# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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.soe.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 1hr6B 443 7.71e-54 1be3A d.185.1.1,d.185.1.1 61166,61167 1ppjA 446 1.03e-50 d.185.1.1,d.185.1.1 104252,104253 2g47A 990 2.44e-49 1q2lA 939 1.45e-47 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 1hr6A 475 3.52e-44 1hr6A d.185.1.1,d.185.1.1 61164,61165 2fgeA 995 7.72e-40 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 133430,133431,133432,133433 1kb9A 431 4.32e-39 d.185.1.1,d.185.1.1 77311,77312 3cx5A 431 5.13e-39 1ppjB 439 1.18e-38 d.185.1.1,d.185.1.1 104254,104255 1ezvA 430 8.75e-38 1be3A d.185.1.1,d.185.1.1 59541,59542 3cx5B 352 6.28e-21 1kb9B 352 2.30e-20 d.185.1.1,d.185.1.1 77313,77314 1ezvB 352 1.53e-19 1ezvB d.185.1.1,d.185.1.1 59543,59544 1k3eA 156 6.19e-02 d.198.1.1 68103 1nrwA 288 2.02e-01 c.108.1.10 86128 2okjA 504 2.57e-01 1f20A 435 2.94e-01 b.43.4.1,c.25.1.4 64932,64933 1js3A 486 4.86e-01 c.67.1.6 67215 2arhA 203 6.98e-01 d.108.1.9 127197 2douA 376 9.19e-01 2z20A 432 9.39e-01 1tllA 688 1.23e+00 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 3cucA 291 1.43e+00 1zejA 293 1.45e+00 3cgvA 397 1.58e+00 1pmmA 466 1.98e+00 c.67.1.6 94901 1t6nA 220 2.01e+00 c.37.1.19 106576 2gnxA 365 2.15e+00 1rh5A 436 2.28e+00 f.41.1.1 97464 2nuwA 288 2.61e+00 2dgmA 466 2.79e+00 c.67.1.6 131508 2jisA 515 2.86e+00 2v7pA 310 2.87e+00 1s9aA 257 2.90e+00 b.3.6.1 105379 1avqA 228 3.04e+00 1avqA c.52.1.13 33326 1wstA 417 3.26e+00 c.67.1.1 121244 2qruA 274 3.48e+00 1o4sA 389 3.52e+00 c.67.1.1 86620 2btoA 473 3.70e+00 2p4fA 299 3.75e+00 1d2fA 390 3.84e+00 1d2fA c.67.1.3 34411 2iksA 293 4.01e+00 1an9A 340 4.14e+00 1an9A c.4.1.2,d.16.1.3 30617,37904 1ve9A 347 4.44e+00 c.4.1.2,d.16.1.3 100571,100572 2yrrA 353 4.68e+00 1n35A 1267 4.92e+00 e.8.1.4 79935 1nh1A 330 5.40e+00 e.45.1.1 91871 1pprM 312 6.10e+00 1pprM a.131.1.1,a.131.1.1 19502,19503 2atfA 200 6.26e+00 b.82.1.19 127290 2b5hA 200 6.26e+00 b.82.1.19 127894 1h2eA 207 6.63e+00 c.60.1.1 70857 1cs8A 316 6.63e+00 1cs8A d.3.1.1 37065 1wyuA 438 6.66e+00 c.67.1.7 121452 2h5nA 133 7.11e+00 2dr1A 386 7.24e+00 7aatA 401 7.40e+00 1ajsA c.67.1.1 34250 1y1uA 585 7.55e+00 1p4xA 250 7.72e+00 a.4.5.28,a.4.5.28 87784,87785 1h6pA 203 8.41e+00 a.146.1.1 60690 1kz7A 353 8.42e+00 a.87.1.1,b.55.1.1 73333,73334 1yc9A 442 8.43e+00 1psdA 409 8.47e+00 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1sc6A 404 8.60e+00 c.2.1.4,c.23.12.1,d.58.18.1 118932,118933,118934 2csgA 424 8.63e+00 b.82.2.12 130768 1gdeA 389 8.76e+00 c.67.1.1 60456 1jyoA 130 8.76e+00 d.198.1.1 67483 1w36B 1180 9.34e+00 c.37.1.19,c.37.1.19,c.52.1.24 