# 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 1iujA 106 3.95e-06 unknown_sccs -9953 1lq9A 112 5.05e-06 d.58.4.3 78129 1edt 271 1.43e-04 2ebn c.1.8.5 28993 1g0cA 364 5.76e-04 7a3hA c.1.8.3 60165 1q4rA 112 2.04e-02 d.58.4.4 -9943 1qysA 106 3.30e-02 unknown_sccs -13432 1a4iA 301 3.39e-02 1a4iA c.2.1.7 30278 c.58.1.2 33926 1o4rA 108 1.08e-01 d.93.1.1 -10624 1q8bA 105 1.17e-01 unknown_sccs -9958 1shdA 107 1.20e-01 1fmk d.93.1.1 40440 1shbA 104 1.25e-01 1fmk d.93.1.1 40425 1g60A 260 1.83e-01 c.66.1.11 70151 1d2kA 392 2.63e-01 1d2kA c.1.8.5 29008 d.26.3.1 38442 1nox 205 2.68e-01 1nox d.90.1.1 40242 1ll7A 392 3.04e-01 c.1.8.5 78085 d.26.3.1 78086 1jayA 212 3.13e-01 c.2.1.6 66478 1icrA 217 3.94e-01 1vfrA d.90.1.1 62274 1sb8A 352 3.98e-01 1bm9A 122 4.02e-01 1bm9A a.4.5.7 16116 1goiA 499 4.90e-01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1c4kA 730 5.32e-01 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1af7 274 5.54e-01 1af7 a.58.1.1 17928 c.66.1.8 34203 1e6pA 499 5.78e-01 1e15A b.72.2.1 59314 c.1.8.5 59315 d.26.3.1 59316 1nmeB 92 6.91e-01 1e4iA 447 7.01e-01 1e70M c.1.8.4 59225 1h09A 338 7.51e-01 b.109.1.1 83420 c.1.8.8 83421 1b5tA 275 8.00e-01 1b5tA c.1.23.1 29676 1h49A 512 8.16e-01 c.1.8.4 83477 1jae 471 8.23e-01 1smd b.71.1.1 27773 c.1.8.1 28760 1v02A 565 8.34e-01 1mwqA 101 8.80e-01 unknown_sccs -9962 1uroA 367 9.76e-01 1uroA c.1.22.1 29675 1r3sA 367 1.01e+00 c.1.22.1 -5648 1e55A 512 1.12e+00 1e70M c.1.8.4 28934 1n2sA 299 1.18e+00 c.2.1.2 79857 1nu0A 138 1.25e+00 unknown_sccs -7658 1iibA 106 1.39e+00 1iibA c.44.2.1 32648 1inp 400 1.44e+00 1inp e.7.1.1 42972 1fcyA 236 1.50e+00 2lbd a.123.1.1 19282 1fiqB 350 1.50e+00 1fiqB d.87.2.1 40229 d.145.1.3 41760 1cnt1 187 1.73e+00 1cnt3 1bag 425 1.78e+00 1bag b.71.1.1 27720 c.1.8.1 28707 1g8kA 825 1.88e+00 1g8jA b.52.2.2 26920 c.81.1.1 35328 1dtdA 303 1.95e+00 1aye c.56.5.1 33823 1s2dA 167 1.97e+00 c.23.14.1 -6469 1m7xA 617 2.09e+00 b.1.18.2 78749 b.71.1.1 78750 c.1.8.1 78751 1qb0A 211 2.20e+00 1c25 c.46.1.1 32699 1forL 210 2.23e+00 8fabA b.1.1.1 19988 b.1.1.2 21044 2myr 501 2.38e+00 1jmtA 104 2.64e+00 d.58.7.3 63180 3ertA 261 2.74e+00 3erdA a.123.1.1 19292 2igd 61 2.81e+00 2igd d.15.7.1 37821 1lkkA 105 2.95e+00 1lckA d.93.1.1 40412 1j34B 123 3.11e+00 d.169.1.1 84049 1js3A 486 3.29e+00 c.67.1.6 67215 1vhh 162 3.42e+00 1vhh d.65.1.2 39550 1bn7A 294 3.51e+00 1bn6A c.69.1.8 34677 1vjtA 483 3.66e+00 c.2.1.5 -5941 d.162.1.2 -11508 1k3eA 