# List of top-scoring protein chains for t04-100-30-str2-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 1l2tA 235 1.04e-02 c.37.1.12 73514 1z47A 355 4.06e-02 2b99A 156 4.82e-02 1c9kA 180 5.34e-02 1c9kB c.37.1.11 32363 1fobA 334 6.27e-02 c.1.8.3 83255 1hp1A 516 8.04e-02 d.114.1.1,d.159.1.2 70976,70977 1z2lA 423 8.90e-02 1yvkA 163 1.05e-01 1xx4A 261 1.08e-01 1ush 550 1.38e-01 1ush d.114.1.1,d.159.1.2 40923,42079 1vypX 364 2.10e-01 c.1.4.1 108905 1y9kA 157 2.15e-01 1obdA 306 2.34e-01 d.143.1.1 86767 1vyrA 364 2.35e-01 c.1.4.1 108906 1gvoA 364 2.36e-01 c.1.4.1 76357 1h61A 364 2.37e-01 1oyc c.1.4.1 60657 2abbA 364 2.55e-01 1mb3A 124 3.10e-01 c.23.1.1 78907 2f5tX 233 3.49e-01 1sg4A 260 3.57e-01 1g0hA 252 3.64e-01 1dk4A e.7.1.1 60171 2reb 352 3.85e-01 2reb c.37.1.11,d.48.1.1 32282,38767 1a48 306 3.91e-01 1a48 d.143.1.1 41590 1b0uA 262 4.40e-01 1b0uA c.37.1.12 32370 2gqrA 237 4.89e-01 1u1wA 298 5.11e-01 1w2xA 758 5.37e-01 c.14.1.4,c.14.1.4 109134,109135 1y10A 407 5.71e-01 1uyrA 737 6.00e-01 c.14.1.4,c.14.1.4 100188,100189 1srrA 124 6.05e-01 1dz3A c.23.1.1 31110 1o0iA 138 6.83e-01 d.38.1.5 86532 1m6iA 493 7.09e-01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1a04A 215 7.83e-01 1a04A a.4.6.2,c.23.1.1 16234,31089 2aa4A 289 8.11e-01 1jf8A 131 8.50e-01 c.44.1.1 66621 1xubA 298 9.13e-01 2ct8A 497 9.30e-01 1vr3A 191 1.02e+00 1ig8A 486 1.09e+00 2yhx c.55.1.3,c.55.1.3 64746,64747 1cr1A 296 1.16e+00 1cr1A c.37.1.11 32286 1phk 298 1.27e+00 1cdkA d.144.1.7 41635 2c31A 568 1.29e+00 1j8yF 297 1.33e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 1w44A 331 1.45e+00 1n13B 113 1.47e+00 1k77A 260 1.49e+00 c.1.15.5 72096 1t6kA 278 1.53e+00 2b6eA 146 1.58e+00 1i39A 225 1.66e+00 1ekeA c.55.3.1 61585 1u9jA 358 1.69e+00 1u0sY 118 1.72e+00 c.23.1.1 107566 1tmy 120 1.85e+00 1dbwA c.23.1.1 31083 1g6hA 257 1.96e+00 1gajA c.37.1.12 60318 2anuA 255 2.05e+00 1w5fA 353 2.08e+00 1z41A 338 2.19e+00 1jmvA 141 2.22e+00 c.26.2.4 66897 2ap1A 327 2.46e+00 1u94A 356 2.49e+00 c.37.1.11,d.48.1.1 107743,107744 1kngA 156 2.50e+00 c.47.1.10 72777 1nu0A 138 2.51e+00 c.55.3.8 92165 1e7rA 321 2.61e+00 1bsvA c.2.1.2 29808 1e19A 314 2.63e+00 1b7bA c.73.1.1 34967 1j8mF 297 2.64e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1e6uA 321 2.72e+00 1bsvA c.2.1.2 29805 1g291 372 2.76e+00 1g291 1vplA 256 2.79e+00 1qe5A 266 2.91e+00 1b8oA c.56.2.1 33784 1p5jA 372 2.98e+00 c.79.1.1 104067 2bllA 345 2.99e+00 1wqaA 455 3.00e+00 1wb4A 297 3.04e+00 1h49A 512 3.20e+00 c.1.8.4 83477 1e55A 512 3.26e+00 1e70M c.1.8.4 28934 1ko7A 314 3.30e+00 c.98.2.1,c.91.1.2 72797,72798 1z7bA 358 3.30e+00 1jkxA 