# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-scores 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 1rz1A 161 5.82e-25 b.45.1.2 -4088 1i0sA 169 1.43e-20 1i0rA b.45.1.2 61491 1uscA 178 1.66e-20 b.45.1.2 -4074 1i0rA 169 1.71e-20 1i0rA b.45.1.2 61489 1ejeA 192 1.31e-19 1ejeA b.45.1.2 25757 1asx 159 2.78e-01 1a6dA c.8.5.2 30821 1iq6A 134 5.28e-01 d.38.1.4 76755 1qmrA 159 8.17e-01 1bv1 d.129.3.1 41314 1bv1 159 8.49e-01 1bv1 d.129.3.1 41313 1gmlA 178 9.70e-01 c.8.5.2 70273 1ojrA 274 1.01e+00 c.74.1.1 -8441 1tlk 154 1.19e+00 1tlk b.1.1.4 21707 1fhgA 154 1.28e+00 1tlk b.1.1.4 21706 1ne2A 200 1.71e+00 c.66.1.32 85586 1fm4A 159 1.82e+00 1bv1 d.129.3.1 76186 1sr4B 261 2.18e+00 1p6oA 161 2.18e+00 c.97.1.2 -8774 1iuhA 198 2.28e+00 d.61.1.2 83711 1g4uS 383 2.29e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1lk5A 229 2.32e+00 unknown_sccs 73960 d.58.40.1 73961 1iukA 140 2.33e+00 c.2.1.8 83712 1ubeA 349 2.52e+00 c.37.1.11 88412 d.48.1.1 88413 1gt7A 274 2.78e+00 c.74.1.1 70398 1s7jA 262 2.97e+00 d.21.1.2 -9424 2reb 352 3.00e+00 2reb c.37.1.11 32282 d.48.1.1 38767 1ass 159 3.00e+00 1a6dA c.8.5.2 30818 1psuA 140 3.02e+00 d.38.1.5 88285 1rxxA 421 3.11e+00 unknown_sccs -10982 1br9 194 3.42e+00 1br9 b.40.3.1 25235 1pswA 348 3.52e+00 c.87.1.7 88287 1p0kA 349 3.72e+00 c.1.4.1 87648 1h6hA 143 3.85e+00 d.189.1.1 65681 1sefA 274 4.14e+00 1h1hA 134 4.53e+00 d.5.1.1 76468 1uj6A 227 4.71e+00 2dnjA 260 5.24e+00 3dni d.151.1.1 41790 1qmtA 134 5.49e+00 7rsa d.5.1.1 37290 1b6fA 159 5.50e+00 1bv1 d.129.3.1 41316 1vpsB 289 5.91e+00 1vpsA b.121.6.1 23337 1miuA 738 5.93e+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 1jb3A 131 6.27e+00 1jc7A b.40.3.2 62833 1mw7A 240 6.46e+00 e.39.1.1 79557 1r9hA 135 6.54e+00 d.26.1.1 -9482 1rusA 490 6.79e+00 1burA c.1.14.1 29388 d.58.9.1 39294 1qwdA 177 6.90e+00 b.60.1.1 -4455 1eulA 994 7.08e+00 1eulA 1httA 423 7.26e+00 1adjA c.51.1.1 33178 d.104.1.1 40727 1vpsA 289 7.55e+00 1vpsA b.121.6.1 23336 1in4A 334 7.69e+00 1hqcA a.4.5.11 62597 c.37.1.20 62598 1vh5A 148 7.76e+00 d.38.1.5 -9677 1kmnD 424 7.82e+00 1adjA c.51.1.1 33185 d.104.1.1 40734 1kmmA 424 8.24e+00 1adjA c.51.1.1 33174 d.104.1.1 40723 1d3bB 91 8.25e+00 1d3bB b.38.1.1 24804 1su4A 994 8.32e+00 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1jofA 365 8.34e+00 b.69.10.1 71775 2rusB 490 8.40e+00 1burA c.1.14.1 29385 d.58.9.1 39291 1j1yA 136 8.49e+00 d.38.1.5 -9671 