# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1tqnA 486 7.14e-49 1po5A 476 6.82e-45 a.104.1.1 -1467 1nr6A 473 1.09e-44 a.104.1.1 -1464 1n6bA 473 1.69e-44 a.104.1.1 85359 1dt6A 473 4.70e-44 1dt6A a.104.1.1 18977 1bu7A 455 2.57e-40 1bu7A a.104.1.1 18937 2bmhA 455 3.27e-40 1bu7A a.104.1.1 18941 1jpzA 473 7.31e-40 a.104.1.1 67069 1jmeA 455 1.17e-39 a.104.1.1 66885 1jipA 403 5.00e-36 a.104.1.1 66748 1e9xA 455 6.37e-36 1ea1A a.104.1.1 18969 1eupA 403 6.60e-36 1rom a.104.1.1 18967 1oxa 403 1.31e-35 1f4tA a.104.1.1 18965 1h5zA 455 2.72e-35 a.104.1.1 -1456 1n97A 389 3.45e-35 a.104.1.1 80335 1u13A 455 5.19e-35 1ea1A 455 5.55e-35 1ea1A a.104.1.1 18970 1odoA 408 5.19e-34 a.104.1.1 -1463 1cmnA 402 1.21e-33 1rom a.104.1.1 18958 1gwiA 411 1.26e-33 a.104.1.1 76364 1jfbA 404 2.20e-33 a.104.1.1 66624 1q5dA 419 2.57e-33 a.104.1.1 -1454 1f24A 402 3.07e-33 1rom a.104.1.1 18953 1rom 403 6.33e-33 1rom a.104.1.1 18963 1cpt 412 3.84e-32 1cpt a.104.1.1 18968 1uedA 406 2.26e-30 a.104.1.1 -1459 1f4tA 368 7.22e-30 1f4tA a.104.1.1 18973 1io7A 368 1.06e-29 1f4tA a.104.1.1 18971 1lfkA 398 6.34e-29 a.104.1.1 77926 1qmqA 414 1.25e-27 1phd a.104.1.1 18907 1phd 414 2.66e-27 1phd a.104.1.1 18913 1phb 414 2.87e-27 1phd a.104.1.1 18906 1phg 414 3.63e-27 1phd a.104.1.1 18910 5cpp 414 4.38e-27 1phd a.104.1.1 18935 1izoA 417 5.63e-27 a.104.1.1 83851 1dz4A 414 7.17e-27 1phd a.104.1.1 18903 1n40A 396 7.09e-25 a.104.1.1 79977 1hm2A 700 1.45e-01 1cb8A a.102.3.2 61083 b.24.1.1 61084 b.30.5.2 61085 1gw9A 388 2.00e-01 c.1.15.3 70658 1jf0A 195 2.02e-01 1ej3A a.39.1.5 62926 1mnzA 388 2.04e-01 c.1.15.3 79328 3xis 387 2.05e-01 4xis c.1.15.3 29423 1xis 387 2.12e-01 4xis c.1.15.3 29422 2xis 387 2.12e-01 4xis c.1.15.3 29427 4xis 387 2.17e-01 4xis c.1.15.3 29421 1cezA 883 2.43e-01 1cezA e.8.1.3 43110 1jf2A 195 2.82e-01 1ej3A a.39.1.5 62930 1muwA 386 3.55e-01 c.1.15.3 79495 1kktA 511 3.90e-01 a.102.2.1 68687 1rkeA 262 4.07e-01 a.24.9.1 -582 a.24.9.1 -583 1t95A 240 4.17e-01 1mdbA 539 4.72e-01 e.23.1.1 79008 1qlnA 883 4.87e-01 1cezA e.8.1.3 43111 1fs7A 485 4.89e-01 1qdbA a.138.1.3 19691 1cb8A 678 5.05e-01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1qv1A 195 5.12e-01 a.39.1.5 -830 1el4A 195 5.97e-01 1ej3A a.39.1.5 59453 1bs2A 607 6.44e-01 1bs2A a.27.1.1 16930 c.26.1.1 31597 d.67.2.1 39563 1ej3A 191 7.12e-01 1ej3A a.39.1.5 17259 1gxmA 332 8.38e-01 a.102.5.1 76371 1epuA 591 1.10e+00 1dn1A e.25.1.1 43358 1dl2A 511 1.22e+00 