# List of top-scoring protein chains for t2k-100-30-bys-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 1esfA 233 1.00e-01 3seb b.40.2.2,d.15.6.1 25146,37735 1zynA 202 2.02e-01 1dyqA 234 2.79e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2rslA 140 5.17e-01 2rslA c.53.1.1 33345 1hyuA 521 9.00e-01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1ghtA 105 1.01e+00 2rslA c.53.1.1 60526 2fclA 169 1.11e+00 2ewrA 170 1.27e+00 1m93A 55 1.27e+00 e.1.1.1 91235 1gdtA 183 1.48e+00 2rslA a.4.1.2,c.53.1.1 16021,33348 1pbgA 468 1.68e+00 1e70M c.1.8.4 28946 2afbA 351 1.74e+00 3pbgA 468 1.75e+00 1e70M c.1.8.4 28951 1agnA 373 1.77e+00 2ohxA b.35.1.2,c.2.1.1 24737,29753 2bg5A 324 2.13e+00 1d2oA 187 2.49e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1a0rP 245 2.78e+00 1b9yC c.47.1.6 33054 1regX 122 3.24e+00 1regX d.58.27.1 39406 1focA 132 3.57e+00 1c52 a.3.1.1 15812 1ih8A 271 4.02e+00 2nsyA c.26.2.1 62377 1j5vA 351 4.56e+00 c.72.1.1 71585 1kqpA 271 4.72e+00 c.26.2.1 72883 1zp4A 304 4.98e+00 1qhlA 227 5.68e+00 1qhlA c.37.1.12 32382 1repC 251 5.77e+00 1repC a.4.5.10,a.4.5.10 16125,16126 2flsA 132 6.26e+00 1xwvA 129 6.46e+00 2asbA 251 6.64e+00 2g9iA 249 6.65e+00 1h72C 296 6.83e+00 d.14.1.5,d.58.26.1 60712,60713 1nsyA 271 6.90e+00 2nsyA c.26.2.1 31614 2nsyA 271 6.95e+00 2nsyA c.26.2.1 31612 1s55A 156 7.02e+00 1gyxA 76 7.02e+00 d.80.1.1 76387 1vr7A 142 7.55e+00 1tiqA 180 8.08e+00 d.108.1.1 107010 1h8vA 218 8.33e+00 2nlrA b.29.1.11 60795 5gcnA 166 8.39e+00 1yghA d.108.1.1 40807 1iqaA 160 8.73e+00 b.22.1.1 71274 2b33A 140 8.82e+00 1oa2A 218 9.44e+00 b.29.1.11 86721 1fwkA 296 9.82e+00 1fwkA d.14.1.5,d.58.26.1 37576,39398 1iz5A 249 1.01e+01 d.131.1.2,d.131.1.2 83834,83835 1c52 131 1.17e+01 1c52 a.3.1.1 15810 2pil 159 1.18e+01 2pil d.24.1.1 38376 1ycyA 71 1.22e+01 2gw6A 123 1.22e+01 1pnsC 206 1.23e+01 i.1.1.1 88170 1qdlB 195 1.33e+01 1qdlB c.23.16.1 31437 1yb2A 275 1.33e+01 1a99A 344 1.34e+01 1pot c.94.1.1 35812 1b25A 619 1.39e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1aogA 485 1.40e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 4uagA 437 1.41e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1uag 437 1.45e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1d2pA 373 1.46e+01 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1wmqA 147 1.46e+01 1k38A 254 1.47e+01 e.3.1.1 84303 1juvA 193 1.47e+01 c.71.1.1 90912 1sqsA 242 1.47e+01 c.23.5.5 98968 2gmqA 118 1.49e+01 2gfgA 193 1.56e+01 1u00A 227 1.57e+01 1gm6A 175 1.58e+01 b.60.1.1 70272 1d2rA 326 1.60e+01 1d2rB c.26.1.1 31572 1i8fA 81 1.65e+01 1i8fA b.38.1.1 61959 1larA 575 1.66e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1grvB 182 1.72e+01 c.61.1.1 76322 1wpuA 147 1.74e+01 2fh7A 595 1.74e+01 1k0rA 366 1.74e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1ap0 73 1.82e+01 1ap0 b.34.13.2 