# List of top-scoring protein chains for t04-100-30-bys 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 4.78e-63 1po5A 476 4.93e-62 a.104.1.1 -1467 1jpzA 473 2.42e-55 a.104.1.1 67069 1bu7A 455 7.91e-55 1bu7A a.104.1.1 18937 1n97A 389 1.68e-53 a.104.1.1 80335 1e9xA 455 1.18e-45 1ea1A a.104.1.1 18969 1h5zA 455 4.16e-45 a.104.1.1 -1456 1u13A 455 1.30e-44 1gwiA 411 1.34e-33 a.104.1.1 76364 1odoA 408 3.92e-33 a.104.1.1 -1463 1jipA 403 6.92e-33 a.104.1.1 66748 1q5dA 419 1.22e-32 a.104.1.1 -1454 1eupA 403 2.88e-32 1rom a.104.1.1 18967 1cpt 412 1.35e-31 1cpt a.104.1.1 18968 1jfbA 404 5.23e-31 a.104.1.1 66624 1uedA 406 5.55e-31 a.104.1.1 -1459 1izoA 417 1.27e-30 a.104.1.1 83851 1f24A 402 6.57e-30 1rom a.104.1.1 18953 1io7A 368 1.08e-28 1f4tA a.104.1.1 18971 1lfkA 398 2.49e-27 a.104.1.1 77926 1qmqA 414 7.45e-25 1phd a.104.1.1 18907 1dz4A 414 1.67e-24 1phd a.104.1.1 18903 1n40A 396 1.25e-22 a.104.1.1 79977 1gnlA 544 7.21e-02 e.26.1.1 70287 1qusA 322 1.43e-01 1ltm d.2.1.6 36991 1pjr 724 1.71e-01 1pjr c.37.1.19 32391 c.37.1.19 32392 1ornA 226 1.74e-01 a.96.1.1 87342 1gnwA 211 2.18e-01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1h3fA 432 3.79e-01 c.26.1.1 76631 d.66.1.4 76632 1dl2A 511 3.94e-01 1dl2A a.102.2.1 18844 1j77A 209 4.18e-01 1j77A a.132.1.2 62674 1qv1A 195 4.51e-01 a.39.1.5 -830 1lci 550 4.67e-01 1lci e.23.1.1 43349 1eswA 500 6.05e-01 1cwyA c.1.8.1 59500 1gw5A 621 6.28e-01 a.118.1.10 70629 1hl9A 449 6.45e-01 unknown_sccs -4694 unknown_sccs -5365 1t95A 240 6.56e-01 1uruA 244 6.77e-01 unknown_sccs -13001 1nxcA 478 7.44e-01 a.102.2.1 -1333 1knqA 175 7.50e-01 c.37.1.17 72786 1r5lA 262 8.52e-01 a.5.3.1 -360 c.13.1.1 -6215 1i3dA 146 9.58e-01 a.1.1.2 61587 4xis 387 9.68e-01 4xis c.1.15.3 29421 2ran 316 9.71e-01 1avc a.65.1.1 18170 1j1jA 240 9.79e-01 a.118.16.1 -1637 3xis 387 1.02e+00 4xis c.1.15.3 29423 1jf2A 195 1.05e+00 1ej3A a.39.1.5 62930 1rpa 342 1.06e+00 1cviA c.60.1.2 33983 1el4A 195 1.18e+00 1ej3A a.39.1.5 59453 1h99A 224 1.28e+00 a.142.1.1 60814 a.142.1.1 60815 1ewqA 765 1.29e+00 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1o0xA 262 1.30e+00 d.127.1.1 80755 2sqcA 631 1.32e+00 2sqcA a.102.4.2 18854 a.102.4.2 18855 1k1xA 659 1.41e+00 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1f0kA 364 1.63e+00 1f0kA c.87.1.2 35465 1mhyD 521 1.70e+00 1mhyD a.25.1.2 16780 1fo3A 460 1.88e+00 1dl2A a.102.2.1 18845 1ubkL 534 1.88e+00 e.18.1.1 88422 1muwA 386 1.90e+00 c.1.15.3 79495 1h2rL 534 1.91e+00 1h2rL e.18.1.1 43298 1ec7A 446 2.09e+00 1bqg c.1.11.2 29218 d.54.1.1 38862 