114122,114123,114124 1dlcA 584 9.46e+00 b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 1r31A 428 9.57e+00 d.58.20.1,d.179.1.1 96897,96898 2hufA 393 9.80e+00 1cjaA 342 9.92e+00 1cjaA d.144.1.3 41708 2g8yA 385 1.04e+01 1wovA 250 1.04e+01 a.132.1.1 121124 1fg7A 356 1.05e+01 1gewA c.67.1.1 59819 1fc4A 401 1.06e+01 1bs0A c.67.1.4 59760 1rkbA 173 1.19e+01 c.37.1.1 111854 104lA 166 1.19e+01 1l92 d.2.1.3 36969 1vbiA 344 1.23e+01 1zymA 258 1.25e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1aisB 200 1.26e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 2i1yA 301 1.28e+01 2ahrA 259 1.28e+01 a.100.1.10,c.2.1.6 126775,126776 2np9A 440 1.30e+01 2uyeA 307 1.32e+01 1w85A 368 1.32e+01 c.36.1.11 114335 3bu8A 235 1.34e+01 2rasA 212 1.35e+01 3cc8A 230 1.35e+01 2r91A 286 1.38e+01 2qypA 91 1.41e+01 1b5pA 385 1.42e+01 c.67.1.1 90403 2d3yA 219 1.43e+01 2gtrA 261 1.43e+01 1zc0A 309 1.45e+01 1a4pA 96 1.47e+01 1b4cA a.39.1.2 17176 1nm8A 616 1.49e+01 c.43.1.3,c.43.1.3 85872,85873 1m5yA 408 1.50e+01 a.223.1.2,d.26.1.1,d.26.1.1 78664,78665,78666 1gpjA 404 1.51e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 2i7qA 402 1.52e+01 3c5iA 369 1.55e+01 2di4A 238 1.56e+01 a.269.1.1 131522 1gewA 356 1.56e+01 1gewA c.67.1.1 60470 1khdA 345 1.57e+01 a.46.2.1,c.27.1.1 77400,77401 1kyqA 274 1.60e+01 c.2.1.11,e.37.1.1 73281,73282 2e9xD 223 1.61e+01 2bwjA 199 1.62e+01 2di3A 239 1.65e+01 1uthA 315 1.65e+01 c.94.1.1 108032 2i57A 438 1.67e+01 2anrA 178 1.68e+01 2yviA 111 1.69e+01 169lA 164 1.72e+01 1l92 d.2.1.3 36963 2f5tX 233 1.73e+01 2e7jA 371 1.73e+01 2dbnA 461 1.76e+01 1j5wA 298 1.80e+01 d.104.1.1 71589 1ddfA 127 1.81e+01 a.77.1.2 18423 2om6A 235 1.82e+01 2jg2A 422 1.82e+01 1e6cA 173 1.84e+01 1shkA c.37.1.2 59296 1sx7A 164 1.85e+01 d.2.1.3 112140 1bjwA 382 1.85e+01 1bjwA c.67.1.1 34349 1qlpA 394 1.86e+01 1ovaA e.1.1.1 42628 1vh4A 435 1.90e+01 b.80.6.1 100640 1wvfA 520 1.97e+01 d.58.32.1,d.145.1.1 121337,121338 2cstA 411 1.99e+01 1ajsA c.67.1.1 34273 1td6A 306 2.01e+01 a.234.1.1 112390 1lvfA 110 2.01e+01 a.47.2.1 74280 2oh1A 179 2.01e+01 1ztuA 341 2.04e+01 2dt9A 167 2.05e+01 2b5aA 77 2.11e+01 a.35.1.3 127882 1xkgA 312 2.11e+01 d.3.1.1 122081 1whzA 70 2.12e+01 d.50.3.2 114656 1xjjA 644 2.18e+01 1vq3A 94 2.19e+01 d.284.1.1 114005 2z9wA 392 2.20e+01 3cnhA 200 2.22e+01 1xl7A 612 2.22e+01 c.43.1.3,c.43.1.3 115438,115439 1paqA 189 2.23e+01 a.118.1.14 94413 1i5gA 144 2.23e+01 1ewxA c.47.1.10 61784 1jlnA 297 2.27e+01 1pty c.45.1.2 63172 1v02A 565 2.27e+01 c.1.8.4 108194 119l 164 2.39e+01 1l92 1s9pA 227 2.39e+01 a.123.1.1 105384 1n7oA 721 2.39e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 2o9cA 342 2.41e+01 2dbbA 151 2.42e+01 