# List of top-scoring protein chains for t04-100-30-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 1zynA 202 2.76e-01 1dyqA 234 3.46e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2rslA 140 5.40e-01 2rslA c.53.1.1 33345 2fclA 169 1.02e+00 2ewrA 170 1.07e+00 1hyuA 521 1.07e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1m93A 55 1.83e+00 e.1.1.1 91235 1pbgA 468 2.24e+00 1e70M c.1.8.4 28946 2afbA 351 2.34e+00 2bg5A 324 2.64e+00 1d2oA 187 2.87e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1a0rP 245 3.27e+00 1b9yC c.47.1.6 33054 1regX 122 4.24e+00 1regX d.58.27.1 39406 1xkiA 162 4.81e+00 1ih8A 271 5.01e+00 2nsyA c.26.2.1 62377 2flsA 132 5.32e+00 1zp4A 304 5.53e+00 1j5vA 351 5.62e+00 c.72.1.1 71585 1kqpA 271 5.81e+00 c.26.2.1 72883 1xwvA 129 6.29e+00 1qhlA 227 6.68e+00 1qhlA c.37.1.12 32382 2g9iA 249 6.81e+00 1vr7A 142 6.88e+00 1repC 251 6.95e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1gyxA 76 8.46e+00 d.80.1.1 76387 2asbA 251 8.66e+00 1tiqA 180 9.21e+00 d.108.1.1 107010 1h8vA 218 9.62e+00 2nlrA b.29.1.11 60795 1s55A 156 1.01e+01 1iz5A 249 1.04e+01 d.131.1.2,d.131.1.2 83834,83835 2b33A 140 1.07e+01 1oa2A 218 1.08e+01 b.29.1.11 86721 2pil 159 1.22e+01 2pil d.24.1.1 38376 1o0pA 104 1.22e+01 d.58.7.1 86535 1iqaA 160 1.23e+01 b.22.1.1 71274 2gmqA 118 1.32e+01 1d2rA 326 1.34e+01 1d2rB c.26.1.1 31572 1ycyA 71 1.35e+01 1a99A 344 1.38e+01 1pot c.94.1.1 35812 1h72C 296 1.40e+01 d.14.1.5,d.58.26.1 60712,60713 1pnsC 206 1.43e+01 i.1.1.1 88170 2gw6A 123 1.45e+01 1c52 131 1.46e+01 1c52 a.3.1.1 15810 1larA 575 1.47e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1juvA 193 1.52e+01 c.71.1.1 90912 1sqsA 242 1.55e+01 c.23.5.5 98968 4uagA 437 1.56e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1b25A 619 1.60e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1yb2A 275 1.66e+01 1i8fA 81 1.67e+01 1i8fA b.38.1.1 61959 1fl2A 310 1.70e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1y96B 85 1.71e+01 1lwjA 441 1.72e+01 b.71.1.1,c.1.8.1 74303,74304 1k38A 254 1.74e+01 e.3.1.1 84303 2gfgA 193 1.75e+01 2fh7A 595 1.78e+01 1wmqA 147 1.81e+01 1m07A 111 1.82e+01 d.5.1.1 78328 1fwkA 296 1.83e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1hdoA 206 1.86e+01 1he2A c.2.1.2 60965 1b56 135 1.94e+01 1hmt b.60.1.2 27183 1u00A 227 1.96e+01 1cjbA 231 2.02e+01 1qk3A c.61.1.1 34079 1tf1A 198 2.04e+01 d.110.2.2 106826 2myr 501 2.07e+01 1wpuA 147 2.14e+01 2b7eA 59 2.19e+01 1ll2A 333 2.26e+01 c.68.1.14 74005 1k0rA 366 2.27e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1x74A 360 2.27e+01 2cxcA 144 2.32e+01 1p35A 299 2.33e+01 1p35A b.28.1.1 23925 1qavA 90 2.36e+01 1qauA b.36.1.1 24777 1quqB 121 2.40e+01 1quqB b.40.4.3 25305 1shsA 147 2.40e+01 1shsA b.15.1.1 23675 1sek 378 2.41e+01 1sek e.1.1.1 42675 1o58A 303 2.46e+01 c.79.1.1 92491 1tygB 87 