# 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 2fe5A 94 3.54e-15 1g9oA 91 2.01e-14 1pdr b.36.1.1 60400 1tp5A 119 2.55e-14 2fcfA 103 2.82e-14 1qavA 90 3.47e-14 1qauA b.36.1.1 24777 1be9A 119 5.61e-14 1pdr b.36.1.1 24774 1n7eA 97 2.14e-13 b.36.1.1 91691 1n7fA 97 2.84e-13 b.36.1.1 91692 1ihjA 98 3.74e-13 1pdr b.36.1.1 62382 1q3oA 109 8.34e-13 b.36.1.1 95700 1l6oA 95 2.64e-12 b.36.1.1 84534 1mfgA 95 3.92e-12 b.36.1.1 79043 1kwaA 88 5.17e-12 1kwaA b.36.1.1 24772 2f0aA 98 1.34e-11 1nf3C 128 1.35e-11 b.36.1.1 85596 1qauA 112 1.73e-11 1qauA b.36.1.1 24779 1wf7A 103 7.20e-11 2f5yA 91 1.15e-10 1nteA 82 1.41e-10 b.36.1.1 86163 1v5lA 103 2.80e-10 b.36.1.1 108378 1r6jA 82 2.86e-10 b.36.1.1 97151 1fc6A 388 6.06e-07 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 9.70e-06 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 1.07e-05 1y8tA 324 5.85e-04 1sotA 320 1.36e-02 b.36.1.4,b.47.1.1 105852,105853 1zn8A 180 7.48e-02 2bsyA 278 8.91e-01 1x3mA 415 9.08e-01 1fxlA 167 1.20e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 1yg9A 330 1.29e+00 1ad3A 452 1.38e+00 1ad3A c.82.1.1 35335 2d4pA 141 1.74e+00 1yjmA 110 1.85e+00 1db3A 372 1.93e+00 1db3A c.2.1.2 29813 2brfA 110 2.24e+00 2fvgA 340 2.41e+00 2f4wA 187 2.50e+00 1h3gA 601 2.75e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1un8A 552 2.78e+00 c.119.1.2,a.208.1.1 103806,99661 1qb7A 236 3.26e+00 1qb7A c.61.1.1 34087 2bsjA 133 3.28e+00 1xdnA 277 3.74e+00 1r13A 148 3.81e+00 d.169.1.1,h.1.1.1 96782,96783 1ftkA 279 3.92e+00 1gr2A c.94.1.1 35819 2bshA 125 4.05e+00 1o6dA 163 4.16e+00 c.116.1.3 92567 2bnjA 303 4.80e+00 2bhoA 130 5.04e+00 1opr 213 5.35e+00 1opr c.61.1.1 34091 2ffmA 91 5.90e+00 2atrA 138 5.97e+00 1vdmA 153 6.21e+00 2bkfA 87 6.92e+00 1vpqA 273 6.99e+00 1mqiA 263 7.07e+00 c.94.1.1 91398 1lh0A 213 7.20e+00 c.61.1.1 73896 1wlsA 328 7.34e+00 1vzqH 250 7.37e+00 2bw3A 534 7.65e+00 1ucyH 150 7.96e+00 1ucyH 1xx6A 191 7.98e+00 1n6aA 259 8.17e+00 b.76.2.1,b.85.7.1 80121,80122 1kk1A 410 8.21e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1g2qA 187 8.43e+00 c.61.1.1 65117 1y96A 86 8.65e+00 1i1wA 303 8.88e+00 c.1.8.3 76732 1u9yA 284 8.89e+00 2aamA 309 9.13e+00 1h8dH 260 9.30e+00 5ptp 1to2I 64 9.31e+00 1w30A 201 9.39e+00 1t6t1 118 9.88e+00 1i52A 236 9.96e+00 1i52A c.68.1.13 61767 1lw6I 64 9.99e+00 d.40.1.1 74294 1vqqA 646 1.00e+01 1ugmA 125 1.00e+01 d.15.1.3 107827 1h72C 296 1.00e+01 d.14.1.5,d.58.26.1 60712,60713 1zsyA 357 1.03e+01 1wnfA 