1vs3A 249 2.44e+01 2owlA 303 2.53e+01 1f06A 320 2.55e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1a6jA 163 2.55e+01 1a6jA d.112.1.1 40915 1pvc3 238 2.55e+01 1aym3 1k3sA 113 2.56e+01 d.198.1.1 68120 2bfwA 200 2.57e+01 c.87.1.8 128456 1v2dA 381 2.59e+01 c.67.1.1 108281 2op5A 117 2.63e+01 1rec 201 2.65e+01 1rec 1tk1A 260 2.65e+01 d.248.1.1 107066 2ec4A 178 2.66e+01 2cxaA 256 2.67e+01 d.108.1.6 130993 180lA 164 2.67e+01 1l92 d.2.1.3 36867 2e2rA 244 2.68e+01 2dgkA 452 2.69e+01 167lA 164 2.69e+01 1l92 d.2.1.3 36937 1jr5A 90 2.70e+01 a.150.1.1 67113 2afrA 231 2.73e+01 1vqoH 171 2.80e+01 d.41.4.1 120369 1w7lA 422 2.81e+01 c.67.1.1 109226 1t1uA 639 2.82e+01 c.43.1.3,c.43.1.3 119110,119111 2pq8A 278 2.86e+01 1lw9A 164 2.86e+01 d.2.1.3 84727 1gx5A 536 2.86e+01 e.8.1.4 70682 3c19A 186 2.95e+01 1gqiA 708 2.98e+01 c.1.8.10,d.92.2.2 76279,76280 1p36A 164 2.99e+01 d.2.1.3 93978 2reb 352 3.06e+01 2reb 2rebA 352 3.06e+01 c.37.1.11,d.48.1.1 32282,38767 1ntyA 311 3.08e+01 a.87.1.1,b.55.1.1 103873,103874 1h6dA 433 3.08e+01 c.2.1.3,d.81.1.5 65656,65657 2plrA 213 3.09e+01 1w24A 182 3.09e+01 d.159.1.7 120579 1g94A 448 3.11e+01 b.71.1.1,c.1.8.1 65169,65170 1mlwA 301 3.13e+01 d.178.1.1 79289 1vjeA 166 3.15e+01 d.185.1.2 100807 175lA 164 3.15e+01 1l92 d.2.1.3 36924 1vh0A 161 3.17e+01 c.116.1.3 100626 1ulyA 192 3.19e+01 a.4.5.58 113297 2p90A 319 3.20e+01 1xi9A 406 3.22e+01 c.67.1.1 115355 1uouA 474 3.22e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1ji6A 589 3.22e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 2nrqA 159 3.24e+01 2ia0A 171 3.25e+01 1ki1B 352 3.26e+01 a.87.1.1,b.55.1.1 72497,72498 1ireB 228 3.26e+01 b.34.4.4 76770 1ugpB 226 3.28e+01 b.34.4.4 107832 2hpvA 208 3.29e+01 174lA 164 3.33e+01 1l92 d.2.1.3 36956 1tfuA 157 3.34e+01 c.26.1.3 106859 1ab4 477 3.34e+01 1ab4 3c3jA 384 3.34e+01 1q1vA 70 3.44e+01 a.159.4.1 104479 2uuuA 584 3.48e+01 1vqqA 646 3.49e+01 d.17.4.5,d.175.1.1,e.3.1.1 114009,114010,114011 1qxoA 388 3.54e+01 d.258.1.1 96539 1eu8A 409 3.57e+01 1eu8A c.94.1.1 59502 1p30A 952 3.57e+01 b.121.2.2,b.121.2.2 93964,93965 1j8fA 323 3.61e+01 1j8fA c.31.1.5 62738 1qlsA 99 3.61e+01 1psrA a.39.1.2 17185 1jgsA 138 3.62e+01 a.4.5.28 66683 2fjtA 182 3.63e+01 1omrA 201 3.63e+01 a.39.1.5 93349 4tmkA 213 3.64e+01 5tmpA c.37.1.1 31930 2dytA 312 3.70e+01 1of8A 370 3.71e+01 c.1.10.4 92819 1b7yB 785 3.71e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,b.153.1.1 16301,16302,25312,39311,40780,41456 176lA 164 3.74e+01 1l92 d.2.1.3 36942 1m7bA 184 3.77e+01 c.37.1.8 74572 2nxoA 291 3.77e+01 2q8nA 460 3.80e+01 2j0fA 482 3.85e+01 1zvpA 133 3.86e+01 d.58.18.9,d.58.18.9 125714,125715 1vrbA 342 3.89e+01 b.82.2.11 