# List of top-scoring protein chains for t2k-w0.5 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 1bza 262 4.51e-01 1btl e.3.1.1 42701 1kktA 511 5.44e-01 a.102.2.1 68687 1i2sA 282 6.35e-01 1eqnA 321 8.98e-01 1dd9A e.13.1.1 43256 1dy6A 267 9.15e-01 1btl e.3.1.1 42732 1g81A 164 9.46e-01 1fw9A d.190.1.1 60336 1g1bA 164 9.57e-01 1fw9A d.190.1.1 60202 4blmA 265 1.06e+00 1btl e.3.1.1 42721 1dd9A 338 1.38e+00 1dd9A e.13.1.1 43254 1ddeA 338 1.38e+00 1dd9A e.13.1.1 43255 1dlpA 236 1.40e+00 1b2pA b.78.1.1 28000 b.78.1.1 28001 1bdfA 235 1.67e+00 1bdfA d.74.3.1 39727 d.181.1.1 42602 1fw9A 164 1.73e+00 1fw9A d.190.1.1 60059 1mblA 256 1.75e+00 1btl e.3.1.1 42723 1fuoA 467 1.84e+00 1furA a.127.1.1 19411 2fusA 467 1.85e+00 1furA a.127.1.1 19409 1furA 467 1.85e+00 1furA a.127.1.1 19403 1fuqA 472 1.86e+00 1furA a.127.1.1 19405 1dceB 331 2.32e+00 1dceB a.102.4.3 18872 1ad1A 266 2.56e+00 1aj2 c.1.21.1 29668 1kyoD 248 2.59e+00 1ezvD 245 2.59e+00 1be3D a.3.1.3 59546 f.2.1.8 59547 1bsg 266 2.70e+00 1btl e.3.1.1 42729 1flcA 432 2.79e+00 1flcA b.19.1.3 23837 c.23.10.2 31337 7prn 289 3.23e+00 3prn f.4.3.1 43768 8prn 289 3.70e+00 3prn f.4.3.1 43767 1aym1 285 3.79e+00 1aym1 1d3e1 285 3.83e+00 2shpA 525 3.98e+00 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1hzoA 271 4.21e+00 1aozA 552 4.50e+00 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 1lnqA 336 4.59e+00 1jd3A 164 4.83e+00 1fw9A d.190.1.1 62896 1i6uA 130 4.92e+00 d.140.1.1 61850 1jljA 189 4.95e+00 c.57.1.1 63169 1ihcA 188 5.05e+00 1di6A c.57.1.1 62379 3prn 289 5.18e+00 3prn f.4.3.1 43761 1cknA 330 5.43e+00 1ckmA b.40.4.6 25360 d.142.2.3 41587 1ckmA 330 5.43e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1kfvA 271 5.44e+00 1cknB 330 5.47e+00 1ckmA b.40.4.6 25361 d.142.2.3 41588 1jvyA 372 5.86e+00 c.94.1.1 63308 1kyfA 247 6.13e+00 1qtsA 247 6.13e+00 1qtsA b.1.10.1 22313 d.105.1.1 40789 1chkA 238 6.39e+00 1chkA d.2.1.7 36999 1jqlB 140 6.77e+00 c.37.1.13 63234 1jf0A 195 6.93e+00 1ej3A a.39.1.5 62926 1prn 289 6.99e+00 3prn f.4.3.1 43762 1mdq 371 7.01e+00 4mbp c.94.1.1 35783 1colA 204 7.53e+00 1a87 f.1.1.1 43378 6prn 289 7.85e+00 3prn f.4.3.1 43765 1fqaA 370 7.89e+00 4mbp c.94.1.1 59984 4mbp 370 7.89e+00 4mbp c.94.1.1 35777 1anf 370 7.89e+00 4mbp c.94.1.1 35776 1omp 370 7.89e+00 4mbp c.94.1.1 35778 1ezoA 370 7.91e+00 4mbp c.94.1.1 59539 1qtpA 247 8.07e+00 1qtsA b.1.10.1 22314 d.105.1.1 40790 1mdaL 121 8.15e+00 2bbkL g.21.1.1 44885 1bh3 289 8.21e+00 3prn f.4.3.1 43766 1mg1A 450 8.25e+00 4mbp c.94.1.1 35790 h.3.2.1 45753 1hsjA 487 8.50e+00 4mbp a.4.5.28 61237 c.94.1.1 61238 1b9kA 238 8.51e+00 1qtsA b.1.10.1 22315 d.105.1.1 40791 2fokA 579 8.53e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1a7lA 389 8.60e+00 4mbp c.94.1.1 35787 1fehA 574 9.49e+00 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1k1zA 78 9.88e+00 b.34.2.1 68026 1dxiA 388 1.00e+01 4xis