1qopB 396 2.23e+00 2tysB c.79.1.1 35270 1vhtA 218 2.23e+00 c.37.1.1 -7004 1exrA 148 2.32e+00 1cll a.39.1.5 17299 1e19A 314 2.35e+00 1b7bA c.73.1.1 34967 1q6hA 224 2.49e+00 d.26.1.1 -9487 1fs7A 485 2.52e+00 1qdbA a.138.1.3 19691 1ui5A 215 2.65e+00 1vduA 172 2.72e+00 unknown_sccs -1651 1r6fA 310 2.77e+00 unknown_sccs -11804 1mdbA 539 2.94e+00 e.23.1.1 79008 1rlr 761 2.95e+00 1rlr a.98.1.1 18753 c.7.1.2 30679 1a8rA 221 3.01e+00 1a8rA d.96.1.1 40587 1otsA 465 3.07e+00 f.20.1.1 87415 1o6uA 403 3.12e+00 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1ho8A 480 3.38e+00 1ho8A a.118.1.9 61107 1pb6A 212 3.46e+00 a.4.1.9 88017 a.121.1.1 88018 1tdtA 259 3.90e+00 3tdt b.81.1.2 28055 1iwhB 146 4.11e+00 a.1.1.2 76883 1ibrB 462 4.36e+00 1qgrA a.118.1.1 19120 12asA 330 4.41e+00 12asA d.104.1.1 40783 1f5qB 252 4.75e+00 1f5qB a.74.1.1 18362 a.74.1.1 18363 2ng1 293 4.88e+00 1ng1 a.24.13.1 16962 c.37.1.10 32273 1oz9A 150 4.90e+00 unknown_sccs -10588 1babB 146 4.97e+00 1abwA a.1.1.2 15414 2gwxA 267 5.03e+00 2prgA a.123.1.1 19323 1rxxA 421 5.24e+00 unknown_sccs -10982 1p2xA 159 5.42e+00 1frb 315 5.47e+00 1frb c.1.7.1 28665 1ggzA 148 5.54e+00 a.39.1.5 70176 1ldjA 760 5.63e+00 a.4.5.34 73847 a.118.17.1 73848 e.40.1.1 73849 1s9rA 410 5.70e+00 unknown_sccs -10989 1e2uA 553 5.70e+00 1e1dA e.26.1.1 43362 1top 162 5.75e+00 1ncx a.39.1.5 17223 1gntA 553 5.86e+00 e.26.1.1 70290 1m2eA 135 5.92e+00 c.23.1.5 78478 1gesA 450 6.11e+00 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1ihp 438 6.14e+00 1ihp c.60.1.2 33993 1cb8A 678 6.39e+00 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1i7kA 179 6.49e+00 1u9aA d.20.1.1 61889 1v7cA 351 6.50e+00 c.79.1.1 -8512 1pixA 587 6.51e+00 c.14.1.4 -6282 1j8mF 297 6.67e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1giqA 413 6.67e+00 d.166.1.1 76224 d.166.1.1 76225 1owqA 361 6.74e+00 1a59 378 6.88e+00 1aj8A a.103.1.1 18902 1t7pA 698 7.03e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1a8b 318 7.11e+00 1avc a.65.1.1 18171 1n7oA 721 7.18e+00 a.102.3.2 80259 b.24.1.1 80260 b.30.5.2 80261 1sqgA 429 7.30e+00 1jeoA 180 7.38e+00 c.80.1.3 66611 1odfA 290 7.43e+00 c.37.1.6 -7045 1o20A 427 7.65e+00 c.82.1.1 86556 2abk 211 7.66e+00 2abk a.96.1.1 18743 1p5sA 203 7.71e+00 a.40.1.1 -900 1g4yR 148 7.71e+00 1cll a.39.1.5 60252 1vkeA 133 7.71e+00 1ps9A 671 7.81e+00 c.1.4.1 -5206 1j8yF 297 7.90e+00 1ng1 a.24.13.1 62747 c.37.1.10 62748 1m3qA 317 7.92e+00 a.96.1.3 -1288 d.129.1.2 -11006 1mkiA 330 7.96e+00 e.3.1.2 84994 1qz9A 416 8.07e+00 c.67.1.3 -8180 1efdN 266 8.51e+00 1efdN