328 1.05e+01 2f69A 261 1.06e+01 2bs3A 656 1.06e+01 1xmrA 243 1.06e+01 1q52A 314 1.07e+01 c.14.1.3 95846 1qlaA 656 1.08e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1eyqA 222 1.09e+01 1eypA d.36.1.1 38534 1fwkA 296 1.17e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1bg4 302 1.20e+01 1taxA c.1.8.3 28806 2c5qA 240 1.23e+01 1w94A 156 1.24e+01 1rl2A 137 1.26e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1ta3B 303 1.26e+01 c.1.8.3 106732 1uh5A 329 1.34e+01 c.2.1.2 107840 1o12A 376 1.36e+01 b.92.1.5,c.1.9.10 80758,80759 1y0bA 197 1.36e+01 1h70A 255 1.42e+01 1h70A d.126.1.3 60711 2affA 120 1.47e+01 1a2yB 116 1.48e+01 1gc1H b.1.1.1 19927 1x6vA 630 1.52e+01 1o63A 219 1.55e+01 c.94.1.1 92540 1zkpA 268 1.63e+01 2b8tA 223 1.67e+01 2fe7A 166 1.72e+01 1xv5A 401 1.75e+01 2a8jA 420 1.75e+01 1vraB 215 1.76e+01 1zm8A 259 1.77e+01 1cq3A 233 1.77e+01 1cq3A b.27.1.1 23923 1p7tA 731 1.78e+01 c.1.13.1 94319 1jalA 363 1.86e+01 c.37.1.8,d.15.10.2 84138,84139 1y07A 128 1.86e+01 1g57A 217 1.86e+01 1g57A d.115.1.2 60253 1g7jB 116 1.87e+01 1f3rB b.1.1.1 19933 1hgxA 183 1.93e+01 1tc1A c.61.1.1 34027 1tzfA 259 1.93e+01 c.68.1.13 107476 1dmgA 225 1.94e+01 1dmgA c.22.1.1 31036 2adcA 229 1.95e+01 1q1rA 431 1.96e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1ecfA 504 1.97e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1l0bA 229 1.98e+01 c.15.1.3,c.15.1.3 73391,73392 1se8A 301 2.00e+01 b.40.4.3 105448 1d8cA 723 2.00e+01 1d8cA c.1.13.1 29325 1tif 78 2.07e+01 1tif d.15.8.1 37836 2az4A 429 2.09e+01 1l1qA 186 2.23e+01 c.61.1.1 77653 1fsgA 233 2.24e+01 1qk3A c.61.1.1 34029 1w78A 422 2.28e+01 2a8lA 420 2.30e+01 2exnA 136 2.31e+01 1dxrH 258 2.35e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1vm7A 311 2.36e+01 c.72.1.1 108884 1s9aA 257 2.37e+01 b.3.6.1 105379 1trb 320 2.43e+01 1trb c.3.1.5,c.3.1.5 30529,30530 1g7sA 594 2.45e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1sflA 238 2.46e+01 1rurH 218 2.51e+01 b.1.1.1,b.1.1.2 97879,97880 1fl2A 310 2.57e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1ypcI 64 2.59e+01 2sniI d.40.1.1 38570 1mkmA 249 2.60e+01 a.4.5.33,d.110.2.2 79242,79243 1ujxA 119 2.61e+01 b.26.1.2 99473 2cyjA 118 2.61e+01 1hzdA 272 2.67e+01 c.14.1.3 65969 1zh1A 163 2.70e+01 1fdr 248 2.74e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1gklA 297 2.77e+01 c.69.1.2 65250 1eceA 358 2.77e+01 1eceA c.1.8.3 28813 1uc2A 481 2.78e+01 d.261.1.1 99161 1whi 122 2.80e+01 1whi b.39.1.1 