212 3.40e+00 c.65.1.1 66813 1gheA 177 3.43e+00 d.108.1.1 76222 1oxxK 353 3.50e+00 b.40.6.3,c.37.1.12 93715,93716 1ig3A 263 3.61e+00 1ig3A b.82.6.1,c.100.1.1 62358,62359 1dq3A 454 3.71e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1n2sA 299 3.86e+00 c.2.1.2 79857 1zn6A 227 3.95e+00 1nekA 588 4.02e+00 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1e9lA 377 4.11e+00 1e9lA c.1.8.5,d.26.3.1 59395,59396 2ae2A 260 4.15e+00 1bdb c.2.1.2 29945 1nrfA 262 4.22e+00 e.3.1.1 92086 7odcA 424 4.30e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 1oxsC 353 4.30e+00 b.40.6.3,c.37.1.12 87519,87520 1ivyA 452 4.32e+00 1ivyA c.69.1.5 34654 1w5qA 337 4.44e+00 2bbsA 290 4.76e+00 1b4kA 337 4.77e+00 1b4kA c.1.10.3 29184 1nxmA 197 4.89e+00 b.82.1.1 86385 1gklA 297 4.89e+00 c.69.1.2 65250 1xwiA 322 5.12e+00 1xbbA 291 5.16e+00 2f5gA 133 5.23e+00 7a3hA 303 5.25e+00 7a3hA c.1.8.3 28817 1zc3B 113 5.42e+00 1ji0A 240 5.53e+00 c.37.1.12 71665 1ru8A 232 5.58e+00 c.26.2.1 97849 1xp8A 366 5.59e+00 1yavA 159 5.74e+00 1u04A 771 5.86e+00 b.34.14.1,c.55.3.10 107539,107540 1wleA 501 5.94e+00 1xmiA 291 6.10e+00 1tp9A 162 6.11e+00 1dkiA 371 6.33e+00 1dkiA d.3.1.1 37090 1vf8A 377 6.37e+00 1z4eA 153 6.46e+00 1g0cA 364 6.66e+00 7a3hA c.1.8.3 60165 1lnsA 763 6.73e+00 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1bqcA 302 6.82e+00 1bqcA c.1.8.3 28831 1h6zA 913 7.02e+00 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1n0wA 243 7.05e+00 c.37.1.11 79772 2fyxA 143 7.10e+00 1eiwA 111 7.11e+00 1eiwA c.23.3.1 31130 1f89A 291 7.13e+00 d.160.1.1 64988 1xfsA 178 7.17e+00 d.129.3.5 109589 1j31A 262 7.26e+00 d.160.1.2 90808 1ctn 540 7.54e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 2azpA 318 7.67e+00 2aq5A 402 7.92e+00 1t0fA 276 7.93e+00 1o70A 324 7.96e+00 b.118.1.1,b.118.1.1 81115,81116 1w78A 422 8.06e+00 1z3eA 132 8.11e+00 2f1fA 164 8.19e+00 1f1zA 273 8.30e+00 1f1zA a.4.5.27,c.52.1.16 16081,33334 1h0hB 214 8.34e+00 d.58.1.5 76437 1cnzA 363 8.36e+00 1cnzA c.77.1.1 35061 1yvoA 172 8.37e+00 1qipA 183 8.37e+00 1qipA d.32.1.1 38470 1s8nA 205 8.39e+00 c.23.1.1 105374 1fvuB 125 8.39e+00 1ixxB d.169.1.1 42346 1zmtA 254 8.47e+00 1qmyA 167 8.47e+00 1qmyA d.3.1.2 37094 1vr5A 547 8.60e+00 1hh1A 143 8.77e+00 1gefA c.52.1.18 61036 1n2eA 300 8.86e+00 c.26.1.4 85268 2f4nA 273 9.17e+00 1c3wA 222 9.44e+00 1c3wA f.13.1.1 43405 1pwxA 254 9.47e+00 c.2.1.2 95262 1jksA 294 9.49e+00 d.144.1.7 71710 1w5nA 337 9.56e+00 2ffcA 353 9.62e+00 1m3uA 264 9.65e+00 c.1.12.8 84784 2pfkA 320 9.65e+00 3pfk c.89.1.1 35577 1ciy 590 9.88e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1k1eA 180 9.96e+00 