156 3.70e+00 d.198.1.1 68103 1g71A 347 3.82e+00 1g71A unknown_sccs 43268 1dpe 507 3.97e+00 1dpe c.94.1.1 35799 1gy8A 397 4.18e+00 c.2.1.2 83376 1rt8A 513 4.43e+00 1tvlA 454 4.45e+00 1uc2A 481 4.77e+00 unknown_sccs -11725 1umhA 184 4.78e+00 unknown_sccs -3127 1e4mM 501 4.82e+00 1e70M c.1.8.4 59226 1pyaB 228 5.01e+00 1pyaB 1nv8A 284 5.10e+00 c.66.1.30 86224 1vhsA 175 5.11e+00 d.108.1.1 -10794 1nx8A 273 5.13e+00 b.82.2.8 86374 1eceA 358 5.19e+00 1eceA c.1.8.3 28813 1e44B 96 5.58e+00 1e44B b.101.1.1 59220 1hkkA 364 5.58e+00 c.1.8.5 -5384 d.26.3.1 -9506 1cnv 299 5.71e+00 1cnv c.1.8.5 28989 1q45A 391 5.75e+00 c.1.4.1 -5199 1ug6A 431 5.84e+00 c.1.8.4 88490 1kpgA 287 5.95e+00 c.66.1.18 68735 1pqnA 127 6.16e+00 c.47.1.8 -7479 1oapA 109 6.21e+00 unknown_sccs -10428 1tz9A 367 6.28e+00 1colA 204 6.45e+00 1a87 f.1.1.1 43378 1twdA 256 6.58e+00 1nhkL 144 6.65e+00 1npk d.58.6.1 39142 1azwA 313 6.85e+00 1qtrA c.69.1.7 34658 1jw9B 249 7.11e+00 c.111.1.1 67377 1bg0 356 7.12e+00 1qh4A a.83.1.1 18476 d.128.1.2 41211 1ro0A 216 7.26e+00 unknown_sccs -11390 1m15A 357 7.51e+00 a.83.1.1 78368 d.128.1.2 78369 1pamA 686 7.58e+00 1cxlA b.1.18.2 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1thfD 253 7.59e+00 1thfD c.1.2.1 28535 1ckeA 227 7.66e+00 1ckeA c.37.1.1 31846 1qkmA 255 7.79e+00 3erdA a.123.1.1 19309 1cb0A 283 7.83e+00 1cb0A c.56.2.1 33790 1miuA 738 7.90e+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 1qgvA 142 8.57e+00 1qgvA c.47.1.8 33056 2mprA 421 8.99e+00 2mprA f.4.3.2 43788 1cb8A 678 9.13e+00 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1itxA 419 9.20e+00 c.1.8.5 71425 d.26.3.1 71426 1b5l 172 9.23e+00 1b5l a.26.1.3 16900 1evhA 112 9.30e+00 1evhA b.55.1.4 26997 1mkeA 152 9.31e+00 b.55.1.4 79231 2hvm 273 9.32e+00 1cnv c.1.8.5 28985 1lvmA 229 9.53e+00 b.47.1.3 78243 1whtA 256 9.54e+00 1ivyA c.69.1.5 34646 1hzoA 271 9.62e+00 e.3.1.1 71092 1vh7A 265 9.66e+00 c.1.2.1 -5159 1sr9A 644 9.73e+00 1tidB 119 9.73e+00 1fi4A 416 9.85e+00 1fi4A d.14.1.5 59847 d.58.26.2 59848 1v0wA 506 9.86e+00 1cf2O 337 9.86e+00 1b7gO c.2.1.3 29994 d.81.1.1 39909 1jyhA 157 9.92e+00 d.60.1.3 71956 1kqzA 273 1.00e+01 c.1.8.5 68844 1n13B 113 1.00e+01 1r1dA 247 1.00e+01 unknown_sccs -8335 1eexB 224 1.04e+01 1dioB c.51.3.1 33213 1owqA 361 1.07e+01 1ro2A 216 1.08e+01 unknown_sccs -11391 1akz 223 1.14e+01 3eugA c.18.1.1 31007 1odzA 386 1.15e+01 c.1.8.3 86889 1lzlA 323 1.16e+01 c.69.1.2 78306 1m6yA 301 1.18e+01 a.60.13.1 