1g291 1dynA 125 2.62e+00 1dynA b.55.1.1 26955 1a49A 530 2.66e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1joa 447 2.82e+00 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1nhs 447 2.96e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1h8eA 510 3.06e+00 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1eysH 259 3.18e+00 6prcH b.41.1.1 25484 f.2.1.2 43517 1aaj 105 3.37e+00 1aac b.6.1.1 22841 1bxaA 105 3.37e+00 1aac b.6.1.1 22839 3hhrB 203 3.47e+00 1axiB b.1.2.1 22005 b.1.2.1 22006 1aac 105 3.61e+00 1aac b.6.1.1 22838 1trb 320 3.68e+00 1trb c.3.1.5 30529 c.3.1.5 30530 2dynA 122 3.91e+00 1dynA b.55.1.1 26957 1i1jA 108 4.09e+00 1i1jA b.34.2.1 61531 1ilr1 152 4.26e+00 1irp 1bxvA 91 4.40e+00 1aac b.6.1.1 22875 1dj7B 75 4.62e+00 1dj7B b.34.4.3 24598 1irp 153 4.92e+00 1irp b.42.1.2 25559 1kbvA 327 5.00e+00 b.6.1.3 68395 b.6.1.3 68396 1fhoA 119 5.02e+00 1fhoA b.55.1.1 26982 1pkn 530 5.12e+00 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1iraX 152 5.35e+00 1irp b.42.1.2 25556 1e32A 458 5.47e+00 1e32A b.52.2.3 59183 c.37.1.13 59184 d.31.1.1 59185 1qniA 581 5.63e+00 1qniA b.6.1.4 23042 b.69.3.1 27642 1d7qA 143 5.64e+00 1d7qA b.40.4.5 25331 1jegA 83 6.01e+00 b.34.2.1 66610 1kawA 135 6.33e+00 3ullA b.40.4.3 25288 1jksA 294 6.35e+00 1awo 62 6.39e+00 1bbzA b.34.2.1 24482 7ahlA 293 6.58e+00 7ahlA f.6.1.1 43812 1hjdA 101 6.82e+00 b.34.2.1 65846 1tuc 63 6.99e+00 1tuc b.34.2.1 24492 1jrkA 156 7.27e+00 1f7sA 139 7.29e+00 1cof d.109.1.2 40857 1nls 237 7.39e+00 1nls b.29.1.1 23928 1gcqA 61 7.63e+00 1ckaA b.34.2.1 60434 1kcw 1046 7.73e+00 1kcw b.6.1.3 23151 b.6.1.3 23152 b.6.1.3 23153 b.6.1.3 23154 b.6.1.3 23155 b.6.1.3 23156 1avaA 403 7.77e+00 1jdc b.71.1.1 27797 c.1.8.1 28784 1qlyA 58 7.81e+00 1bbzA b.34.2.1 24530 1kypA 237 7.98e+00 1e9pA 151 8.66e+00 1mfmA b.1.8.1 22215 1scs 237 8.75e+00 1nls b.29.1.1 23930 1xsoA 150 9.59e+00 1mfmA b.1.8.1 22273 1k2eA 156 9.81e+00 1g5vA 88 9.86e+00 1g5vA b.34.9.1 60292 1hdkA 141 1.01e+01 b.29.1.3 65807 1jacA 133 1.02e+01 1jotA 1jotA 133 1.04e+01 1jotA 1ggxA 223 1.06e+01 1ggxA d.22.1.1 38367 1lvoA 302 1.06e+01 1lnh 857 1.06e+01 1yge a.119.1.1 19237 b.12.1.1 23637 1ksiA 642 1.07e+01 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1k26A 156 1.09e+01 1ema 236 1.09e+01 1ema d.22.1.1 38339 1cskA 71 1.09e+01 1ckaA b.34.2.1 24513 1jnyA 435 1.11e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1imvA 398 1.11e+01 e.1.1.1 62591 1ksiB 642 1.14e+01 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1wkt 88 1.15e+01 1wkt b.11.1.2 23630 2emo 237 1.15e+01 1ema d.22.1.1 38366 1griA 217 1.17e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 1m26A 133 1.17e+01 1jacC 133 1.17e+01 1jotA 1g86A 142 1.18e+01 1lcl 142 1.18e+01 1lcl b.29.1.3 24216 1fonA 240 1.19e+01 5ptp b.47.1.2 26231 1ku8A 133 1.24e+01 1pse 69 1.25e+01 1pse b.34.4.2 24595 1dgsA 667 