c.108.1.5 67995 1ekeA 230 9.97e+00 1ekeA c.55.3.1 33572 1gzgA 337 9.98e+00 c.1.10.3 70805 1dbiA 280 1.00e+01 1gci c.41.1.1 32543 2czdA 208 1.01e+01 1juhA 350 1.01e+01 b.82.1.5 71884 1wab 232 1.02e+01 1wab c.23.10.3 31341 1q8bA 105 1.02e+01 d.58.4.6 96201 1auk 489 1.03e+01 1auk c.76.1.2 35030 1vfvA 366 1.03e+01 c.37.1.9 108592 2az4A 429 1.03e+01 2ethA 154 1.04e+01 1vm0A 130 1.05e+01 d.68.6.2 108873 2gkeA 274 1.06e+01 1g7fA 298 1.06e+01 1pty c.45.1.2 60330 1pfkA 320 1.06e+01 3pfk c.89.1.1 35575 1es9A 232 1.10e+01 1wab c.23.10.3 31340 1tqzA 133 1.14e+01 1zmoA 244 1.15e+01 1vdwA 254 1.16e+01 e.7.1.1 100569 1w0dA 337 1.16e+01 1edqA 540 1.17e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1r0wA 286 1.18e+01 c.37.1.12 96754 1pm3A 78 1.20e+01 b.41.1.2 94889 1on0A 158 1.25e+01 d.108.1.1 87095 1pwhA 327 1.25e+01 c.79.1.1 95224 1ne9A 335 1.25e+01 d.108.1.4,d.108.1.4 91839,91840 1f28A 297 1.26e+01 1bkpA d.117.1.1 59608 2ac2A 309 1.26e+01 1jykA 254 1.26e+01 c.68.1.13 67458 1eo1A 124 1.27e+01 1eo1A c.55.5.1 33739 1v5eA 590 1.28e+01 1ezm 301 1.30e+01 1hyt d.92.1.2 58980 2a84A 300 1.31e+01 1vp8A 201 1.31e+01 1gmlA 178 1.34e+01 c.8.5.2 70273 2f71A 298 1.34e+01 1mvoA 136 1.34e+01 c.23.1.1 79513 2fexA 188 1.36e+01 2b0vA 153 1.39e+01 1hkkA 364 1.39e+01 c.1.8.5,d.26.3.1 90634,90635 2aefA 234 1.40e+01 1meoA 209 1.42e+01 c.65.1.1 79035 1jlnA 297 1.42e+01 1pty c.45.1.2 63172 1vk9A 151 1.44e+01 c.139.1.1 108640 1wb0A 445 1.44e+01 1yu6A 275 1.45e+01 1qvbA 481 1.46e+01 1qvbA c.1.8.4 28983 1bg4 302 1.47e+01 1taxA c.1.8.3 28806 1uj6A 227 1.47e+01 c.124.1.4,d.58.40.1 107898,107899 1iy8A 267 1.48e+01 c.2.1.2 83774 1zy9A 564 1.51e+01 1i6iA 366 1.52e+01 1bg2 c.37.1.9 61844 1yqzA 438 1.53e+01 2cw9A 194 1.54e+01 1orrA 347 1.54e+01 c.2.1.2 93460 1qo2A 241 1.55e+01 1qo2A c.1.2.1 28533 1i60A 278 1.56e+01 c.1.15.4 71118 1zarA 282 1.56e+01 1r0rE 274 1.56e+01 c.41.1.1 96735 1szoA 257 1.57e+01 c.14.1.3 106164 1khdA 345 1.58e+01 a.46.2.1,c.27.1.1 77400,77401 1ac5 483 1.59e+01 1ac5 c.69.1.5 34653 1q74A 303 1.59e+01 c.134.1.1 96019 1a9xB 379 1.60e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 2bl1A 172 1.61e+01 1hjsA 332 1.61e+01 c.1.8.3 83492 1cseE 274 1.63e+01 1gci c.41.1.1 32481 2ac4A 309 1.64e+01 1o8uA 257 1.64e+01 c.14.1.3 81194 1qv9A 283 1.65e+01 c.127.1.1 96356 1s72H 171 1.65e+01 d.41.4.1 105327 1io2A 213 1.66e+01 1ekeA c.55.3.1 62612 1f9vA 347 1.66e+01 1bg2 c.37.1.9 59745 1jmxB 349 1.66e+01 b.69.2.2 66906 2b0mA 393 1.67e+01 1lam 484 1.67e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1sjwA 144 1.68e+01 d.17.4.9 98899 2cw5A 255 1.69e+01 2b49A 287 1.69e+01 2pia 321 