24810 1xebA 150 2.83e+01 1fxrA 64 2.86e+01 1fxd d.58.1.4 38993 1cl1A 395 2.87e+01 1cl2A c.67.1.3 34395 1wb4A 297 2.87e+01 2cw8A 537 2.88e+01 1l7bA 92 2.88e+01 c.15.1.2 91053 2a8mA 420 2.89e+01 1m65A 245 2.90e+01 c.6.3.1 84847 1xtmA 175 2.97e+01 1mzhA 225 3.00e+01 c.1.10.1 79698 1y7lA 316 3.02e+01 1cliA 345 3.07e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1nepA 130 3.15e+01 b.1.18.7 80440 1e7uA 961 3.15e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1vchA 175 3.16e+01 1jp4A 308 3.18e+01 1jp4A e.7.1.1 63223 1dg6A 191 3.19e+01 1d4vB b.22.1.1 23883 1uheA 97 3.30e+01 1gpl 432 3.31e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1rxxA 421 3.32e+01 d.126.1.4 98061 1stzA 338 3.37e+01 a.4.5.51,d.110.2.3 106009,106010 1fr3A 67 3.50e+01 1fr3A b.40.6.1 25436 1d4oA 184 3.54e+01 1d4oA c.31.1.4 31748 1t5hX 504 3.58e+01 e.23.1.1 106449 1jnyA 435 3.59e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1rypB 250 3.62e+01 1rypB d.153.1.4 41933 1rpxA 230 3.63e+01 1rpxA c.1.2.2 28536 2ptd 298 3.64e+01 2plc c.1.18.2 29605 1hyuA 521 3.65e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1ppfE 218 3.66e+01 1a7s b.47.1.2 26234 1js8A 394 3.72e+01 a.86.1.1,b.112.1.1 67219,67220 1t4gA 322 3.72e+01 a.60.4.1,c.37.1.11 106418,106419 2f6rA 281 3.72e+01 1koe 172 3.73e+01 1koe d.169.1.5 42448 1ako 268 3.74e+01 1ako d.151.1.1 41779 1y9wA 140 3.79e+01 1kliH 254 3.81e+01 b.47.1.2 77435 1ten 90 3.85e+01 1ten b.1.2.1 21990 1zkkA 167 3.86e+01 1wd5A 208 3.87e+01 1vkmA 297 3.88e+01 c.138.1.1 108670 1poiA 317 3.89e+01 1poiA c.124.1.2 34153 2f4iA 197 3.92e+01 1mpxA 615 3.97e+01 b.18.1.13,c.69.1.21 85041,85042 1rutX 188 3.98e+01 1iscA 192 4.00e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1llnA 262 4.01e+01 d.165.1.1 84625 1j9qA 341 4.03e+01 1nif b.6.1.3,b.6.1.3 62765,62766 2fpmA 322 4.06e+01 2f1wA 158 4.12e+01 1v93A 296 4.14e+01 c.1.23.1 100532 1hrkA 359 4.16e+01 1hrkA c.92.1.1 61228 1xznA 179 4.17e+01 1tc5A 194 4.18e+01 c.110.1.1 106752 2f6uA 234 4.23e+01 1bo4A 168 4.23e+01 1bo4A d.108.1.1 40798 1dq3A 454 4.34e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1wwzA 159 4.36e+01 1o7iA 119 4.39e+01 b.40.4.3 86642 2bepA 159 4.43e+01 1wxxA 382 4.43e+01 1cruA 454 4.46e+01 1c9uA b.68.2.1 27617 1y9kA 157 4.46e+01 1qmvA 197 4.48e+01 1qq2A c.47.1.10 33066 1vkcA 158 4.52e+01 1qzzA 374 4.55e+01 a.4.5.29,c.66.1.12 96719,96720 1u09A 476 4.63e+01 e.8.1.4 107545 1oroA 213 4.66e+01 1opr c.61.1.1 34093 2fnjA 226 