# List of top-scoring protein chains for t2k-100-30-alpha 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 1nt4A 391 1.77e-01 c.60.1.2 92102 1zvdA 380 1.15e+00 1sgg 75 1.57e+00 1b4fA a.60.1.2 17943 1s5lX 50 2.18e+00 1qmzB 259 2.39e+00 1vin a.74.1.1 18338 a.74.1.1 18339 1m3yA 413 2.40e+00 b.121.2.3 78579 b.121.2.3 78580 1j5qA 437 2.44e+00 b.121.2.3 77084 b.121.2.3 77085 1t7pA 698 2.63e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1r5zA 323 3.49e+00 f.40.1.1 97135 1zk7A 467 3.55e+00 1dfoA 417 3.76e+00 1bj4A c.67.1.4 34480 1k0nA 241 3.83e+00 a.45.1.1 67953 c.47.1.5 67954 1x9mA 698 3.87e+00 1zsxA 347 4.02e+00 2cohA 202 4.15e+00 1urqA 63 4.50e+00 h.1.15.1 107994 1vk9A 151 4.50e+00 c.139.1.1 108640 1m6dA 214 4.54e+00 d.3.1.1 84849 1k9tA 540 4.80e+00 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1yaxA 153 4.86e+00 1eni 138 5.11e+00 2end a.18.1.1 16403 1yw0A 276 5.23e+00 1edqA 540 5.32e+00 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 2end 138 5.37e+00 2end a.18.1.1 16400 1n2sA 299 5.49e+00 c.2.1.2 79857 1k0mA 241 5.57e+00 a.45.1.1 67949 c.47.1.5 67950 1f07A 321 5.69e+00 1ezwA c.1.16.3 59560 1exbA 332 5.77e+00 1qrqA c.1.7.1 28666 1ctn 540 6.31e+00 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1qrqA 325 6.35e+00 1qrqA c.1.7.1 28667 1bx4A 345 6.42e+00 1bx4A c.72.1.1 34935 1ffkV 143 6.69e+00 1ffkV c.9.2.1 30849 2lbp 346 8.43e+00 2liv c.93.1.1 35709 1ze3H 122 8.47e+00 1lvmA 229 9.02e+00 b.47.1.3 78243 1vasA 137 9.16e+00 2end a.18.1.1 16404 1b4fG 82 9.44e+00 1b4fA a.60.1.2 17940 1rylA 167 9.67e+00 d.276.1.1 105124 2a6qA 86 9.74e+00 1r12A 258 9.80e+00 e.4.1.1 96780 1vin 268 9.97e+00 1vin a.74.1.1 18354 a.74.1.1 18355 1f0mA 82 1.02e+01 1b4fA a.60.1.2 17942 1rwtA 232 1.03e+01 f.43.1.1 97992 1b4fA 82 1.03e+01 1b4fA a.60.1.2 17934 1uelB 48 1.04e+01 j.105.1.1 99266 1wpgA 994 1.06e+01 1m2eA 135 1.07e+01 c.23.1.5 78478 2afwA 329 1.09e+01 1enk 138 1.10e+01 2end a.18.1.1 16402 1ou8A 111 1.10e+01 b.136.1.1 93543 1nfiA 301 1.13e+01 1a3qA b.1.18.1 21942 b.2.5.3 22455 1h2eA 207 1.13e+01 c.60.1.1 70857 1lj8A 493 1.15e+01 a.100.1.9 90392 c.2.1.6 90393 1qhtA 775 1.16e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 2aefA 234 1.27e+01 1k8mA 93 1.27e+01 b.84.1.1 68314 1h8lA 380 1.28e+01 b.3.2.1 65737 c.56.5.1 65738 1hnnA 282 1.34e+01 c.66.1.15 65895 1nfiC 301 1.36e+01 b.1.18.1 21943 b.2.5.3 22456 1t0qA 498 1.38e+01 a.25.1.2 106220 1klpA 115 1.48e+01 a.28.1.1 72721 1p9cA 45 1.49e+01 j.105.1.1 94386 1vflA 356 1.50e+01 1qmuA 380 1.51e+01 1qmuA b.3.2.1 22534 c.56.5.1 33827 1ebbA 202 1.53e+01 c.60.1.1 64900 1ll2A 333 1.55e+01 c.68.1.14 74005 1aa7A 158 1.57e+01 1aa7A a.95.1.1 18741 1xc0A 33 1.58e+01 j.6.1.1 109542 1vp6A 138 1.65e+01 1yydA 357 1.67e+01 1jtdB 273 1.67e+01 b.69.5.2 67265 1ovnA 248 1.68e+01 a.71.1.1 93602 c.47.1.7 93603 1vqoY 241 1.71e+01 1enj 138 1.82e+01 2end a.18.1.1 16401 1u5tA 233 1.83e+01 a.4.5.54 107684 a.4.5.54 107685 1zsyA 357 1.84e+01 1yfnA 118 1.88e+01 1usgA 346 1.89e+01 c.93.1.1 99864 1ea3A 164 1.90e+01 1aa7A a.95.1.1 59398 1pgs 314 1.97e+01 1pgs