1dl2A a.102.2.1 18844 1umdA 367 1.24e+00 c.36.1.11 -6969 1p9qC 256 1.38e+00 1a99A 344 1.39e+00 1pot c.94.1.1 35812 1gnlA 544 1.43e+00 e.26.1.1 70287 1epwA 1290 1.53e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1nt4A 391 1.56e+00 c.60.1.2 -7942 1foeA 377 1.63e+00 1foeA a.87.1.1 18517 b.55.1.1 26969 1gnd 447 1.69e+00 1gnd c.3.1.3 30423 d.16.1.6 37987 1f7uA 607 1.91e+00 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1d5tA 433 2.03e+00 1gnd c.3.1.3 30422 d.16.1.6 37986 2sas 185 2.05e+00 2sas a.39.1.5 17258 1aijL 281 2.36e+00 6prcL f.26.1.1 43461 2pflA 759 2.49e+00 1cm5A c.7.1.1 30675 1nxcA 478 3.25e+00 a.102.2.1 -1333 1h16A 759 3.51e+00 c.7.1.1 76462 1rzhM 307 3.54e+00 f.26.1.1 -12227 1jk0B 345 3.54e+00 a.25.1.2 63143 1qq8A 214 3.81e+00 1qq8A 1cm5A 759 3.83e+00 1cm5A c.7.1.1 30671 1exrA 148 3.88e+00 1cll a.39.1.5 17299 1dxrL 273 4.03e+00 6prcL f.26.1.1 43431 1rzhL 281 4.11e+00 f.26.1.1 -12215 1qoxN 449 4.24e+00 1qoxN c.1.8.4 28978 1osa 148 4.26e+00 1cll a.39.1.5 17300 1dpgA 485 4.44e+00 1dpgA c.2.1.3 30074 d.81.1.5 39989 1c4oA 664 4.46e+00 1d2mA c.37.1.19 32415 c.37.1.19 32416 1hcuA 503 4.46e+00 a.102.2.1 65796 2ts1 419 4.65e+00 2ts1 c.26.1.1 31564 1m9nA 613 4.69e+00 c.24.1.3 78870 c.97.2.1 78871 1hyeA 313 4.83e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1fo3A 460 4.86e+00 1dl2A a.102.2.1 18845 1eemA 241 4.91e+00 1eemA a.45.1.1 17717 c.47.1.5 33011 1rpa 342 5.39e+00 1cviA c.60.1.2 33983 1iqrA 420 5.54e+00 a.99.1.1 66275 c.28.1.1 66276 1kp0A 402 5.60e+00 c.55.2.1 72834 d.127.1.1 72835 3pflA 759 5.84e+00 1cm5A c.7.1.1 30673 6prcL 273 6.00e+00 6prcL f.26.1.1 43434 1dquA 538 6.27e+00 1dquA c.1.12.7 29314 1g8mA 593 6.27e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1ewqA 765 6.51e+00 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1enp 312 6.64e+00 1enp c.2.1.2 29906 1eno 312 6.69e+00 1enp c.2.1.2 29905 1j77A 209 6.77e+00 1j77A a.132.1.2 62674 1ndbA 596 6.79e+00 c.43.1.3 80411 c.43.1.3 80412 1ggzA 148 6.81e+00 a.39.1.5 70176 1k3rA 268 7.00e+00 b.40.4.10 72018 c.116.1.2 72019 1nktA 922 7.04e+00 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1d7oA 297 7.13e+00 1enp c.2.1.2 29907 1bgp 309 7.16e+00 1bgp a.93.1.1 18690 1abwA 283 7.31e+00 1abwA a.1.1.2 15288 a.1.1.2 15289 4xiaA 393 7.53e+00 4xis c.1.15.3 29439 1owlA 484 7.84e+00 a.99.1.1 -1296 c.28.1.1 -6646 1ub3A 220 7.85e+00 c.1.10.1 88395 1h49A 512 8.06e+00 c.1.8.4 83477 1v02A 565 8.11e+00 1h38C 