c.92.2.1 35597 1ebmA 317 8.66e+00 1ebmA a.96.1.3 18751 d.129.1.2 41300 1ii7A 333 8.84e+00 1ii7A d.159.1.4 62415 1vjxA 157 9.02e+00 a.25.1.1 -654 1fp2A 352 9.04e+00 1fpxA a.4.5.29 59941 c.66.1.12 59942 1rxwA 336 9.05e+00 a.60.7.1 -1041 c.120.1.2 -6680 1gqeA 365 9.06e+00 e.38.1.1 70351 1rkeA 262 9.67e+00 a.24.9.1 -582 a.24.9.1 -583 1gxmA 332 9.82e+00 a.102.5.1 76371 1epwA 1290 9.88e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1l8aA 886 9.91e+00 c.36.1.6 73678 c.36.1.10 73677 c.48.1.1 73679 1fm9D 272 1.00e+01 2prgA a.123.1.1 19313 1v8gA 329 1.01e+01 a.46.2.1 -953 c.27.1.1 -6644 1rwzA 245 1.01e+01 d.131.1.2 -11106 d.131.1.2 -11107 1vd5A 377 1.01e+01 1irdB 146 1.02e+01 a.1.1.2 66287 1s96A 219 1.02e+01 c.37.1.1 -6972 1uumA 372 1.04e+01 c.1.4.1 -5193 1qwoA 442 1.06e+01 1h6kA 757 1.08e+01 unknown_sccs 60675 unknown_sccs 60676 unknown_sccs 60677 2cb5A 453 1.08e+01 3gcb d.3.1.1 37035 3tdt 274 1.08e+01 3tdt b.81.1.2 28053 1b4kA 337 1.10e+01 1b4kA c.1.10.3 29184 1m7gA 211 1.12e+01 c.37.1.4 78724 1rvgA 305 1.13e+01 c.1.10.2 -5500 1c3cA 429 1.18e+01 1c3cA a.127.1.1 19425 1gzgA 337 1.20e+01 c.1.10.3 70805 1pg4A 652 1.20e+01 e.23.1.1 88067 1ub3A 220 1.25e+01 c.1.10.1 88395 3gcb 470 1.25e+01 3gcb d.3.1.1 37032 1pmmA 466 1.29e+01 c.67.1.6 -8159 1keaA 221 1.30e+01 a.96.1.2 68491 1knzA 164 1.30e+01 e.34.1.1 68709 1di1A 300 1.32e+01 1di1A a.128.1.4 19446 1rjdA 334 1.37e+01 unknown_sccs -8079 1iw8A 231 1.39e+01 a.111.1.1 76866 1dosA 358 1.40e+01 1dosA c.1.10.2 29175 1cqxA 403 1.41e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 2reb 352 1.43e+01 2reb c.37.1.11 32282 d.48.1.1 38767 1q16A 1247 1.44e+01 b.52.2.2 -4337 c.81.1.1 -8547 1eguA 731 1.44e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.5.2 24423 1rwhA 757 1.45e+01 a.102.3.2 -1340 b.24.1.1 -3300 b.30.5.2 -3508 1g0oA 283 1.46e+01 1ybvA c.2.1.2 60181 1furA 467 1.50e+01 1furA a.127.1.1 19403 1ua4A 455 1.55e+01 c.72.1.3 -8416 1dc1A 323 1.57e+01 1dc1A c.52.1.11 33321 1se0A 116 1.59e+01 g.52.1.1 -12841 4ubpA 101 1.59e+01 1ubpA d.8.1.1 37352 1oz2A 331 1.59e+01 b.34.9.3 -3597 b.34.9.3 -3598 b.34.9.3 -3599 1k0fA 277 1.60e+01 c.92.2.2 71974 1hnnA 282 1.60e+01 c.66.1.15 65895 1gvnB 287 1.62e+01 c.37.1.21 76354 2ts1 419 1.62e+01 2ts1 c.26.1.1 31564 1p32A 209 1.62e+01 1p32A d.25.1.1 38379 1ut8A 291 1.65e+01 a.60.7.1 -1036 c.120.1.2 -6675 1e6yA 569 1.65e+01 1mroA a.89.1.1 18529 d.58.31.2 39447 1f75A 249 1.68e+01 1f75A c.101.1.1 59662 1qzzA 374 1.69e+01 a.4.5.29 -277 c.66.1.12 -8045 1s4qA 228 1.69e+01 c.37.1.1 -6975 1e6pA 499 1.71e+01 1e15A