37475 1bib 321 1.83e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 3uagA 437 1.86e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1lwjA 441 1.86e+01 b.71.1.1,c.1.8.1 74303,74304 1shsA 147 1.88e+01 1shsA b.15.1.1 23675 1x74A 360 1.94e+01 2b7eA 59 1.97e+01 1he2A 206 2.00e+01 1he2A c.2.1.2 60966 1wjcA 47 2.00e+01 1wjcA a.4.10.1 16261 1cjbA 231 2.01e+01 1qk3A c.61.1.1 34079 1qavA 90 2.03e+01 1qauA b.36.1.1 24777 1p35A 299 2.05e+01 1p35A b.28.1.1 23925 2cxcA 144 2.07e+01 1ge8A 249 2.08e+01 1plq d.131.1.2,d.131.1.2 41398,41399 1tf1A 198 2.14e+01 d.110.2.2 106826 1fc2D 224 2.16e+01 1igtB b.1.1.2,b.1.1.2 21516,21517 1qlmA 316 2.16e+01 1qlmA d.147.1.1 41765 1ll2A 333 2.17e+01 c.68.1.14 74005 2myr 501 2.18e+01 1m07A 111 2.20e+01 d.5.1.1 78328 1qoxN 449 2.25e+01 1qoxN c.1.8.4 28978 1sek 378 2.27e+01 1sek e.1.1.1 42675 1t0aA 159 2.39e+01 2adoA 196 2.40e+01 1bc4 111 2.41e+01 1onc d.5.1.1 37279 1tluA 130 2.42e+01 d.156.1.2 107139 1qi9A 556 2.50e+01 1qhbA a.111.1.2 19053 1a9v 129 2.54e+01 1a9v b.1.18.7 21946 1s9rA 410 2.54e+01 d.126.1.4 98758 1y96B 85 2.57e+01 1lxyA 409 2.59e+01 d.126.1.4 91154 1zpvA 91 2.60e+01 1tygB 87 2.64e+01 d.15.3.2 107455 2ohxA 374 2.66e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1f8nA 839 2.68e+01 1yge a.119.1.1,b.12.1.1 59703,59704 1ll0A 339 2.69e+01 c.68.1.14 73995 1wjbA 55 2.75e+01 1wjcA a.4.10.1 16265 1hdoA 206 2.78e+01 1he2A c.2.1.2 60965 3kar 346 2.79e+01 1bg2 c.37.1.9 32198 1wlyA 333 2.80e+01 1ma3A 253 2.81e+01 c.31.1.5 78883 2aefA 234 2.83e+01 1axgA 374 2.95e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1ydmA 187 2.96e+01 1fc1A 224 2.97e+01 1igtB b.1.1.2,b.1.1.2 21520,21521 1quqB 121 3.05e+01 1quqB b.40.4.3 25305 1cbg 490 3.06e+01 1e70M c.1.8.4 28933 1ay2 159 3.11e+01 2pil d.24.1.1 38377 1al0F 426 3.14e+01 2bpa1 b.121.5.1 23274 1o58A 303 3.16e+01 c.79.1.1 92491 2bby 69 3.18e+01 2bby a.4.5.15 16148 1e9rA 437 3.21e+01 c.37.1.11 64827 1ur1A 378 3.21e+01 c.1.8.3 99804 1xdpA 687 3.22e+01 1ft5A 211 3.24e+01 1bvb a.138.1.3 19681 1wlzA 105 3.26e+01 1bg6 359 3.27e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1njhA 119 3.32e+01 b.128.1.1 85787 3nll 138 3.34e+01 5nul c.23.5.1 31206 1pnsB 234 3.35e+01 i.1.1.1 88169 1i6kA 328 3.37e+01 c.26.1.1 66040 1b56 135 3.37e+01 1hmt b.60.1.2 27183 1ns5A 155 3.38e+01 c.116.1.3 80705 1juk 248 3.41e+01 1a53 c.1.2.4 28567 1qrkA 731 3.58e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1ee2A 373 3.61e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1ktjA 129 3.65e+01 b.1.18.7 72974 1adqA 206 3.66e+01 1igtB b.1.1.2,b.1.1.2 21518,21519 1ibsA 317 3.68e+01 c.61.1.2,c.61.1.2 66107,66108 2bspA 420 3.69e+01 1pcl b.80.1.1 28023 1m4jA 142 3.72e+01 d.109.1.2 78602 1uc7A 125 3.76e+01 c.47.1.1 99163 1duvG 333 3.78e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1b5tA 275 3.81e+01 1b5tA