883 8.12e+00 e.8.1.3 76627 1f0kA 364 8.56e+00 1f0kA c.87.1.2 35465 1h2aL 567 8.67e+00 1h2rL e.18.1.1 43299 1n45A 233 8.86e+00 a.132.1.1 79981 1jb0A 755 8.90e+00 1jb0A f.29.1.1 62820 1mmsA 140 8.91e+00 1mmsA a.4.7.1 16247 d.47.1.1 38766 1o0xA 262 9.44e+00 d.127.1.1 80755 1a8rA 221 9.81e+00 1a8rA d.96.1.1 40587 2dpg 485 9.90e+00 1dpgA c.2.1.3 30076 d.81.1.5 39991 1h38B 883 1.02e+01 e.8.1.3 76626 1i19A 561 1.02e+01 1i19A d.58.32.3 61522 d.145.1.1 61523 1gnxA 479 1.05e+01 c.1.8.4 76241 2sqcA 631 1.07e+01 2sqcA a.102.4.2 18854 a.102.4.2 18855 1fftB 315 1.12e+01 1cyx b.6.1.2 23025 f.17.2.1 43628 1h38D 883 1.16e+01 e.8.1.3 76628 1jbaA 204 1.22e+01 1rec a.39.1.5 17330 1otvA 259 1.23e+01 unknown_sccs -1915 1f3aA 222 1.26e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1jilA 420 1.26e+01 c.26.1.1 66745 1eswA 500 1.27e+01 1cwyA c.1.8.1 59500 1s96A 219 1.32e+01 c.37.1.1 -6972 1r6fA 310 1.32e+01 unknown_sccs -11804 1ltqA 301 1.34e+01 c.108.1.9 78208 c.37.1.1 78209 2ng1 293 1.34e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1tr1A 447 1.39e+01 1e70M c.1.8.4 28957 1h3fA 432 1.39e+01 c.26.1.1 76631 d.66.1.4 76632 1ka1A 357 1.42e+01 e.7.1.1 68369 1qgxA 357 1.42e+01 1qgxA e.7.1.1 42973 1ncx 162 1.43e+01 1ncx a.39.1.5 17222 1llwA 1520 1.44e+01 b.80.4.1 74017 c.1.4.1 74018 d.153.1.1 74019 1qdbA 473 1.44e+01 1qdbA a.138.1.3 19688 1eia 207 1.46e+01 1eia a.28.3.1 16951 a.73.1.1 18331 3bct 457 1.47e+01 3bct a.118.1.1 19112 1d2mA 665 1.50e+01 1d2mA c.37.1.19 32417 c.37.1.19 32418 1o0wA 252 1.51e+01 a.149.1.1 80751 d.50.1.1 80752 1h2rL 534 1.51e+01 1h2rL e.18.1.1 43298 1l1lA 739 1.52e+01 c.7.1.4 73470 1toh 343 1.56e+01 4pah d.178.1.1 42573 1dgjA 907 1.56e+01 1alo a.56.1.1 17909 d.15.4.2 37694 d.41.1.1 38585 d.133.1.1 41415 1top 162 1.58e+01 1ncx a.39.1.5 17223 1e2uA 553 1.58e+01 1e1dA e.26.1.1 43362 1l1qA 186 1.58e+01 c.61.1.1 77653 1ltm 320 1.62e+01 1ltm d.2.1.6 36992 1qusA 322 1.65e+01 1ltm d.2.1.6 36991 1qnf 484 1.67e+01 1qnf a.99.1.1 18777 c.28.1.1 31632 1hr6B 443 1.70e+01 1be3A d.185.1.1 61166 d.185.1.1 61167 1tqyB 415 1.71e+01 2reb 352 1.75e+01 2reb c.37.1.11 32282 d.48.1.1 38767 1cwyA 500 1.76e+01 1cwyA c.1.8.1 28789 1lxyA 409 1.76e+01 unknown_sccs -10987 1mpgA 282 1.78e+01 1mpgA a.96.1.3 18747 d.129.1.2 41296 1gntA 553 1.79e+01 e.26.1.1 70290 1ls1A 295 1.79e+01 a.24.13.1 78170 c.37.1.10 78171 1ubpA 101 1.80e+01 1ubpA d.8.1.1 37353 4ubpA 101 1.80e+01 1ubpA d.8.1.1 37352 1anxA 319 