1.25e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1ciy 590 1.29e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 9apiA 347 1.29e+01 1ovaA e.1.1.1 42630 1b56 135 1.29e+01 1hmt b.60.1.2 27183 1qs1A 462 1.31e+01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1aipE 405 1.33e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1gthB 1025 1.35e+01 1gt8B 1025 1.36e+01 1qfmA 710 1.37e+01 1qfmA b.69.7.1 27673 c.69.1.4 34641 1e8nA 710 1.42e+01 1qfmA b.69.7.1 27675 c.69.1.4 34643 1vif 62 1.42e+01 1vie b.34.4.1 24593 1jdiA 231 1.42e+01 c.74.1.1 66551 1ystH 260 1.42e+01 6prcH b.41.1.1 25482 f.2.1.2 43511 1ckaA 57 1.42e+01 1ckaA b.34.2.1 24459 1i0cA 60 1.43e+01 1aojA b.34.2.1 61485 1gr2A 279 1.44e+01 1gr2A c.94.1.1 35825 1jxmA 301 1.45e+01 b.34.2.1 67420 c.37.1.1 67421 1ftkA 279 1.47e+01 1gr2A c.94.1.1 35819 2mcm 112 1.47e+01 2mcm b.1.7.1 22207 1fwxA 595 1.48e+01 b.6.1.4 60069 b.69.3.1 60070 1rl6A 177 1.53e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1gt8A 1025 1.54e+01 1cbjA 151 1.55e+01 1mfmA b.1.8.1 22213 1gteD 1025 1.56e+01 1h7xD 1025 1.58e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1kz7A 353 1.58e+01 2ms2A 129 1.59e+01 1msc d.85.1.1 40049 1jyoA 130 1.61e+01 d.198.1.1 67483 1gutA 68 1.63e+01 b.40.6.1 65576 1gt8C 1025 1.63e+01 1ef1A 294 1.65e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1pszA 303 1.65e+01 1toaA c.92.2.2 35600 1g2iA 166 1.70e+01 1g2iA c.23.16.2 31438 1gpr 162 1.71e+01 1gpr b.84.3.1 28267 1fcdA 401 1.73e+01 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1e5mA 416 1.74e+01 1dd8A c.95.1.1 58973 c.95.1.1 58974 1jb0E 75 1.75e+01 1pse b.34.4.2 62824 1qqjA 419 1.76e+01 1qcnA b.34.8.1 59034 d.177.1.1 59035 1gthA 1025 1.77e+01 2sodB 152 1.78e+01 1mfmA b.1.8.1 22242 1kk1A 410 1.81e+01 1jztA 246 1.82e+01 c.104.1.1 63319 1h7wB 1025 1.88e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1bjt 793 1.88e+01 1bjt e.11.1.1 43249 1l5jA 865 1.88e+01 1qcnA 421 1.89e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1skyB 502 1.89e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1vie 62 1.89e+01 1vie b.34.4.1 24592 1qs2A 401 1.91e+01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1hyoA 421 1.91e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1fdr 248 1.93e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1qvcA 145 1.96e+01 3ullA b.40.4.3 25284 1gt8D 1025 1.99e+01 1vhrA 184 2.00e+01 1vhrA c.45.1.1 32651 1h7wD 1025 2.01e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1h7wA 1025 2.01e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1tbgA 340 2.01e+01 1tbgA b.69.4.1 27649 1kjwA 295 2.01e+01 b.34.2.1 68643 c.37.1.1 68644 1gteA 1025 2.02e+01 1gthC 1025 2.03e+01 1h7xA 1025 2.04e+01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1h7xC 1025 2.04e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1h7xB 1025 