b.72.2.1 59314 c.1.8.5 59315 d.26.3.1 59316 1euhA 475 1.72e+01 1euhA c.82.1.1 35369 1eexG 173 1.77e+01 1dioG a.23.2.1 16490 1gakA 141 1.79e+01 1gakA a.19.1.1 16415 1p9qC 256 1.79e+01 1mzhA 225 1.80e+01 c.1.10.1 79698 1ud9A 245 1.80e+01 1n3jA 119 1.81e+01 b.85.7.2 79963 1kblA 873 1.83e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1nu5A 370 1.84e+01 c.1.11.2 -5565 d.54.1.1 -9823 1ps1A 337 1.86e+01 1ps1A a.128.1.4 19450 1d6jA 211 1.88e+01 1d6jA c.37.1.4 31940 1nd6A 354 1.89e+01 c.60.1.2 80407 1goiA 499 1.91e+01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1e3dB 542 1.92e+01 1h2rL e.18.1.1 59189 1m1cA 680 1.98e+01 e.42.1.1 78395 1dqaA 467 2.02e+01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1ekeA 230 2.03e+01 1ekeA c.55.3.1 33572 1ad3A 452 2.06e+01 1ad3A c.82.1.1 35335 2ahjA 206 2.06e+01 2ahjA d.149.1.1 41772 1qlnA 883 2.10e+01 1cezA e.8.1.3 43111 1fx2A 235 2.10e+01 1fx2A d.58.29.1 39430 1n1jA 93 2.10e+01 a.22.1.3 79813 1dik 874 2.13e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1dm5A 315 2.14e+01 1avc a.65.1.1 18186 1rt8A 513 2.14e+01 1plq 258 2.15e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1ireA 204 2.17e+01 d.149.1.1 76769 1jlvA 209 2.20e+01 a.45.1.1 71729 c.47.1.5 71730 1o0wA 252 2.20e+01 a.149.1.1 80751 d.50.1.1 80752 1nw3A 416 2.21e+01 c.66.1.31 86288 1v8aA 265 2.24e+01 c.72.1.2 -8379 1n5uA 585 2.36e+01 a.126.1.1 85339 a.126.1.1 85340 a.126.1.1 85341 1fjhA 257 2.41e+01 1fjhB c.2.1.2 29870 1qq8A 214 2.42e+01 1qq8A 1ejxA 100 2.47e+01 d.8.1.1 83182 1fts 295 2.47e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1uf2A 1019 2.47e+01 unknown_sccs -12036 1uzbA 516 2.47e+01 c.82.1.1 -8552 2occA 514 2.48e+01 2occA f.24.1.1 43518 1d2tA 231 2.48e+01 1d2tA a.111.1.1 19052 1eca 136 2.48e+01 1flp a.1.1.2 15209 2scpA 174 2.50e+01 2scpA a.39.1.5 17256 1gr0A 367 2.50e+01 c.2.1.3 70379 d.81.1.3 70380 1q4gA 553 2.56e+01 a.93.1.2 -1248 g.3.11.1 -12492 1rqlA 267 2.57e+01 c.108.1.3 -6814 1oglA 283 2.59e+01 unknown_sccs -1512 1or7C 90 2.59e+01 a.180.1.1 87336 1omrA 201 2.60e+01 a.39.1.5 -854 1toaA 313 2.62e+01 1toaA c.92.2.2 35598 1fcyA 236 2.62e+01 2lbd a.123.1.1 19282 1lbvA 252 2.65e+01 e.7.1.1 73813 1r3sA 367 2.65e+01 c.1.22.1 -5648 1j5sA 463 2.65e+01 c.1.9.8 71580 3grs 478 2.66e+01 3grs c.3.1.5 30441 c.3.1.5 30442 d.87.1.1 40152 1plzA 189 2.68e+01 b.82.1.7 88160 1f2eA 201 2.68e+01 1a0fA a.45.1.1 17745 c.47.1.5 33039 1uurA 473 2.69e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1otvA 259 2.70e+01 unknown_sccs -1915 1qxrA 189 2.71e+01 b.82.1.7 -4834 1he7A 