4.67e+01 1vheA 373 4.70e+01 b.49.3.1,c.56.5.4 100669,100670 2bh8A 101 4.73e+01 2bgzA 299 4.75e+01 1r0vA 305 4.75e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1uwfA 158 4.80e+01 1s3zA 165 4.81e+01 d.108.1.1 105250 1c44A 123 4.83e+01 1qndA d.106.1.1 40795 1ok7A 366 4.90e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 2awpA 198 4.98e+01 1kuuA 202 5.00e+01 d.153.2.1 73019 2cc0A 195 5.02e+01 2f51A 118 5.02e+01 2polA 366 5.03e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 2b8wA 328 5.08e+01 1qsmA 152 5.17e+01 1qsmA d.108.1.1 40808 1zuoA 186 5.17e+01 1npuA 117 5.17e+01 b.1.1.1 92038 1s1iG 119 5.21e+01 i.1.1.1 105181 1rypI 222 5.23e+01 d.153.1.4 41877 1o50A 157 5.24e+01 d.37.1.1,d.37.1.1 92478,92479 1scuA 288 5.27e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1ydgA 211 5.28e+01 1svy 114 5.29e+01 1svy d.109.1.1 40831 1rz3A 201 5.31e+01 c.37.1.6 98132 1tr7A 164 5.32e+01 1dljA 402 5.32e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1ub3A 220 5.34e+01 c.1.10.1 88395 1g6sA 427 5.34e+01 1eps d.68.2.2 39584 2fb5A 205 5.34e+01 1rypH 205 5.36e+01 d.153.1.4 41876 2ghpA 292 5.36e+01 1ec7A 446 5.38e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1qstA 160 5.42e+01 1yghA d.108.1.1 40804 1uekA 275 5.49e+01 d.14.1.5,d.58.26.5 88483,88484 1wrvA 308 5.52e+01 1nonA 179 5.54e+01 c.61.1.1 103868 1xm7A 195 5.57e+01 1g31A 111 5.58e+01 1g31A b.35.1.1 24656 1b25A 619 5.62e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 2fojA 155 5.65e+01 1th7A 81 5.67e+01 1z9lA 128 5.71e+01 1nm1G 125 5.71e+01 d.109.1.1 80653 1a8y 367 5.73e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1n3jA 119 5.77e+01 b.85.7.2 79963 1h65A 270 5.90e+01 c.37.1.8 65640 1xvsA 126 5.92e+01 1wlgA 299 5.94e+01 1reqB 637 5.96e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1ti6A 875 5.97e+01 b.52.2.2,c.81.1.1 106974,106975 2anuA 255 5.99e+01 1y7rA 133 6.00e+01 1htrB 329 6.00e+01 1smrA 1mmiA 366 6.01e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1bxaA 105 6.02e+01 1aac b.6.1.1 22839 1a44 185 6.05e+01 1a44 b.17.1.1 23704 1iwlA 182 6.11e+01 b.125.1.1 83757 1ifyA 49 6.13e+01 a.5.2.1 71207 1bx4A 345 6.16e+01 1bx4A c.72.1.1 34935 1w99A 558 6.18e+01 1sffA 426 6.18e+01 c.67.1.4 105482 1yy6A 155 6.18e+01 2cy2A 174 6.21e+01 1k8mA 93 6.25e+01 b.84.1.1 68314 1qunB 279 6.26e+01 b.2.3.2,b.2.3.2 22411,22412 1z90A 469 6.27e+01 1gv3A 248 6.27e+01 a.2.11.1,d.44.1.1 70585,70586 1zq1C 633 6.31e+01 1a53 247 6.32e+01 1a53 c.1.2.4 