120450 1ynpA 317 3.89e+01 2fji1 399 3.96e+01 1z2wA 192 3.96e+01 d.159.1.7 124390 2hi0A 240 3.96e+01 2acaA 189 3.97e+01 d.63.1.2 126545 2vj4A 294 3.98e+01 2hxwA 237 3.99e+01 2plgA 163 4.00e+01 2hnlA 225 4.00e+01 2rexB 197 4.01e+01 2ay1A 394 4.01e+01 1ajsA c.67.1.1 34357 2be3A 226 4.03e+01 d.218.1.8 128349 2j0eA 266 4.05e+01 1sr9A 644 4.07e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 2dmeA 120 4.08e+01 2j59M 168 4.09e+01 1jmsA 381 4.11e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 2gzmA 267 4.14e+01 1l7mA 211 4.15e+01 c.108.1.4 73664 2axyA 73 4.15e+01 d.51.1.1 127532 2ethA 154 4.18e+01 a.4.5.28 132358 1g8iA 190 4.20e+01 1rec a.39.1.5 60363 1yreA 197 4.22e+01 d.108.1.1 123919 2obeA 932 4.23e+01 3cg6A 146 4.33e+01 2oayA 391 4.34e+01 1uuyA 167 4.34e+01 c.57.1.1 108059 1ekqA 272 4.35e+01 1c3qA c.72.1.2 34941 2dbyA 368 4.37e+01 1t0fA 276 4.39e+01 a.4.5.27,c.52.1.16 112195,112196 2dx6A 159 4.43e+01 1a3aA 148 4.44e+01 1a3aA d.112.1.1 40917 2nppB 449 4.46e+01 a.118.1.20 138445 2yykA 481 4.46e+01 1yaaA 412 4.46e+01 1ajsA c.67.1.1 34280 1jfuA 186 4.47e+01 c.47.1.10 62940 1xteA 154 4.47e+01 d.189.1.1 116017 2g4rA 160 4.49e+01 2nogA 173 4.50e+01 1lfwA 470 4.57e+01 c.56.5.4,d.58.19.1 77942,77943 1eguA 731 4.57e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 2gpuA 230 4.58e+01 a.123.1.1 135493 2qmaA 497 4.62e+01 2hehA 387 4.66e+01 2rcyA 262 4.68e+01 1w3iA 293 4.70e+01 c.1.10.1 109152 1xrkA 124 4.71e+01 d.32.1.2 115881 1t71A 281 4.72e+01 d.159.1.9 112283 2fa5A 162 4.73e+01 2e8eA 132 4.78e+01 2jd3A 130 4.78e+01 2aorA 223 4.80e+01 2h4tA 626 4.83e+01 1swvA 267 4.84e+01 c.108.1.3 112134 2egtA 132 4.85e+01 2vdeA 460 4.87e+01 2qmwA 267 4.88e+01 2o8gI 225 4.91e+01 2ppwA 216 4.94e+01 1dd9A 338 4.95e+01 1dd9A e.13.1.1 43254 2gojA 197 4.97e+01 2au3A 407 4.98e+01 2pa8L 92 5.02e+01 1jliA 112 5.05e+01 a.26.1.2 16884 1u6mA 199 5.15e+01 d.108.1.1 113069 1prxA 224 5.18e+01 1prxA c.47.1.10 33076 1xccA 220 5.18e+01 c.47.1.10 115113 2arkA 188 5.19e+01 c.23.5.8 127202 1wtjA 343 5.22e+01 2jejA 358 5.22e+01 d.240.1.1,e.8.1.7 138284,138285 2dc4A 165 5.23e+01 2v0vA 194 5.26e+01 1ef1C 90 5.27e+01 1ef1C a.137.5.1 19642 2rk0A 136 5.31e+01 1vkdA 338 5.32e+01 b.67.2.4 108644 1r71A 178 5.33e+01 a.4.14.1 104823 1nrjB 218 5.38e+01 c.37.1.8 86125 2j69A 695 5.39e+01 1yseA 141 5.45e+01 a.35.1.7 123970 137lA 164 5.46e+01 1l92 d.2.1.3 36791 2eqxA 105 5.47e+01 1topA 162 5.51e+01 a.39.1.5 17223 1wycA 392 5.52e+01 1b3uA 588 5.54e+01 1b3uA a.118.1.2 19135 2a4xA 138 5.54e+01 d.32.1.2 126166 2ddhA 661 5.55e+01 a.29.3.2,a.29.3.2,e.6.1.2 131394,131395,131396 1vp4A 425 5.58e+01 c.67.1.1 113935 1ctqA 166 5.65e+01 1ctqA c.37.1.8 31965 1x2mA 64 5.68e+01 