c.1.15.3 29407 2prn 289 1.02e+01 3prn f.4.3.1 43763 1mup 166 1.03e+01 1mup b.60.1.1 27133 1jv4A 162 1.03e+01 b.60.1.1 67343 1dsfL 112 1.04e+01 8fabA b.1.1.1 20246 1i06A 180 1.10e+01 1mup b.60.1.1 27131 1i05A 180 1.10e+01 1mup b.60.1.1 27130 1bjqB 253 1.12e+01 1led b.29.1.1 24118 1qdmA 478 1.13e+01 1smrA a.64.1.2 18141 b.50.1.2 26838 4matA 278 1.14e+01 1c24A d.127.1.1 41150 1c24A 263 1.14e+01 1c24A d.127.1.1 41148 3matA 265 1.14e+01 1c24A d.127.1.1 41149 2matA 264 1.14e+01 1c24A d.127.1.1 41146 1a8p 258 1.17e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 1cqqA 180 1.25e+01 1cqqA b.47.1.4 26422 1btl 263 1.26e+01 1btl e.3.1.1 42691 1ck3A 263 1.26e+01 1btl e.3.1.1 42698 1gghA 753 1.26e+01 1cf9A c.23.16.3 31465 e.5.1.1 42839 1ggeA 753 1.26e+01 1cf9A c.23.16.3 31449 e.5.1.1 42823 1gg9A 753 1.27e+01 1cf9A c.23.16.3 31445 e.5.1.1 42819 1pd21 199 1.27e+01 1pd21 1qf7A 753 1.28e+01 1cf9A c.23.16.3 31461 e.5.1.1 42835 1mpb 370 1.30e+01 4mbp c.94.1.1 35780 1jgjA 217 1.33e+01 1c3wA f.2.1.1 62952 1bcpD 110 1.34e+01 1bcpD b.40.2.1 25132 1prtD 110 1.34e+01 1bcpD b.40.2.1 25128 1cf9A 753 1.38e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1im5A 180 1.39e+01 c.33.1.2 66211 1fdjA 363 1.39e+01 1fbaA c.1.10.1 59772 1hqvA 191 1.43e+01 1hqvA a.39.1.8 61160 1hngA 176 1.44e+01 1cczA b.1.1.1 19752 b.1.1.3 21681 1oen 540 1.45e+01 1ayl c.91.1.1 64750 c.109.1.1 64751 6xia 387 1.48e+01 4xis c.1.15.3 29406 4xis 387 1.49e+01 4xis c.1.15.3 29421 3xis 387 1.49e+01 4xis c.1.15.3 29423 2xis 387 1.49e+01 4xis c.1.15.3 29427 1jwvA 263 1.49e+01 1gw9A 388 1.50e+01 1c1eL 216 1.51e+01 8fabA b.1.1.1 20238 b.1.1.2 21250 1htzA 263 1.51e+01 1btl e.3.1.1 61262 1h68A 239 1.53e+01 f.2.1.1 60664 1esuA 263 1.54e+01 1btl e.3.1.1 42696 1l7uA 263 1.54e+01 1erqA 263 1.54e+01 1btl e.3.1.1 42697 1jwzA 263 1.54e+01 1jvjA 263 1.55e+01 1fqgA 263 1.56e+01 1btl e.3.1.1 42699 1jtdA 263 1.56e+01 e.3.1.1 67264 1ermA 263 1.59e+01 1btl e.3.1.1 42690 1l0yD 221 1.61e+01 1jvxA 372 1.67e+01 c.94.1.1 63307 1jr3D 343 1.71e+01 a.80.1.1 63251 c.37.1.13 63252 1mat 264 1.75e+01 1c24A d.127.1.1 41152 1k82A 268 1.77e+01 1ggkA 753 1.80e+01 1cf9A c.23.16.3 31453 e.5.1.1 42827 2mysC 149 1.81e+01 1wdcC a.39.1.5 17323 1aj0 282 1.82e+01 1aj2 c.1.21.1 29667 1aj2 282 1.82e+01 1aj2 c.1.21.1 29665 1e8xA 961 1.83e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1e7uA 961 1.83e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1gegA 256 1.83e+01 1ybvA c.2.1.2 29888 1hd8A 363 1.85e+01 b.105.1.1 65803 e.3.1.1 65804 1bueA 265 1.89e+01 1btl e.3.1.1 42727 1fnyA 237 1.91e+01 1led b.29.1.1 59920 1clkA 387 1.93e+01 4xis c.1.15.3 29438 1qt1A 387 1.96e+01 4xis c.1.15.3 29436 1dcnA 424 2.04e+01 1auwA a.127.1.1 19420 1dcnC 434 2.04e+01 1auwA a.127.1.1 19422 1qo5A 363 2.08e+01 1fbaA c.1.10.1 29102 1dcnD 436 2.09e+01 1auwA a.127.1.1 19423 1ehxA 94 2.10e+01 1ehxA b.1.1.6 21950 1kobA 387 2.13e+01 