b.121.1.1 23653 b.121.1.1 23654 1ash 150 1.99e+01 1ash a.1.1.2 15622 1jeyB 565 2.02e+01 1jeqB b.131.1.2 90372 c.62.1.4 90373 1dv2A 452 2.05e+01 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1lbeA 258 2.08e+01 1lbeA e.4.1.1 42773 1tueB 218 2.10e+01 b.91.1.1 107324 1o51A 114 2.11e+01 d.58.5.4 92480 1w9yA 319 2.11e+01 1dv1A 449 2.14e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1jud 232 2.15e+01 1qq5A c.108.1.1 43325 2cz1A 206 2.16e+01 1bncB 449 2.16e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1zrn 232 2.18e+01 1qq5A c.108.1.1 43323 1pbgA 468 2.22e+01 1e70M c.1.8.4 28946 1ll0A 339 2.22e+01 c.68.1.14 73995 2c3vA 102 2.24e+01 3pflA 759 2.24e+01 1cm5A c.7.1.1 30673 1mn1 357 2.26e+01 1arv a.93.1.1 18667 1crkA 380 2.27e+01 1qh4A a.83.1.1 18458 d.128.1.2 41193 1mnp 357 2.28e+01 1arv a.93.1.1 18668 1a17 166 2.36e+01 1a17 a.118.8.1 19206 1z83A 196 2.37e+01 2aamA 309 2.40e+01 3adk 195 2.42e+01 1zin c.37.1.1 31885 1oyb 400 2.44e+01 1oyc c.1.4.1 28602 1oyc 400 2.46e+01 1oyc c.1.4.1 28603 1ds6B 180 2.50e+01 1rhoA b.1.18.8 21898 2lhb 149 2.50e+01 2fal a.1.1.2 15597 1bpyA 335 2.51e+01 1bpyA a.60.6.1 17980 a.60.12.1 75819 d.218.1.2 75820 1quqB 121 2.52e+01 1quqB b.40.4.3 25305 2f96A 224 2.56e+01 1cm5A 759 2.65e+01 1cm5A c.7.1.1 30671 2ahjA 206 2.66e+01 2ahjA d.149.1.1 41772 1yp5A 58 2.68e+01 1mioA 534 2.71e+01 1qguA c.92.2.3 35601 1tgoA 773 2.73e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1ahjA 207 2.74e+01 2ahjA d.149.1.1 41774 1jeqB 565 2.76e+01 1jeqB b.131.1.2 90368 c.62.1.4 90369 2pflA 759 2.77e+01 1cm5A c.7.1.1 30675 3pbgA 468 2.79e+01 1e70M c.1.8.4 28951 1y0hA 105 2.81e+01 1jj2X 240 2.86e+01 1ffkV c.9.2.1 63109 1g4yR 148 2.87e+01 1cll a.39.1.5 60252 1xfxO 149 2.93e+01 1zpvA 91 2.94e+01 1s72Y 241 2.95e+01 c.9.2.1 105344 1h8eI 50 2.96e+01 1e79I a.137.8.1 60758 1c0pA 363 2.97e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1s1iD 361 3.08e+01 i.1.1.1 105178 1tv9A 335 3.10e+01 1h16A 759 3.16e+01 c.7.1.1 76462 1lqtA 456 3.21e+01 c.3.1.1 74198 c.4.1.1 74199 1f88A 348 3.21e+01 1f88A f.13.1.2 43429 1kfuS 184 3.23e+01 a.39.1.8 68574 1bncA 449 3.25e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1a3aC 148 3.30e+01 1a3aA d.112.1.1 40919 1a3aA 148 3.31e+01 1a3aA d.112.1.1 40917 2aw4Q 117 3.31e+01 1am4A 199 3.35e+01 1tx4A a.116.1.1 19100 1lbvA 252 3.36e+01 e.7.1.1 73813 1b22A 114 3.38e+01 1b22A a.60.4.1 17969 1yruB 74 3.44e+01 1hqsA 423 3.51e+01 1iso c.77.1.1 61154 1nekC 129 3.51e+01 f.21.2.2 80431 1fsu 492 3.53e+01 1auk c.76.1.2 35032 1ox8A 107 3.60e+01 b.136.1.1 93671 3thiA 371 3.63e+01 2thiA c.94.1.1 35792 1ds1A 324 3.69e+01 1drtA b.82.2.2 28127 1y0vH 146 3.70e+01 1u04A 771 3.70e+01 b.34.14.1 107539 c.55.3.10 107540 1ruwA 69 3.71e+01 2ahjC 206 3.72e+01 2ahjA d.149.1.1 41773 1v9mA 323 3.75e+01 f.40.1.1 100543 2c5uA 375 3.76e+01 2thiA 379 3.80e+01 2thiA c.94.1.1 35794 1qqhA 144 3.81e+01 1dtoA b.91.1.1 28404 2d00A 109 3.84e+01 1oya 400 3.87e+01 1oyc c.1.4.1 28604 1ko3A 230 3.87e+01 d.157.1.1 90974 1xkwA 665 3.88e+01 1irxA 523 3.90e+01 a.97.1.2 71378 c.26.1.1 71379