1.81e+01 1avc a.65.1.1 18161 1pj5A 830 1.88e+01 unknown_sccs -4066 c.3.1.2 -6031 d.16.1.5 -9251 unknown_sccs -10171 1se0A 116 1.89e+01 g.52.1.1 -12841 1tqyA 424 1.92e+01 1jlvA 209 1.92e+01 a.45.1.1 71729 c.47.1.5 71730 1a27 289 1.94e+01 1fds c.2.1.2 29839 1jndA 420 1.97e+01 c.1.8.5 71757 d.26.3.1 71758 1kblA 873 1.99e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1vduA 172 2.00e+01 unknown_sccs -1651 1s9rA 410 2.03e+01 unknown_sccs -10989 1q9uA 130 2.04e+01 unknown_sccs -11025 1dik 874 2.04e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1jk0A 419 2.05e+01 a.25.1.2 63142 1obdA 306 2.07e+01 d.143.1.1 86767 1cii 602 2.08e+01 1cii f.1.1.1 43381 h.4.3.1 45787 1ng1 294 2.09e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1cc1L 498 2.09e+01 1h2rL e.18.1.1 43301 1hv9A 456 2.11e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 2cb5A 453 2.14e+01 3gcb d.3.1.1 37035 1nnmA 652 2.14e+01 1pg4A 652 2.14e+01 e.23.1.1 88067 1mkeA 152 2.16e+01 b.55.1.4 79231 1dkqA 410 2.16e+01 1dklA c.60.1.2 33998 1eg5A 384 2.27e+01 1ecxA c.67.1.3 34429 1e55A 512 2.28e+01 1e70M c.1.8.4 28934 1mlwA 301 2.29e+01 d.178.1.1 79289 1jpnA 296 2.36e+01 a.24.13.1 67039 c.37.1.10 67040 1pii 452 2.36e+01 1pii c.1.2.4 28559 c.1.2.4 28563 1uor 585 2.36e+01 1bj5 a.126.1.1 19396 a.126.1.1 19397 a.126.1.1 19398 1fnmA 691 2.37e+01 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 1dfoA 417 2.41e+01 1bj4A c.67.1.4 34480 1pmi 440 2.42e+01 1pmi b.82.1.3 28114 1ku2A 241 2.44e+01 a.4.13.1 83096 a.177.1.1 83097 1ecxA 384 2.46e+01 1ecxA c.67.1.3 34431 1ko9A 345 2.48e+01 a.96.1.3 68717 d.129.1.2 68718 1knqA 175 2.49e+01 c.37.1.17 72786 1di1A 300 2.50e+01 1di1A a.128.1.4 19446 1q16A 1247 2.54e+01 b.52.2.2 -4337 c.81.1.1 -8547 1cydA 244 2.55e+01 1cydA c.2.1.2 29825 1a02F 56 2.56e+01 1a02F h.1.3.1 45534 1r5lA 262 2.58e+01 a.5.3.1 -360 c.13.1.1 -6215 1lkvX 232 2.60e+01 a.118.14.1 73980 1vtmP 158 2.62e+01 1rmvA a.24.5.1 16587 1qhtA 775 2.64e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1i82A 189 2.65e+01 1i82A b.1.9.2 61937 1i8aA 189 2.65e+01 1i82A b.1.9.2 61951 1gwuA 309 2.68e+01 a.93.1.1 83351 1sqc 631 2.69e+01 2sqcA a.102.4.2 18858 a.102.4.2 18859 1pvaA 110 2.70e+01 1a75A a.39.1.4 17207 1a48 306 2.77e+01 1a48 d.143.1.1 41590 1p94A 76 2.81e+01 unknown_sccs -916 1ornA 226 2.82e+01 a.96.1.1 87342 1dc1A 323 2.87e+01 1dc1A c.52.1.11 33321 1uruA 244 2.88e+01 unknown_sccs -13001 1vlbA 907 2.89e+01 1g4yR 148 2.91e+01 