5rubA 490 8.73e+00 1burA c.1.14.1 29382 d.58.9.1 39288 1lp4A 332 9.00e+00 d.144.1.7 74170 1om1A 332 9.47e+00 d.144.1.7 -11318 1axj 122 9.63e+00 1axj b.45.1.1 25749 1ryp2 233 9.86e+00 1ryp2 1l3iA 192 9.90e+00 c.66.1.22 77676 1nezG 128 9.92e+00 b.1.1.1 85592 1l1eA 287 1.01e+01 c.66.1.18 73454 1mx3A 347 1.01e+01 c.2.1.4 79638 c.23.12.1 79639 1vg0A 650 1.07e+01 1ltlA 279 1.09e+01 b.40.4.11 84701 1pxfA 111 1.10e+01 b.40.4.4 88341 1lpuA 332 1.13e+01 d.144.1.7 74177 1uaqA 158 1.14e+01 c.97.1.2 88386 1f7lA 121 1.14e+01 1f7lA d.150.1.2 59666 1krhA 338 1.14e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1mqsA 671 1.18e+01 e.25.1.1 79414 1hruA 188 1.25e+01 1hruA d.115.1.1 40926 1fbnA 230 1.25e+01 1fbnA c.66.1.3 34181 1fxlA 167 1.27e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1f2aA 215 1.27e+01 1cs8A d.3.1.1 37040 1kzlA 208 1.29e+01 b.43.4.3 77635 b.43.4.3 77636 1gjuA 637 1.30e+01 b.71.1.1 60580 c.1.8.1 60581 1k2fA 190 1.32e+01 b.8.1.2 68054 1csbB 205 1.36e+01 1theB 1jalA 363 1.36e+01 c.37.1.8 84138 d.15.10.2 84139 2phh 394 1.38e+01 1pbe c.3.1.2 30353 d.16.1.2 37884 1fthA 122 1.38e+01 d.150.1.2 60028 1riqA 465 1.42e+01 unknown_sccs -1295 d.104.1.1 -10769 1ytw 306 1.45e+01 1ytw c.45.1.2 32689 1aisA 182 1.46e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1in6A 334 1.46e+01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1g4wR 383 1.47e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1cdkA 350 1.49e+01 1cdkA d.144.1.7 41620 1dytA 133 1.51e+01 7rsa d.5.1.1 37288 1s0uA 408 1.51e+01 b.43.3.1 -4053 b.44.1.1 -4061 c.37.1.8 -7096 2omf 340 1.52e+01 2omf f.4.3.1 43749 1louA 101 1.53e+01 1ris d.58.14.1 39323 1ewfA 456 1.55e+01 1bp1 d.83.1.1 40024 d.83.1.1 40025 1fljA 260 1.56e+01 2cba b.74.1.1 27954 1d06A 130 1.57e+01 1drmA d.110.3.2 40906 1hxxA 340 1.57e+01 2omf f.4.3.1 61385 1h6qA 168 1.59e+01 1h6qA b.88.1.2 60692 1i58A 189 1.60e+01 1b3qA d.122.1.3 61773 1fe8A 196 1.61e+01 1atzA c.62.1.1 59783 1dcuA 357 1.62e+01 1frpA e.7.1.1 42943 1g8sA 230 1.62e+01 c.66.1.3 -8047 1gd7A 109 1.63e+01 b.40.4.4 60441 1stfI 98 1.66e+01 1stfI d.17.1.2 38006 1kebA 108 1.69e+01 c.47.1.1 77341 1pxvA 183 1.71e+01 d.3.1.1 -8881 1jc7A 131 1.71e+01 1jc7A b.40.3.2 62873 1qhtA 775 1.71e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1ekgA 127 1.73e+01 1dlxA d.82.2.1 40021 1aim 215 1.74e+01 1cs8A d.3.1.1 37044 1g6q2 328 1.76e+01 1g6q2 1b6rA 355 