2.52e+01 d.15.3.2 107455 2adoA 196 2.52e+01 1tluA 130 2.54e+01 d.156.1.2 107139 1qi9A 556 2.55e+01 1qhbA a.111.1.2 19053 1njhA 119 2.65e+01 b.128.1.1 85787 1zpvA 91 2.67e+01 1qlmA 316 2.74e+01 1qlmA d.147.1.1 41765 1ma3A 253 2.75e+01 c.31.1.5 78883 1s9rA 410 2.82e+01 d.126.1.4 98758 2ohxA 374 2.88e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1a53 247 2.96e+01 1a53 c.1.2.4 28564 1exg 110 2.96e+01 1exg b.2.2.1 22387 1ktjA 129 3.01e+01 b.1.18.7 72974 1ydmA 187 3.01e+01 1igs 248 3.04e+01 1a53 c.1.2.4 28565 2aefA 234 3.07e+01 1t0aA 159 3.09e+01 1fc1A 224 3.12e+01 1igtB b.1.1.2,b.1.1.2 21520,21521 1lid 131 3.13e+01 1hmt b.60.1.2 27184 1ex0A 731 3.23e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1h4gA 207 3.25e+01 b.29.1.11 70863 1wlzA 105 3.27e+01 1evuA 731 3.35e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1ur1A 378 3.37e+01 c.1.8.3 99804 1ns5A 155 3.39e+01 c.116.1.3 80705 1ft5A 211 3.45e+01 1bvb a.138.1.3 19681 1ve6A 582 3.46e+01 1bg6 359 3.52e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1xdpA 687 3.55e+01 1nijA 318 3.57e+01 c.37.1.10,d.237.1.1 85741,85742 1qh7A 207 3.63e+01 1axkA b.29.1.11 24317 1wlyA 333 3.64e+01 1v04A 355 3.69e+01 b.68.6.2 100240 1e4mM 501 3.76e+01 1e70M c.1.8.4 59226 1g7nA 131 3.77e+01 b.60.1.2 83274 1ri7A 171 3.83e+01 a.4.5.32,d.58.4.2 97504,97505 2etxA 209 3.84e+01 1b5tA 275 3.88e+01 1b5tA c.1.23.1 29676 1epwA 1290 3.89e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1o6dA 163 3.90e+01 c.116.1.3 92567 1uc7A 125 3.93e+01 c.47.1.1 99163 1xyiA 66 3.96e+01 1hqz1 141 3.98e+01 1duvG 333 3.98e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1bn8A 420 4.05e+01 1pcl b.80.1.1 28022 1i6lA 328 4.06e+01 c.26.1.1 66041 1zthA 258 4.09e+01 1bby 69 4.11e+01 2bby a.4.5.15 16149 1wr1B 58 4.13e+01 1xtoA 311 4.15e+01 1o0yA 260 4.17e+01 c.1.10.1 80756 2amyA 246 4.21e+01 2cxaA 256 4.24e+01 1dkuA 317 4.25e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1o1zA 234 4.25e+01 c.1.18.3 86555 2bwbA 46 4.29e+01 2ffeA 311 4.34e+01 1fg7A 356 4.36e+01 1gewA c.67.1.1 59819 2bo4A 397 4.37e+01 1ej0A 180 4.39e+01 1ej0A c.66.1.2 34179 1of8A 370 4.59e+01 c.1.10.4 92819 1j1vA 94 4.63e+01 a.4.12.2 83981 1vcvA 226 4.65e+01 1mmiA 366 4.66e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1n8jA 186 4.71e+01 c.47.1.10 85401 2bce 581 4.76e+01 2bce c.69.1.1 34625 2dfkA 402 4.76e+01 1t8qA 336 4.78e+01 c.1.18.3 106669 1tueA 212 4.78e+01 c.37.1.20 107323 1p8xA 344 4.78e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1v0lA 313 4.88e+01 c.1.8.3 108207 1oj4A 283 4.91e+01 d.14.1.5,d.58.26.5 93083,93084 3seb 238 5.06e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1qzgA 187 5.08e+01 b.40.4.3 96643 1ti6B 274 5.08e+01 b.3.5.1,d.58.1.5 106976,106977 1v93A 296 5.09e+01 c.1.23.1 100532 1ta8A 332 5.14e+01 1vicA 262 5.18e+01 c.68.1.13 100756 2bw0A 