126 2.73e+01 1wwcA b.1.1.4 60970 2gsq 202 2.77e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1n45A 233 2.78e+01 a.132.1.1 79981 1anv 356 2.78e+01 1anv a.54.1.1 17890 g.51.1.1 45365 g.51.1.1 45371 1n93X 375 2.79e+01 unknown_sccs -1540 4icb 76 2.82e+01 4icb a.39.1.1 17145 1jqgA 433 2.85e+01 c.56.5.1 71791 d.58.3.1 71792 1rpjA 288 2.91e+01 2dri c.93.1.1 35656 1a0cA 438 2.92e+01 1a0cA c.1.15.3 29529 1o57A 291 2.92e+01 unknown_sccs -249 c.61.1.1 -7960 1nthA 458 2.94e+01 c.1.25.1 80730 1ugpA 203 2.97e+01 1r85A 379 2.99e+01 1q5qA 259 3.00e+01 d.153.1.4 -11433 1fecA 490 3.02e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1jqeA 292 3.06e+01 c.66.1.19 71789 2hbg 147 3.07e+01 2hbg a.1.1.2 15014 2ctc 307 3.09e+01 1aye c.56.5.1 33802 1o0uA 429 3.11e+01 c.118.1.1 80743 1qvbA 481 3.13e+01 1qvbA c.1.8.4 28983 1l1qA 186 3.13e+01 c.61.1.1 77653 1dxrL 273 3.14e+01 6prcL f.26.1.1 43431 1ku1A 230 3.24e+01 a.118.3.1 72996 1qpcA 279 3.25e+01 1fgkA d.144.1.7 41685 1q7eA 428 3.25e+01 c.123.1.1 -8768 1l8wA 348 3.25e+01 a.154.1.1 73704 1nigA 152 3.27e+01 a.25.2.1 85740 1uroA 367 3.27e+01 1uroA c.1.22.1 29675 1mmq 170 3.30e+01 1hfc d.92.1.11 40396 1fvuB 125 3.32e+01 1ixxB d.169.1.1 42346 1cc1L 498 3.35e+01 1h2rL e.18.1.1 43301 1tag 324 3.35e+01 1cipA a.66.1.1 18197 c.37.1.8 32080 1im5A 180 3.37e+01 unknown_sccs 66211 1e3mA 800 3.38e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1pp7U 131 3.39e+01 unknown_sccs -304 1umdA 367 3.40e+01 c.36.1.11 -6969 1xwl 580 3.45e+01 1xwl c.55.3.5 33708 e.8.1.1 43001 1qq5A 253 3.45e+01 1qq5A c.108.1.1 43327 1jjiA 311 3.47e+01 c.69.1.2 66766 1otkA 249 3.53e+01 a.25.1.2 -695 8rucI 123 3.54e+01 1rboC d.73.1.1 39629 1nv8A 284 3.54e+01 c.66.1.30 86224 1gcb 454 3.62e+01 3gcb d.3.1.1 37034 1axdA 209 3.62e+01 1gnwA a.45.1.1 17730 c.47.1.5 33024 1gnxA 479 3.63e+01 c.1.8.4 76241 1pwhA 327 3.66e+01 c.79.1.1 -8524 1cg5B 141 3.67e+01 1cg5B a.1.1.2 15585 1n7kA 234 3.69e+01 c.1.10.1 85374 1qq7A 253 3.70e+01 1qq5A c.108.1.1 43329 1hyeA 313 3.72e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 2vsgA 358 3.72e+01 2vsgA h.4.1.1 45780 1sesA 421 3.73e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1pbgA 468 3.74e+01 1e70M c.1.8.4 28946 1tx4A 198 3.75e+01 1tx4A a.116.1.1 19098 1hz4A 373 3.75e+01 a.118.8.2 65960 1p7gA 222 3.76e+01 a.2.11.1 -108 d.44.1.1 -9742 1ekgA 127 3.77e+01 1dlxA d.82.2.1 40021 1o6yA 299 3.83e+01 d.144.1.7 81106 1fioA 196 3.85e+01 1fioA a.47.2.1 17773 1k87A 669 3.86e+01 a.176.1.1 77286 c.1.23.2 77287 1qpoA 284 3.89e+01 1qpoA c.1.17.1 29561 d.41.2.1 38597