78716 c.66.1.23 78717 2aaa 484 1.20e+01 7taa b.71.1.1 27777 c.1.8.1 28764 1j5vA 351 1.21e+01 c.72.1.1 71585 2ebn 289 1.24e+01 2ebn c.1.8.5 28990 1v97A 1332 1.24e+01 1mml 265 1.30e+01 1mml e.8.1.2 43015 1p1xA 260 1.33e+01 1jclA 260 1.34e+01 c.1.10.1 66501 1oz9A 150 1.37e+01 unknown_sccs -10588 1q6cA 495 1.39e+01 c.1.8.1 -5300 1tx4B 178 1.39e+01 1ctqA c.37.1.8 32045 1h9dB 134 1.41e+01 2jhbA b.54.1.1 60822 1pk6B 132 1.42e+01 b.22.1.1 -3290 3c2c 112 1.43e+01 1ycc a.3.1.1 15885 1hjxA 362 1.48e+01 c.1.8.5 83512 d.26.3.1 83513 1v84A 253 1.54e+01 1fgyA 127 1.54e+01 1faoA b.55.1.1 26976 1bjx 110 1.54e+01 1bjx c.47.1.2 32774 1pbgA 468 1.57e+01 1e70M c.1.8.4 28946 1vjzA 341 1.61e+01 c.1.8.3 -5318 1h10A 125 1.61e+01 b.55.1.1 83446 1i37A 260 1.64e+01 1a28A a.123.1.1 61583 1on0A 158 1.68e+01 d.108.1.1 87095 1kqfB 294 1.68e+01 d.58.1.5 75900 f.23.22.1 75901 1nwaA 203 1.68e+01 d.58.28.1 86295 1n0wA 243 1.69e+01 c.37.1.11 79772 1b3tA 147 1.70e+01 1b3tA d.58.8.1 39228 1uzcA 71 1.72e+01 a.159.2.1 -339 1q7zA 566 1.73e+01 c.1.21.2 -5638 c.1.26.1 -5666 1kdgA 546 1.76e+01 c.3.1.2 77337 d.16.1.1 77338 1o6dA 163 1.79e+01 c.116.1.3 -6689 1jj2O 148 1.79e+01 1ffkM a.94.1.1 63100 1s72P 149 1.81e+01 1sr7A 259 1.82e+01 1gqiA 708 1.89e+01 c.1.8.10 76279 d.92.2.2 76280 1cuk 203 1.90e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1t3uA 104 1.90e+01 unknown_sccs -9325 1iybA 208 1.91e+01 d.124.1.1 -10977 1a28A 256 1.99e+01 1a28A a.123.1.1 19290 1jdlA 121 1.99e+01 a.3.1.1 66557 1a99A 344 1.99e+01 1pot c.94.1.1 35812 1v33A 366 2.00e+01 unknown_sccs -11384 1vhiA 142 2.00e+01 1b3tA d.58.8.1 39230 1fxlA 167 2.00e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1usmA 80 2.05e+01 d.74.1.1 -10334 1dciA 275 2.07e+01 1dciA c.14.1.3 30918 1bia 321 2.10e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1umdB 324 2.11e+01 c.36.1.7 -6929 c.48.1.2 -7539 1c7sA 858 2.11e+01 1qba b.1.18.2 21812 b.2.2.3 22408 c.1.8.6 29011 d.92.2.1 40410 1o98A 511 2.12e+01 c.105.1.1 86684 c.76.1.3 86685 1gqeA 365 2.13e+01 e.38.1.1 70351 1j9yA 385 2.14e+01 1j9yA c.1.8.3 62791 1r2qA 170 2.15e+01 c.37.1.8 -7071 2irfG 113 2.18e+01 2irfG a.4.5.23 16185 1m55A 197 2.18e+01 d.89.1.3 74469 1pwhA 327 2.19e+01 c.79.1.1 -8524 1d3gA 367 2.20e+01 1d3gA c.1.4.1 28600 1npk 154 2.21e+01 1npk d.58.6.1 39099 1f0iA 504 2.25e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1eg7A 557 2.25e+01 1eg7A c.37.1.10 32241 1jj2M 186 2.26e+01 1ffkK c.55.4.1 63098 1ftkA 279 