2.04e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1l3aA 228 2.08e+01 1exmA 405 2.13e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ah9 71 2.14e+01 1ah9 b.40.4.5 25330 1g2qA 187 2.15e+01 c.61.1.1 65117 1im3D 95 2.15e+01 1im3D b.1.1.6 62568 1luzA 88 2.15e+01 1d6mA 653 2.17e+01 1d6mA e.10.1.1 43248 1kafA 108 2.17e+01 d.199.1.1 68372 1mjc 69 2.22e+01 1mjc b.40.4.5 25319 1jg1A 235 2.29e+01 c.66.1.7 66661 1jh2A 99 2.35e+01 b.35.1.1 63038 1f6fB 210 2.38e+01 1axiB b.1.2.1 22033 b.1.2.1 22034 1ebpA 211 2.39e+01 1eerB b.1.2.1 22023 b.1.2.1 22024 1konA 249 2.41e+01 1dfx 125 2.42e+01 1dfx b.1.13.1 22367 g.41.5.2 45255 2plc 274 2.44e+01 2plc c.1.18.2 29614 1h4rA 314 2.45e+01 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1cbs 137 2.49e+01 1hmt b.60.1.2 27201 1ekrA 161 2.50e+01 1ekrA d.58.21.1 39380 1gkuB 1054 2.50e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1fa4A 105 2.52e+01 1plc b.6.1.1 22867 1feuA 206 2.56e+01 1feuA b.53.1.1 59801 1eerB 227 2.58e+01 1eerB b.1.2.1 22011 b.1.2.1 22012 1shg 62 2.59e+01 1ckaA b.34.2.1 24493 1f89A 291 2.63e+01 d.160.1.1 64988 1pwt 61 2.63e+01 1tud b.34.2.1 24490 1pcs 98 2.77e+01 1plc b.6.1.1 22871 1i39A 225 2.96e+01 1ekeA c.55.3.1 61585 1b8aA 438 3.07e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1cl2A 395 3.08e+01 1cl2A c.67.1.3 34397 1dcs 311 3.08e+01 1dcs b.82.2.1 28124 1eikA 77 3.08e+01 1eikA d.78.1.1 39751 1a3qA 285 3.09e+01 1a3qA b.1.1.5 21932 b.2.5.1 22447 1i7dA 659 3.12e+01 1d6mA e.10.1.1 61886 1qcoA 423 3.12e+01 1qcnA b.34.8.1 59021 d.177.1.1 59022 1ffk1 177 3.18e+01 1ffk1 1dwmA 70 3.21e+01 1hymA d.40.1.1 38583 1lpuA 332 3.24e+01 1g0u1 266 3.31e+01 1hdmB 193 3.31e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 2dabA 282 3.33e+01 1daaA e.17.1.1 43274 1gotB 340 3.36e+01 1tbgA b.69.4.1 27648 1hr0W 71 3.39e+01 1ah9 b.40.4.5 25329 1b6cB 342 3.39e+01 1b6cB d.144.1.1 41673 1aszB 490 3.40e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1c9oA 66 3.43e+01 1mjc b.40.4.5 25325 1ha3A 405 3.46e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1p32A 209 3.46e+01 1p32A d.25.1.1 38379 1hzgA 295 3.46e+01 1hzgA d.194.1.1 61436 1j7nB 776 3.54e+01 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1dzfA 215 3.55e+01 1dzfA c.52.3.1 33344 d.78.1.1 39753 1j7nA 776 3.55e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1e1aA 314 3.59e+01 1e1aA b.68.6.1 59155 1semA 58 3.60e+01 1ckaA b.34.2.1 24544 1qr4A 186 3.60e+01 1qr4B b.1.2.1 21986 b.1.2.1 21987 1el5A 389 3.63e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1i60A 278 3.72e+01 1i78A 297 3.73e+01 f.4.4.1 66046 1bawA 105 3.75e+01 1plc b.6.1.1 22868 7taa 478 3.76e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1g2bA 62 3.77e+01 1tud b.34.2.1 24488 1qlpA 394 3.90e+01 1ovaA e.1.1.1 42628 3pbgA 468 3.96e+01 1e70M c.1.8.4 28951 1azeA 56 3.99e+01 b.34.2.1 24536 1cl1A 395 4.00e+01 1cl2A c.67.1.3 34395