c.1.23.1 29676 1o6dA 163 3.82e+01 c.116.1.3 92567 1a53 247 3.82e+01 1a53 c.1.2.4 28564 1j5eB 256 3.83e+01 c.23.15.1 71543 2etxA 209 3.84e+01 1ri7A 171 3.85e+01 a.4.5.32,d.58.4.2 97504,97505 1a71A 374 3.90e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1hqz1 141 3.92e+01 1igs 248 3.92e+01 1a53 c.1.2.4 28565 1o0yA 260 3.92e+01 c.1.10.1 80756 1wr1B 58 3.94e+01 1kfiA 572 3.99e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 1bn8A 420 4.01e+01 1pcl b.80.1.1 28022 1xyiA 66 4.02e+01 1e4mM 501 4.04e+01 1e70M c.1.8.4 59226 2amyA 246 4.08e+01 1bby 69 4.08e+01 2bby a.4.5.15 16149 1e6qM 501 4.12e+01 1e70M c.1.8.4 28920 1dkuA 317 4.18e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 2bwbA 46 4.20e+01 1zthA 258 4.31e+01 1j5eC 239 4.40e+01 d.52.3.1,d.53.1.1 71544,71545 2fox 138 4.45e+01 5nul c.23.5.1 31197 2bo4A 397 4.50e+01 1d2rB 326 4.51e+01 1d2rB c.26.1.1 31573 2bce 581 4.54e+01 2bce c.69.1.1 34625 1vcvA 226 4.54e+01 1e70M 501 4.54e+01 1e70M c.1.8.4 28926 1epwA 1290 4.55e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1o1zA 234 4.57e+01 c.1.18.3 86555 1j1vA 94 4.59e+01 a.4.12.2 83981 1bvb 211 4.62e+01 1bvb a.138.1.3 19683 1mmiA 366 4.68e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1xtoA 311 4.71e+01 1p8xA 344 4.73e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1fg7A 356 4.74e+01 1gewA c.67.1.1 59819 2dfkA 402 4.75e+01 1axeA 374 4.77e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 8adh 374 4.80e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1f76A 336 4.80e+01 c.1.4.1 76160 1t8qA 336 4.83e+01 c.1.18.3 106669 1n8jA 186 4.90e+01 c.47.1.10 85401 1pk9A 237 4.91e+01 c.56.2.1 94823 1ex0A 731 4.92e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1ghr 306 5.05e+01 1aq0A c.1.8.3 28844 1se4 239 5.06e+01 3seb b.40.2.2,d.15.6.1 25187,37776 2a41C 32 5.06e+01 1smrA 335 5.12e+01 1smrA b.50.1.2 26878 1wrjA 156 5.13e+01 1v93A 296 5.15e+01 c.1.23.1 100532 1vpzA 73 5.16e+01 1qzgA 187 5.19e+01 b.40.4.3 96643 1v0lA 313 5.25e+01 c.1.8.3 108207 1ti6B 274 5.31e+01 b.3.5.1,d.58.1.5 106976,106977 1ydyA 356 5.31e+01 3pfk 319 5.32e+01 3pfk c.89.1.1 35581 3seb 238 5.34e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1ve6A 582 5.39e+01 1f6dA 376 5.41e+01 1f6dA c.87.1.3 35467 1azpA 66 5.41e+01 1azpA b.34.13.1 37467 1ck2A 104 5.44e+01 1ck9A d.79.3.1 39809 2cxaA 256 5.52e+01 2fcjA 119 5.55e+01 1fhgA 154 5.60e+01 1tlk b.1.1.4 21706 1evuA 731 5.65e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1bf4A 63 5.65e+01 1azpA b.34.13.1 37461 1dkrA 317 5.73e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 2bwfA 77 5.75e+01 1xkiA 162 5.76e+01 1wcdJ 441 5.77e+01 1xkqA 280 5.78e+01 1h4gA 207 5.79e+01 b.29.1.11 70863 1wu3I 161 5.87e+01 1yr2A 741 5.91e+01 1fgqA 839 5.92e+01 1yge a.119.1.1,b.12.1.1 59826,59827 1gh6A 114 5.95e+01 a.2.3.1 65191 1oj4A 283 5.95e+01 