2.27e+01 1gr2A c.94.1.1 35819 1bcfA 158 2.31e+01 1bcfA a.25.1.1 16648 1s72N 187 2.32e+01 1mjfA 281 2.35e+01 c.66.1.17 79198 5nul 138 2.36e+01 5nul c.23.5.1 31191 1uu1A 335 2.38e+01 c.67.1.1 -8146 1jipA 403 2.39e+01 a.104.1.1 66748 7taa 478 2.40e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1rgyA 360 2.41e+01 e.3.1.1 -11768 1esiA 262 2.43e+01 1skf e.3.1.1 42682 1v4vA 376 2.45e+01 c.87.1.3 -8583 1eqjA 511 2.46e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1byb 495 2.47e+01 1byb c.1.8.1 28790 1btkA 169 2.48e+01 1btkA b.55.1.1 26959 1urrA 102 2.48e+01 1ly1A 181 2.48e+01 c.37.1.1 74334 1gt91 357 2.49e+01 1v3hA 495 2.51e+01 7a3hA 303 2.51e+01 7a3hA c.1.8.3 28817 2apr 325 2.51e+01 2er7E b.50.1.2 26819 1khbA 625 2.53e+01 c.91.1.1 68606 c.109.1.1 68607 1eupA 403 2.53e+01 1rom a.104.1.1 18967 2bltA 361 2.53e+01 1gceA e.3.1.1 42739 1on3A 523 2.54e+01 c.14.1.4 87107 c.14.1.4 87108 2fokA 579 2.55e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1k8vA 40 2.56e+01 j.6.1.1 72182 1oflA 481 2.58e+01 1k28D 391 2.58e+01 b.106.1.1 68052 b.106.1.1 68053 1atiA 505 2.59e+01 1atiA c.51.1.1 33196 d.104.1.1 40745 1vjjA 692 2.59e+01 b.1.18.9 -2758 b.1.5.1 -2786 b.1.5.1 -2787 d.3.1.4 -8893 1cxc 124 2.62e+01 1ycc a.3.1.1 15890 2pviA 157 2.62e+01 3pviA c.52.1.6 33302 1im8A 244 2.63e+01 c.66.1.14 66212 1eexA 554 2.64e+01 1dioA c.1.19.3 29650 2cxbA 124 2.65e+01 1ycc a.3.1.1 15891 1j6pA 418 2.67e+01 b.92.1.4 77089 c.1.9.9 77090 1i8jA 323 2.68e+01 1b4kA c.1.10.3 61968 1od6A 160 2.71e+01 c.26.1.3 86836 1q1oA 98 2.73e+01 d.15.2.2 -9172 1p1mA 406 2.75e+01 b.92.1.4 87696 c.1.9.9 87697 1l6sA 323 2.79e+01 c.1.10.3 73627 1j9bA 141 2.81e+01 c.47.1.12 66459 1ta3B 303 2.84e+01 1a8s 273 2.86e+01 1brt c.69.1.12 34710 1q8rA 120 2.88e+01 unknown_sccs -10422 1aq0A 306 2.88e+01 1aq0A c.1.8.3 28842 1va4A 279 2.88e+01 1hh1A 143 2.89e+01 1gefA c.52.1.18 61036 1kafA 108 2.92e+01 d.199.1.1 68372 1d3cA 686 2.92e+01 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721 1ac5 483 2.95e+01 1ac5 c.69.1.5 34653 1jidA 128 2.97e+01 d.201.1.1 66735 1st9A 143 3.01e+01 c.47.1.10 -7503 1o60A 292 3.02e+01 c.1.10.4 -5549 1gdhA 320 3.06e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1h1nA 305 3.06e+01 c.1.8.3 70855 1dbgA 506 3.06e+01 1dbgA b.80.1.4 28033 1kqqA 139 3.06e+01 a.4.3.1 72885 1k1xA 659 3.07e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1wod 233 3.07e+01 1wod c.94.1.1 35832 1bh9B 89 3.09e+01 1bh9B a.22.1.3 16485 