1.70e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1oneA 436 1.73e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1izcA 339 1.73e+01 c.1.12.5 83838 1pa1A 310 1.74e+01 c.45.1.2 94404 1z2iA 358 1.74e+01 1h8gA 95 1.75e+01 b.109.1.1 65735 2grrA 161 1.76e+01 1ei6A 406 1.76e+01 c.76.1.4 90443 1mzjA 339 1.77e+01 c.95.1.2,c.95.1.2 79700,79701 1yr0A 175 1.79e+01 1r94A 118 1.81e+01 b.124.1.1 97251 2av4A 162 1.82e+01 1ri6A 343 1.84e+01 b.69.11.1 97503 1dozA 309 1.85e+01 1ak1 c.92.1.1 35592 1z5oA 242 1.86e+01 1u9aA 160 1.90e+01 1u9aA d.20.1.1 38333 1ntvA 152 1.91e+01 b.55.1.2 86168 1vpqA 273 1.92e+01 1kutA 230 1.93e+01 d.143.1.1 73017 1z5nA 242 1.94e+01 2cy2A 174 1.95e+01 4enl 436 1.96e+01 4enl c.1.11.1,d.54.1.1 29202,38846 1ma3A 253 1.97e+01 c.31.1.5 78883 1ye8A 178 1.97e+01 1tqmA 282 2.01e+01 a.4.5.56,d.144.1.9 107236,107237 1tq5A 242 2.01e+01 1u4gA 301 2.02e+01 d.92.1.2 107670 1yuwA 554 2.03e+01 1y4oA 104 2.04e+01 1u2eA 289 2.04e+01 1t9bA 677 2.10e+01 1gteA 1025 2.12e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1y0gA 191 2.12e+01 1r8gA 372 2.13e+01 d.128.1.3 104845 1nu7D 282 2.13e+01 a.8.6.1,a.8.6.1 92191,92192 1rvgA 305 2.15e+01 c.1.10.2 97920 1vetA 124 2.15e+01 d.110.7.1 108553 1m8jA 181 2.17e+01 c.26.1.3 84875 1m2oA 768 2.20e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1bu6O 501 2.21e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 2bryA 497 2.21e+01 2fp8A 322 2.21e+01 1b74A 254 2.21e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1nxuA 333 2.22e+01 c.122.1.1 86389 2a67A 167 2.23e+01 1vl8A 267 2.24e+01 c.2.1.2 108733 1v9wA 130 2.25e+01 c.47.1.16 108453 1kyfA 247 2.26e+01 b.1.10.1,d.105.1.1 73220,73221 1eqjA 511 2.27e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1yd9A 193 2.27e+01 1v04A 355 2.28e+01 b.68.6.2 100240 1vjoA 393 2.28e+01 c.67.1.3 100827 1bg2 325 2.29e+01 1bg2 c.37.1.9 32189 1xc3A 302 2.29e+01 2ai4A 119 2.32e+01 1ijtA 128 2.34e+01 1bfg b.42.1.1 62510 1o98A 511 2.35e+01 c.105.1.1,c.76.1.3 86684,86685 1wbsA 360 2.37e+01 1hzdA 272 2.40e+01 c.14.1.3 65969 1c0pA 363 2.41e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1uoyA 64 2.42e+01 g.3.19.1 99709 1yd7A 395 2.45e+01 1ptvA 321 2.45e+01 1pty c.45.1.2 32665 2frnA 278 2.47e+01 1a0i 348 2.49e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 2fhxA 246 2.49e+01 1bl3A 160 2.49e+01 1b9dA c.55.3.2 33655 1te0A 318 2.50e+01 1npuA 117 2.50e+01 b.1.1.1 92038 1n8jA 186 2.53e+01 c.47.1.10 85401 1jtdB 273 2.53e+01 b.69.5.2 67265 1gs5A 258 2.53e+01 c.73.1.2 70395 1yh6A 179 2.54e+01 1ccwA 137 2.54e+01 1be1 c.23.6.1 31238 1jx7A 117 2.55e+01 c.114.1.1 77195 1ws0A 