1tkiA d.144.1.1 41640 1dcnB 418 2.16e+01 1auwA a.127.1.1 19421 1ae6L 219 2.22e+01 8fabA b.1.1.1 20210 b.1.1.2 21222 1qcqA 148 2.23e+01 1u9aA d.20.1.1 38329 1alq 266 2.28e+01 1btl e.3.1.1 42707 2frvA 264 2.30e+01 2frvA e.19.1.1 43303 1frvA 264 2.32e+01 2frvA e.19.1.1 43308 1epxA 370 2.34e+01 1fbaA c.1.10.1 29150 1iud 380 2.45e+01 4mbp c.94.1.1 35786 1csyA 112 2.49e+01 1lckA d.93.1.1 40519 1qpaA 345 2.55e+01 1arv a.93.1.1 18585 1ibfA 151 2.61e+01 1yaiA b.1.8.1 62158 1shvA 265 2.63e+01 1btl e.3.1.1 42703 1ei5A 520 2.67e+01 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1jnrA 643 2.67e+01 a.7.3.1 66966 c.3.1.4 66967 d.168.1.1 66968 1pskL 213 2.72e+01 8fabA b.1.1.1 20138 b.1.1.2 21168 1regX 122 2.75e+01 1regX d.58.27.1 39406 1div 149 2.77e+01 1div d.99.1.1 40692 d.100.1.1 40693 2cas 548 2.84e+01 2cas b.10.1.4 23376 1jsxA 207 2.88e+01 1rsy 152 2.94e+01 1rsy b.7.1.2 23192 1auwA 468 2.97e+01 1auwA a.127.1.1 19416 1cunA 213 2.99e+01 1cunA a.7.1.1 16313 a.7.1.1 16314 1jjyA 636 2.99e+01 1jjyA e.26.1.2 63141 1rpxA 230 3.00e+01 1rpxA c.1.2.2 28536 4dpvZ 584 3.09e+01 2cas b.10.1.4 23377 1tnw 162 3.12e+01 1ncx a.39.1.5 17235 1rp1 441 3.16e+01 1gpl b.12.1.2 23646 c.69.1.19 34794 1f66C 128 3.24e+01 1aoiC a.22.1.1 16442 1aihA 170 3.25e+01 1aihA d.163.1.1 42149 1k4wA 252 3.29e+01 1i7wB 151 3.29e+01 1i7wB j.71.1.1 61910 5tnc 162 3.32e+01 1ncx a.39.1.5 17246 1ldg 316 3.34e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1jf2A 195 3.38e+01 1ej3A a.39.1.5 62930 5prn 289 3.42e+01 3prn f.4.3.1 43764 1thi 207 3.42e+01 1thv b.25.1.1 23906 1ceqA 316 3.45e+01 1ceqA c.2.1.5 30163 d.162.1.1 42130 1ayl 541 3.46e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1k3cA 540 3.46e+01 c.91.1.1 68099 c.109.1.1 68100 1f3z 161 3.47e+01 1gpr b.84.3.1 28273 1ci0A 228 3.51e+01 1ci0A b.45.1.1 25750 1kezA 300 3.53e+01 c.69.1.22 68546 1bfoA 214 3.53e+01 8fabA b.1.1.1 20310 b.1.1.2 21302 1jbjA 186 3.54e+01 b.1.1.4 66482 b.1.1.4 66483 1glaF 168 3.54e+01 1gpr b.84.3.1 28274 1omeA 242 3.54e+01 1btl e.3.1.1 42717 1c8dA 584 3.55e+01 2cas b.10.1.4 23375 1ggjA 753 3.59e+01 1cf9A c.23.16.3 31457 e.5.1.1 42831 1el4A 195 3.62e+01 1ej3A a.39.1.5 59453 1cbg 490 3.62e+01 1e70M c.1.8.4 28933 1thw 207 3.63e+01 1thv b.25.1.1 23903 1e79H 146 3.63e+01 1e79H a.2.10.1 15721 b.93.1.1 28438 1h8eH 146 3.63e+01 1e79H b.93.1.1 60757 2tplA 456 3.66e+01 1ax4A c.67.1.2 34389 1gcqC 70 3.69e+01 1gcpA b.34.2.1 60436 1gcpA 70 3.69e+01 1gcpA b.34.2.1 60430 1i7xB 151 3.76e+01 1i7xB j.71.1.1 61914 1thv 207 3.77e+01 1thv b.25.1.1 23904 1top 162 3.85e+01 1ncx a.39.1.5 17223 1ncx 162 3.85e+01 1ncx a.39.1.5 17222 1ibdA 151 3.92e+01 1yaiA b.1.8.1 62157 1ce7A 241 3.95e+01 1mrj d.165.1.1 42194 4tnc 162 3.96e+01 1ncx a.39.1.5 17228 1c8gA 548 3.98e+01 2cas b.10.1.4 23380 1hy1C 468 4.00e+01 1auwA a.127.1.1 61396 1dghC 498 4.00e+01 1cf9A e.5.1.1 42792 1dgfA 497 4.00e+01 1cf9A e.5.1.1 42782