28564 1kw4A 89 6.33e+01 a.60.1.2 73077 2f9dA 125 6.34e+01 1hvyA 288 6.40e+01 1bkpA d.117.1.1 41049 1rovA 857 6.42e+01 a.119.1.1,b.12.1.1 97674,97675 1w77A 228 6.44e+01 1rm6B 324 6.46e+01 1e4mM 501 6.52e+01 1e70M c.1.8.4 59226 1oi7A 288 6.53e+01 c.2.1.8,c.23.4.1 87049,87050 1t9bA 677 6.63e+01 1fjrA 195 6.63e+01 1fjrA b.102.1.1 59855 1xtqA 177 6.65e+01 2bz6H 254 6.66e+01 1x67A 146 6.66e+01 1d4xG 126 6.72e+01 1d0nA d.109.1.1 59109 1l7yA 94 6.74e+01 d.15.1.6 73676 1enp 312 6.77e+01 1enp c.2.1.2 29906 1xtlA 175 6.79e+01 1egpA 45 6.84e+01 1egpA d.40.1.1 38561 2bb3A 221 6.85e+01 1xtoA 311 6.86e+01 1fm0E 150 6.86e+01 1fmaE d.41.5.1 38629 1t3qB 788 6.91e+01 d.41.1.1,d.133.1.1 106369,106370 1yloA 348 6.92e+01 1fcjA 322 6.94e+01 1oasA c.79.1.1 35289 2g8mA 264 6.99e+01 2bw4A 340 7.05e+01 1d7oA 297 7.06e+01 1enp c.2.1.2 29907 1iieA 75 7.10e+01 1iieA a.109.1.1 19039 2f7fA 494 7.11e+01 2g8oA 264 7.12e+01 1a79A 171 7.13e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1l1dA 152 7.16e+01 b.88.1.3 73452 1klfB 279 7.20e+01 b.2.3.2,b.2.3.2 72684,72685 1fa8A 135 7.24e+01 1qipA d.32.1.1 38486 1zxxA 319 7.24e+01 1hw7A 255 7.30e+01 1i7fA d.193.1.1 61297 1r4aA 165 7.31e+01 c.37.1.8 96986 1snrA 341 7.35e+01 b.6.1.3,b.6.1.3 105823,105824 1viuA 203 7.41e+01 d.113.1.1 100771 1id2A 106 7.43e+01 1aac b.6.1.1 62288 1yfuA 174 7.43e+01 1eq9A 222 7.50e+01 5ptp b.47.1.2 26068 1c9oA 66 7.53e+01 1mjc b.40.4.5 25325 1zm0A 114 7.55e+01 1aac 105 7.57e+01 1aac b.6.1.1 22838 1r7lA 110 7.58e+01 d.277.1.1 104837 1evfA 264 7.59e+01 1bkpA d.117.1.1 40932 2c3zA 222 7.61e+01 1ojhA 65 7.62e+01 a.214.1.1 103976 1qqqA 264 7.63e+01 1bkpA d.117.1.1 40931 2ahuA 531 7.71e+01 1voqa 90 7.75e+01 1xe1A 116 7.83e+01 b.43.3.1 109571 1ow1A 195 7.90e+01 b.131.1.3 93625 1sdjA 310 7.91e+01 d.21.1.2,d.21.1.2 98807,98808 1kcbA 340 7.95e+01 b.6.1.3,b.6.1.3 90951,90952 1wvhA 134 7.95e+01 1p99A 295 7.98e+01 c.94.1.1 94384 2plc 274 7.99e+01 2plc c.1.18.2 29614 1bqhG 129 7.99e+01 1cd8 b.1.1.1 19715 1h30A 422 7.99e+01 b.29.1.4,b.29.1.4 76604,76605 1evuA 731 8.00e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1ikpA 613 8.09e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1igs 248 8.12e+01 1a53 c.1.2.4 28565 1ze3H 122 8.12e+01 1rzmA 338 8.14e+01 c.1.10.4 105137 1uwzA 136 8.30e+01 c.97.1.1 108081 1gvhA 396 8.30e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1orrA 347 8.41e+01 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100016,100017,100018