156 2.57e+01 1h7wA 1025 2.58e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1h3fA 432 2.62e+01 c.26.1.1,d.66.1.4 76631,76632 1pvdA 537 2.63e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1vrmA 325 2.63e+01 1bolA 222 2.63e+01 1bolA d.124.1.1 41120 1zhvA 134 2.63e+01 1qk8A 146 2.63e+01 1ewxA c.47.1.10 33061 2ge3A 170 2.64e+01 1qd1A 325 2.64e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1augA 215 2.65e+01 1a2zA c.56.4.1 33798 1gqzA 274 2.65e+01 d.21.1.1,d.21.1.1 83311,83312 1uf5A 303 2.67e+01 d.160.1.2 107808 1u24A 337 2.68e+01 1erzA 303 2.69e+01 1erzA d.160.1.2 59498 1vmoA 163 2.69e+01 1vmoA b.77.1.1 27974 2eueA 279 2.70e+01 1fzqA 181 2.70e+01 1hurA c.37.1.8 32060 2al1A 436 2.73e+01 2al2A 436 2.73e+01 1mwqA 101 2.73e+01 d.58.4.7 91481 1thm 279 2.74e+01 1gci c.41.1.1 32544 1vqoH 171 2.75e+01 1m7xA 617 2.79e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 2b7oA 464 2.81e+01 1ofuA 320 2.81e+01 c.32.1.1,d.79.2.1 86972,86973 1jysA 242 2.84e+01 c.56.2.1 77216 1s7iA 124 2.85e+01 d.58.4.9 105353 1m0wA 491 2.86e+01 c.30.1.4,d.142.1.6 78363,78364 1nhkL 144 2.86e+01 1npk d.58.6.1 39142 1uh5A 329 2.87e+01 c.2.1.2 107840 1g7sA 594 2.87e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1brwA 433 2.89e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1qhtA 775 2.91e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1svdA 473 2.92e+01 1zh2A 121 2.92e+01 1ek0A 170 2.94e+01 1ctqA c.37.1.8 32076 1pcxA 810 2.94e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 2gtrA 261 2.95e+01 2dkaA 544 2.95e+01 1onxA 390 2.99e+01 b.92.1.7,c.1.9.13 87176,87177 2bvpA 276 3.02e+01 1qwgA 251 3.03e+01 c.1.27.1 96473 1wg8A 285 3.03e+01 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c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1wlsA 328 8.54e+01 1o0yA 260 8.59e+01 c.1.10.1 80756 2bv9A 290 8.60e+01 1wjvA 79 8.63e+01 1vjeA 166 8.65e+01 d.185.1.2 100807 1g5aA 628 8.69e+01 b.71.1.1,c.1.8.1 65152,65153 1ag6 99 8.69e+01 1plc b.6.1.1 22857 1nzjA 298 8.69e+01 c.26.1.1 92377 2a1xA 308 8.70e+01 1zesA 125 8.71e+01 1dfuP 94 8.72e+01 1dfuP b.53.1.1 26936 1ro5A 201 8.72e+01 d.108.1.3 105023 1qnf 484 8.78e+01 1qnf a.99.1.1,c.28.1.1 18777,31632 1xfoA 357 8.81e+01 1ng4A 390 8.83e+01 c.3.1.2,d.16.1.3 85666,85667 2b5dX 528 8.83e+01 1wkvA 389 8.84e+01 1dz3A 130 8.88e+01 1dz3A c.23.1.1 31105 1th0A 226 8.88e+01 d.3.1.7 106903 1vh5A 148 8.91e+01 d.38.1.5 100642 1su0B 159 8.91e+01 d.224.1.2 106015 1huxA 270 8.95e+01 1huxA c.55.1.5 61278 1rznA 205 8.96e+01 1f0kA 364 8.98e+01 1f0kA c.87.1.2 35465 1o91A 178 8.98e+01 b.22.1.1 92656 1i4uA 181 9.00e+01 b.60.1.1 61732