1.78e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1i82A 189 1.79e+01 1i82A b.1.9.2 61937 1hi2A 135 1.82e+01 7rsa d.5.1.1 61057 1atzA 189 1.82e+01 1atzA c.62.1.1 34132 1bp3A 191 1.85e+01 1huw a.26.1.1 16838 1qqp2 218 1.86e+01 1qqp2 1nytA 271 1.87e+01 c.2.1.7 86417 c.58.1.5 86418 1m2rA 327 1.90e+01 d.144.1.7 84760 1jkgA 140 1.92e+01 d.17.4.2 66795 3dni 260 1.92e+01 3dni d.151.1.1 41791 1mal 421 1.93e+01 2mprA f.4.3.2 43784 1ah6 220 1.93e+01 1yer d.122.1.1 41094 1me3A 215 1.97e+01 d.3.1.1 79022 1dxy 333 1.97e+01 1dxy c.2.1.4 30094 c.23.12.1 31354 1vk3A 615 2.00e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1q8uA 350 2.00e+01 d.144.1.7 -11331 1fzoB 99 2.02e+01 1agdB b.1.1.2 60157 1qg6A 261 2.05e+01 1eny c.2.1.2 29919 1bqhG 129 2.06e+01 1cd8 b.1.1.1 19715 1ew0A 130 2.09e+01 1drmA d.110.3.2 40905 1d7qA 143 2.09e+01 1d7qA b.40.4.5 25331 1dekA 241 2.09e+01 1dekA c.37.1.1 31842 1b8aA 438 2.12e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1b1cA 181 2.13e+01 1amoA c.23.5.2 31212 1i1qA 520 2.16e+01 1qdlA d.161.1.1 61543 1f7tA 122 2.17e+01 1f7lA d.150.1.2 59667 1ixlA 131 2.18e+01 d.38.1.5 -9705 1sq9A 397 2.21e+01 1pv5A 264 2.22e+01 unknown_sccs -10182 1avpA 204 2.26e+01 1avpA d.3.1.7 37132 1adjA 421 2.31e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1nqcA 217 2.35e+01 d.3.1.1 86024 1qmyA 167 2.44e+01 1qmyA d.3.1.2 37094 1b6sA 355 2.50e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1h4vB 421 2.50e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1m6dA 214 2.51e+01 d.3.1.1 84849 1yptA 305 2.52e+01 1ytw c.45.1.2 32686 1pzdA 322 2.53e+01 unknown_sccs -2848 unknown_sccs -10778 1i2aA 219 2.54e+01 e.24.1.1 -12012 1u2fA 90 2.54e+01 1u2fA d.58.7.1 39168 1uq5A 263 2.57e+01 d.165.1.1 -11555 1jn5A 140 2.58e+01 d.17.4.2 66921 1kcmA 270 2.58e+01 d.129.3.4 72300 1nlnA 204 2.62e+01 d.3.1.7 -8897 1nnxA 109 2.63e+01 unknown_sccs -3899 1n16A 381 2.64e+01 a.83.1.1 79781 d.128.1.2 79782 1juk 248 2.64e+01 1a53 c.1.2.4 28567 1dlhB 188 2.67e+01 1iakB b.1.1.2 21598 d.19.1.1 38172 1e69B 322 2.68e+01 1e69B c.37.1.12 32377 2bosA 68 2.68e+01 2bosA b.40.2.1 25025 1xnaA 183 2.72e+01 1xnaA b.18.1.8 23773 1r89A 437 2.73e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1igs 248 2.74e+01 1a53 c.1.2.4 28565 1g0u1 266 2.74e+01 1i8aA 189 2.78e+01 1i82A b.1.9.2 61951 1fzkB 99 2.78e+01 1agdB b.1.1.2 60151 1lk2B 99 2.80e+01 b.1.1.2 -2576 1g0uL 241 2.80e+01 d.153.1.4 41894 1a53 247 