1cll a.39.1.5 60252 1qvbA 481 2.93e+01 1qvbA c.1.8.4 28983 1mpxA 615 2.98e+01 b.18.1.13 85041 c.69.1.21 85042 1f5qB 252 2.98e+01 1f5qB a.74.1.1 18362 a.74.1.1 18363 1lvk 762 3.00e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 1ho8A 480 3.01e+01 1ho8A a.118.1.9 61107 1qlpA 394 3.01e+01 1ovaA e.1.1.1 42628 1a8b 318 3.02e+01 1avc a.65.1.1 18171 1hvd 319 3.04e+01 1avc a.65.1.1 18154 7atjA 308 3.04e+01 1bgp a.93.1.1 18673 1rro 108 3.06e+01 1a75A a.39.1.4 17195 1pjr 724 3.06e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 1fosE 60 3.07e+01 h.1.3.1 45535 1l8qA 324 3.13e+01 a.4.12.2 77809 c.37.1.20 77810 1hlrA 907 3.17e+01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1rxxA 421 3.18e+01 unknown_sccs -10982 1uc2A 481 3.21e+01 unknown_sccs -11725 1irxA 523 3.23e+01 a.97.1.2 71378 c.26.1.1 71379 1mjgM 729 3.23e+01 e.26.1.3 79204 1qxrA 189 3.24e+01 b.82.1.7 -4834 1mswD 883 3.24e+01 e.8.1.3 79427 1sr9A 644 3.24e+01 1qpcA 279 3.25e+01 1fgkA d.144.1.7 41685 1d2rA 326 3.26e+01 1d2rB c.26.1.1 31572 1ei7A 158 3.31e+01 1rmvA a.24.5.1 16584 1sesA 421 3.33e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1qpoA 284 3.36e+01 1qpoA c.1.17.1 29561 d.41.2.1 38597 1cll 148 3.37e+01 1cll a.39.1.5 17263 1ub0A 258 3.39e+01 c.72.1.2 88394 1plzA 189 3.40e+01 b.82.1.7 88160 1e9rA 437 3.40e+01 c.37.1.11 64827 1lci 550 3.43e+01 1lci e.23.1.1 43349 1e1dA 553 3.45e+01 1e1dA e.26.1.1 43363 1ur5A 309 3.49e+01 c.2.1.5 -5910 d.162.1.1 -11477 1pnkA 209 3.50e+01 1ajqA d.153.1.2 41839 1h6zA 913 3.52e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1ubkL 534 3.56e+01 e.18.1.1 88422 1p9aG 290 3.56e+01 c.10.2.7 87990 1v25A 541 3.61e+01 1m93A 55 3.61e+01 e.1.1.1 -11751 1nnwA 252 3.62e+01 d.159.1.5 80674 1tx4A 198 3.64e+01 1tx4A a.116.1.1 19098 1apxA 249 3.65e+01 1ryc a.93.1.1 18669 1nm8A 616 3.68e+01 c.43.1.3 85872 c.43.1.3 85873 1gmjC 84 3.70e+01 h.4.8.1 65312 1e6qM 501 3.72e+01 1e70M c.1.8.4 28920 1hl8A 449 3.73e+01 unknown_sccs -4690 unknown_sccs -5361 1kijA 390 3.75e+01 d.14.1.3 72514 d.122.1.2 72515 1nv8A 284 3.75e+01 c.66.1.30 86224 1i5rA 327 3.76e+01 c.2.1.2 83668 1eysL 280 3.86e+01 6prcL f.26.1.1 43515 1iq0A 592 3.89e+01 a.27.1.1 66257 c.26.1.1 66258 d.67.2.1 66259 1rlzA 369 3.90e+01 1fdt 327 3.92e+01 1fds c.2.1.2 29841 1e4iA 447 3.94e+01 1e70M c.1.8.4 59225 3lck 271 3.94e+01 1fmk d.144.1.7 41686 2iadB 205 3.95e+01 1iakB b.1.1.2 21640 d.19.1.1 38214 1scjB 71 3.95e+01 1scjB d.58.3.2 39069