329 5.18e+01 2a41C 32 5.20e+01 1wrjA 156 5.22e+01 1wu3I 161 5.23e+01 1azpA 66 5.31e+01 1azpA b.34.13.1 37467 1smrA 335 5.31e+01 1smrA b.50.1.2 26878 1f6dA 376 5.33e+01 1f6dA c.87.1.3 35467 1fhgA 154 5.34e+01 1tlk b.1.1.4 21706 1ydyA 356 5.36e+01 1p6pA 125 5.37e+01 b.60.1.2 87839 1vr4A 103 5.42e+01 2gi3A 476 5.45e+01 1tyjA 170 5.47e+01 1vpzA 73 5.50e+01 1wcdJ 441 5.54e+01 1vjpA 394 5.62e+01 c.2.1.3,d.81.1.3 100828,100829 2fcjA 119 5.66e+01 2bwfA 77 5.71e+01 1f9vA 347 5.81e+01 1bg2 c.37.1.9 59745 1z2uA 150 5.82e+01 1xkqA 280 5.92e+01 1hetA 374 6.08e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 5nul 138 6.11e+01 5nul c.23.5.1 31191 1n8kA 374 6.22e+01 b.35.1.2,c.2.1.1 80298,80299 1vm6A 228 6.26e+01 c.2.1.3,d.81.1.3 108876,108877 1yr2A 741 6.26e+01 1r64A 481 6.29e+01 b.18.1.20,c.41.1.1 97140,97141 1vddA 228 6.36e+01 e.49.1.1 108519 1u3wA 374 6.38e+01 1f2tB 148 6.38e+01 1f2tB 1r5jA 337 6.42e+01 c.77.1.5 97097 1xrjA 261 6.44e+01 1mixA 206 6.55e+01 a.11.2.1,b.55.1.5 79166,79167 1ok7A 366 6.62e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1cfr 285 6.64e+01 1cfr c.52.1.7 33312 1a8q 274 6.66e+01 1brt c.69.1.12 34702 1gewA 356 6.71e+01 1gewA c.67.1.1 60470 1iwmA 186 6.72e+01 b.125.1.2 83758 2trcP 217 6.72e+01 1b9yC c.47.1.6 33051 1jy5A 212 6.74e+01 d.124.1.1 71940 1mjc 69 6.78e+01 1mjc b.40.4.5 25319 1f5jA 199 6.79e+01 1axkA b.29.1.11 24342 1tlk 154 6.79e+01 1tlk b.1.1.4 21707 1f0cA 305 6.87e+01 1c8oA e.1.1.1 42676 1m4jA 142 6.89e+01 d.109.1.2 78602 2b4rO 345 6.91e+01 1vqoL 165 6.91e+01 1squA 155 6.95e+01 d.252.1.1 98971 1xn9A 101 7.01e+01 1rr7A 129 7.02e+01 a.4.1.14 105075 1uj2A 252 7.06e+01 c.37.1.6 99452 1lk2A 274 7.07e+01 b.1.1.2,d.19.1.1 91056,91057 1s0pA 176 7.09e+01 a.192.1.1 98300 2f42A 179 7.12e+01 2as9A 210 7.14e+01 1gs5A 258 7.18e+01 c.73.1.2 70395 1iruK 201 7.37e+01 d.153.1.4 71362 1r1a1 287 7.37e+01 1aym1 2aioA 269 7.45e+01 1a4yB 123 7.47e+01 7rsa d.5.1.1 37296 2pooA 355 7.50e+01 1qlgA b.68.3.1 27626 1q3lA 69 7.52e+01 2a3mA 130 7.55e+01 1ryjA 70 7.61e+01 d.15.3.2 98104 1mdc 133 7.70e+01 1hmt b.60.1.2 27198 1txvB 440 7.78e+01 1pyfA 312 7.79e+01 c.1.7.1 95334 1h6lA 353 7.82e+01 b.68.3.1 60687 1ouwA 152 7.83e+01 b.77.3.1 93571 2b2aA 199 7.84e+01 2f6hX 419 7.89e+01 1idk 359 7.96e+01 1qcxA b.80.1.2 28025 1x23A 155 8.02e+01 1w9zA 283 8.12e+01 1od8A 313 8.21e+01 c.1.8.3 86838 1mdwA 328 8.43e+01 d.3.1.3 84934 1fsgA 233 8.46e+01 1qk3A c.61.1.1 34029 1ede 310 8.52e+01 1b6g c.69.1.8 34662 1snlA 103 8.63e+01 a.39.1.7 105820 2av5A 120 8.68e+01 2trxA 108 8.73e+01 1thx c.47.1.1 32719 1o57A 291 8.74e+01 a.4.5.40,c.61.1.1 92483,92484 2a74A 643 8.88e+01 1xhfA 123 8.89e+01 1kshA 186 8.89e+01 c.37.1.8 72914 1tt8A 164 8.95e+01 3csuA 310 8.97e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 1vjjA 692 8.99e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817