d.14.1.5,d.58.26.5 93083,93084 5nul 138 5.97e+01 5nul c.23.5.1 31191 1cvmA 353 5.98e+01 1qlgA b.68.3.1 27628 1hetA 374 5.98e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1i6lA 328 6.05e+01 c.26.1.1 66041 1n8kA 374 6.05e+01 b.35.1.2,c.2.1.1 80298,80299 1qk3A 233 6.18e+01 1qk3A c.61.1.1 34031 1vjpA 394 6.28e+01 c.2.1.3,d.81.1.3 100828,100829 1nijA 318 6.29e+01 c.37.1.10,d.237.1.1 85741,85742 1qh7A 207 6.32e+01 1axkA b.29.1.11 24317 1cfr 285 6.34e+01 1cfr c.52.1.7 33312 1f0cA 305 6.35e+01 1c8oA e.1.1.1 42676 1exg 110 6.35e+01 1exg b.2.2.1 22387 1heuA 374 6.36e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1f9vA 347 6.40e+01 1bg2 c.37.1.9 59745 1mixA 206 6.46e+01 a.11.2.1,b.55.1.5 79166,79167 1p6pA 125 6.48e+01 b.60.1.2 87839 1ponB 36 6.49e+01 1ponB 1hqz9 141 6.56e+01 1ok7A 366 6.61e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1a4yB 123 6.67e+01 7rsa d.5.1.1 37296 1vqoL 165 6.72e+01 1u3wA 374 6.73e+01 2trcP 217 6.76e+01 1b9yC c.47.1.6 33051 1r5jA 337 6.80e+01 c.77.1.5 97097 1vgvA 384 6.85e+01 c.87.1.3 100608 1rr7A 129 6.92e+01 a.4.1.14 105075 1xrjA 261 6.95e+01 1azqA 66 6.97e+01 1azpA b.34.13.1 37469 1o57A 291 7.01e+01 a.4.5.40,c.61.1.1 92483,92484 1jy5A 212 7.04e+01 d.124.1.1 71940 1gs5A 258 7.07e+01 c.73.1.2 70395 1r64A 481 7.09e+01 b.18.1.20,c.41.1.1 97140,97141 1vicA 262 7.10e+01 c.68.1.13 100756 1b9xC 246 7.10e+01 1b9yC c.47.1.6 33053 1tueA 212 7.11e+01 c.37.1.20 107323 2pgi 445 7.14e+01 2pgi c.80.1.2 35308 1b0zA 445 7.14e+01 2pgi c.80.1.2 35309 2f42A 179 7.15e+01 1xn9A 101 7.15e+01 1a8q 274 7.16e+01 1brt c.69.1.12 34702 2as9A 210 7.21e+01 1s0pA 176 7.28e+01 a.192.1.1 98300 1mjc 69 7.32e+01 1mjc b.40.4.5 25319 1tlk 154 7.33e+01 1tlk b.1.1.4 21707 1uj2A 252 7.43e+01 c.37.1.6 99452 2b4rO 345 7.51e+01 1irxA 523 7.56e+01 a.97.1.2,c.26.1.1 71378,71379 2trxA 108 7.59e+01 1thx c.47.1.1 32719 1gewA 356 7.60e+01 1gewA c.67.1.1 60470 1dbrA 231 7.74e+01 1qk3A c.61.1.1 34041 1g0dA 695 7.74e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 1iwmA 186 7.75e+01 b.125.1.2 83758 1pmt 203 7.83e+01 1a0fA a.45.1.1,c.47.1.5 17740,33034 1idk 359 7.85e+01 1qcxA b.80.1.2 28025 2snv 151 7.97e+01 1svpA b.47.1.3 26394 1pyfA 312 7.98e+01 c.1.7.1 95334 1kal 29 7.99e+01 g.3.3.1 44077 2f6hX 419 8.01e+01 1iruK 201 8.03e+01 d.153.1.4 71362 1q3lA 69 8.05e+01 1squA 155 8.06e+01 d.252.1.1 98971 1ac5 483 8.09e+01 1ac5 c.69.1.5 34653 1qlgA 355 8.11e+01 1qlgA b.68.3.1 27627 1b1eA 123 8.16e+01 7rsa d.5.1.1 37300 1k8yB 396 8.19e+01 c.79.1.1 72184 2pooA 355 8.29e+01 1qlgA b.68.3.1 27626 1h6lA 353 8.54e+01 b.68.3.1 60687 1wq8A 110 8.77e+01 1ptf 88 8.80e+01 1ptf d.94.1.1 40549 1snlA 103 8.88e+01 a.39.1.7 105820 2b2aA 199 8.88e+01 1gnf 46 8.89e+01 1gatA g.39.1.1 45107 1o0vA 327 8.90e+01 b.1.1.2,b.1.1.2,b.1.1.2 80745,80746,80747 1ta8A 332 8.94e+01 1jsg 114 8.98e+01 1a1x b.63.1.1 27513