1v7zA 260 3.09e+01 unknown_sccs -6353 1pvdA 537 3.10e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1dyr 206 3.11e+01 1aoeA c.71.1.1 34916 1cr1A 296 3.15e+01 1cr1A c.37.1.11 32286 1mqiA 263 3.15e+01 c.94.1.1 -8681 1udh 244 3.17e+01 3eugA c.18.1.1 31015 1o6uA 403 3.20e+01 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1omzA 293 3.20e+01 c.68.1.15 87093 1fcqA 350 3.24e+01 c.1.8.9 65006 1oef 24 3.28e+01 j.39.1.1 46299 5hpgA 84 3.29e+01 5hpgA g.14.1.1 44642 1ve9A 347 3.30e+01 c.4.1.2 -6056 d.16.1.3 -9214 1eokA 290 3.30e+01 1eokA c.1.8.5 28991 1oaoC 729 3.31e+01 e.26.1.3 86746 1ccwB 483 3.31e+01 1cb7B c.1.19.2 29646 1e5rA 290 3.32e+01 1e5rA b.82.2.4 59276 1ixkA 315 3.35e+01 unknown_sccs -8099 1sacA 204 3.38e+01 1sacA b.29.1.5 24237 1kte 105 3.38e+01 1kte c.47.1.1 32771 1p5sA 203 3.41e+01 a.40.1.1 -900 1hyhA 309 3.41e+01 1hyhA c.2.1.5 30150 d.162.1.1 42117 1bjt 793 3.41e+01 1bjt e.11.1.1 43249 1axdA 209 3.41e+01 1gnwA a.45.1.1 17730 c.47.1.5 33024 1kmqA 184 3.42e+01 c.37.1.8 84412 1kao 167 3.43e+01 1ctqA c.37.1.8 32014 1bt0A 76 3.43e+01 1ubi d.15.1.1 37607 1uc8A 280 3.46e+01 unknown_sccs -6718 unknown_sccs -11230 1b7yB 785 3.46e+01 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 1oiaA 95 3.46e+01 d.58.7.1 87051 1jkxA 212 3.48e+01 c.65.1.1 66813 1bg4 302 3.50e+01 1taxA c.1.8.3 28806 1an9A 340 3.51e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1o0pA 104 3.52e+01 d.58.7.1 86535 1l8nA 679 3.54e+01 c.1.8.10 84564 d.92.2.2 84565 1acc 735 3.62e+01 1acc f.11.1.1 43828 1whsA 255 3.64e+01 1ivyA c.69.1.5 34649 3aprE 325 3.65e+01 2er7E b.50.1.2 26820 1j5yA 187 3.66e+01 a.4.5.1 71592 d.94.2.1 71593 1hjzA 192 3.68e+01 c.50.1.2 83520 1otgA 125 3.68e+01 1otgA d.80.1.2 39831 1bif 469 3.69e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1exbA 332 3.69e+01 1qrqA c.1.7.1 28666 1al3 324 3.71e+01 1al3 c.94.1.1 35835 1dl5A 317 3.75e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1aa8A 347 3.76e+01 1an9A 1nthA 458 3.77e+01 c.1.25.1 80730 1ef8A 261 3.81e+01 1ef8A c.14.1.3 30921 1p2xA 159 3.83e+01 1rkuA 206 3.84e+01 unknown_sccs -6823 1mjhA 162 3.87e+01 1mjhA c.26.2.4 31639 1f4pA 147 3.91e+01 5nul c.23.5.1 59651 1g7sA 594 3.92e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1cvrA 435 3.94e+01 1cvrA b.1.18.12 21949 c.17.1.2 31006 1om0A 274 3.94e+01 c.1.8.5 87058 1iapA 211 3.94e+01 a.91.1.1 62119 1cem 363 3.95e+01 1cem a.102.1.2 18826 1j4aA 333 3.96e+01 c.2.1.4 71502 c.23.12.1 71503