2.84e+01 1a53 c.1.2.4 28564 1ckiA 317 2.85e+01 1csn d.144.1.7 41660 1h70A 255 2.86e+01 1h70A d.126.1.3 60711 1kpuB 99 2.88e+01 b.1.1.2 84458 1g7pB 99 2.94e+01 b.1.1.2 70155 1me4A 215 3.01e+01 d.3.1.1 79023 1h2wA 710 3.03e+01 b.69.7.1 76596 c.69.1.4 76597 1nh9A 87 3.03e+01 d.68.6.1 -10287 1c14A 262 3.04e+01 1eny c.2.1.2 29927 1ift 263 3.04e+01 1mrj d.165.1.1 42211 2fmr 65 3.06e+01 2fmr d.51.1.1 38808 1umgA 362 3.08e+01 1jj2A 239 3.09e+01 1rl2A b.34.5.3 63084 b.40.4.5 63085 1h3gA 601 3.09e+01 b.1.18.2 -2725 b.71.1.1 -4653 c.1.8.1 -5277 1tgoA 773 3.10e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1nd4A 264 3.14e+01 d.144.1.6 -11381 1l1sA 113 3.14e+01 c.114.1.1 73484 1gqvA 135 3.14e+01 d.5.1.1 70376 1jksA 294 3.17e+01 d.144.1.7 71710 1zxq 192 3.20e+01 1zxq b.1.1.3 21657 b.1.1.4 21693 1ytn 306 3.32e+01 1ytw c.45.1.2 32688 1e8nA 710 3.32e+01 1qfmA b.69.7.1 27675 c.69.1.4 34643 1qrrA 394 3.32e+01 1qrrA c.2.1.2 29824 1kobA 387 3.32e+01 1tkiA d.144.1.7 41640 1kyoA 430 3.34e+01 d.185.1.1 73249 d.185.1.1 73250 1b7yB 785 3.38e+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 1qd9A 124 3.39e+01 1qu9A d.79.1.1 39758 1m5sA 297 3.40e+01 d.58.33.1 74511 d.58.33.1 74512 1kyfA 247 3.41e+01 b.1.10.1 73220 d.105.1.1 73221 1hrnA 337 3.42e+01 1smrA b.50.1.2 26869 1cmkE 350 3.45e+01 1cdkA d.144.1.7 41623 1nb5I 98 3.47e+01 d.17.1.2 80381 1se8A 301 3.48e+01 1nxzA 246 3.49e+01 b.122.1.2 86391 c.116.1.5 86392 1d7yA 408 3.49e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1qtsA 247 3.49e+01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1h2xA 710 3.55e+01 b.69.7.1 76598 c.69.1.4 76599 1n71A 180 3.55e+01 d.108.1.1 85370 1quqB 121 3.59e+01 1quqB b.40.4.3 25305 1jdqA 98 3.66e+01 d.68.3.3 66559 1af6A 421 3.69e+01 2mprA f.4.3.2 43772 1qamA 244 3.70e+01 2ercA c.66.1.24 34220 1atzB 189 3.72e+01 1atzA c.62.1.1 34133 1h6uA 308 3.73e+01 b.1.18.15 65688 c.10.2.1 65689 1eljA 381 3.75e+01 4mbp c.94.1.1 35791 1dpe 507 3.75e+01 1dpe c.94.1.1 35799 1ny6A 267 3.77e+01 c.37.1.20 -7221 1quqA 129 3.79e+01 1quqA b.40.4.3 25303 1cjsA 219 3.83e+01 1cjsA e.24.1.1 43354 1bvoA 175 3.83e+01 1a3qA b.2.5.3 22457 1dr8B 344 3.85e+01 1cnzA c.77.1.1 35052 1i3cA 149 3.85e+01 c.23.1.1 71112 1n08A 163 3.87e+01 b.43.5.1 79730 1bovA 69 3.88e+01 2bosA b.40.2.1 25070 1ddjA 247 3.90e+01 5ptp b.47.1.2 26362 1g19A 350 3.91e+01 2reb c.37.1.11 32284 d.48.1.1 38770 1f37A 110 3.92e+01 1f37A c.47.1.11 33088