a.4.1.1 121645 3crrA 323 5.68e+01 2a1vA 144 5.70e+01 d.198.3.1 126019 2ot4A 525 5.70e+01 2erxA 172 5.75e+01 c.37.1.8 132304 2dcfA 392 5.76e+01 2ig7A 401 5.76e+01 1j97A 211 5.78e+01 1f5sA c.108.1.4 62753 1yozA 116 5.79e+01 a.253.1.1 123796 2dkhA 639 5.84e+01 2debA 653 5.92e+01 1womA 271 5.92e+01 2yufA 142 5.94e+01 1p2zA 968 5.95e+01 b.121.2.2,b.121.2.2 93962,93963 3cnwA 148 5.96e+01 1ml8A 134 5.97e+01 d.227.1.2 85013 1ezvD 245 6.02e+01 1be3D a.3.1.3,f.23.11.1 59546,59547 1q77A 138 6.03e+01 c.26.2.4 96023 2b79A 144 6.03e+01 1qnxA 209 6.04e+01 1qnxA d.111.1.1 40914 1v9nA 360 6.05e+01 2fm8A 135 6.07e+01 d.198.1.1 133767 2pebA 122 6.08e+01 1ccwB 483 6.13e+01 1cb7B c.1.19.2 29646 1bcpB 199 6.14e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 1uzmA 247 6.15e+01 c.2.1.2 119811 1p16A 395 6.16e+01 b.40.4.6,d.142.2.3 87661,87662 1g4wR 383 6.21e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1wcgA 464 6.23e+01 c.1.8.4 120888 1uehA 253 6.23e+01 c.101.1.1 99259 1ywfA 296 6.25e+01 c.45.1.5 124144 1rydA 387 6.27e+01 c.2.1.3,d.81.1.5 118801,118802 1opd 85 6.28e+01 1ptf 1opdA 85 6.28e+01 d.94.1.1 40560 2oznB 140 6.31e+01 1k2yX 463 6.32e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1twfK 120 6.32e+01 d.74.3.2 112736 1jx4A 352 6.35e+01 d.240.1.1,e.8.1.7 90378,90379 1hx0A 496 6.36e+01 b.71.1.1,c.1.8.1 61346,61347 1j98A 157 6.37e+01 1j98A d.185.1.2 62755 2ntxA 365 6.40e+01 2hszA 243 6.41e+01 c.108.1.6 136726 1odfA 290 6.48e+01 c.37.1.6 92782 2qndA 144 6.49e+01 168lA 164 6.52e+01 1l92 d.2.1.3 36975 1vzyA 291 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7.12e+01 2polA 366 7.22e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1yoeA 322 7.23e+01 2bpqA 373 7.25e+01 1m12A 84 7.28e+01 a.64.1.1 84745 2hp1A 432 7.31e+01 2gsaA 432 7.34e+01 2gsaA c.67.1.4 34446 2o18A 340 7.38e+01 3b98A 475 7.42e+01 1jhgA 101 7.47e+01 1jhgA a.4.12.1 19009 1vl8A 267 7.51e+01 c.2.1.2 108733 1xs5A 241 7.51e+01 c.94.1.1 115912 2q4eA 362 7.52e+01 3cz6A 168 7.52e+01 3cniA 156 7.53e+01 2o4aA 93 7.54e+01 2zg5A 397 7.58e+01 1ldjA 760 7.58e+01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 3b5mA 205 7.59e+01 1iugA 352 7.59e+01 c.67.1.3 90699 1wyuB 474 7.62e+01 c.67.1.7 121453 2phcB 225 7.63e+01 1xp8A 366 7.64e+01 c.37.1.11,d.48.1.1 115735,115736 1qo7A 394 7.66e+01 1qo7A c.69.1.11 34697 1d8wA 426 7.67e+01 1de5A c.1.15.2 29394 2nybA 192 7.72e+01 a.2.11.1,d.44.1.1 138804,138805 1u94A 356 7.73e+01 c.37.1.11,d.48.1.1 107743,107744 1mtpA 323 7.77e+01 e.1.1.1 85107 2nrkA 173 7.78e+01 1uhnA 189 7.80e+01 a.39.1.5 99399 1qzzA 374 7.80e+01 a.4.5.29,c.66.1.12 96719,96720 2agaA 190 7.80e+01 2qryA 330 7.82e+01 1gw5S 142 7.95e+01 d.110.4.2 70633