# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1umgA 362 2.94e-01 1o8uA 257 4.70e-01 c.14.1.3 81194 1ho1A 242 5.17e-01 1ho1A c.1.24.1 61097 1abrA 251 8.53e-01 1mrj d.165.1.1 42196 1p32C 209 1.10e+00 1p32A d.25.1.1 38381 1szoA 257 1.12e+00 1jkmA 358 1.17e+00 1jkmA c.69.1.2 34633 1p32A 209 1.32e+00 1p32A d.25.1.1 38379 1m5wA 243 1.46e+00 c.1.24.1 84836 1jkmB 361 1.56e+00 1jkmA c.69.1.2 34634 1pgx 83 2.01e+00 2igd d.15.7.1 37823 1mg7A 417 2.55e+00 d.14.1.6 84954 d.58.26.6 84955 1v7rA 186 2.58e+00 c.51.4.1 -7546 1vkdA 338 3.25e+00 1vk3A 615 3.55e+00 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1mumA 295 3.55e+00 c.1.12.7 85108 1az3A 244 3.60e+00 1rvaA c.52.1.2 33276 1sqzA 121 3.71e+00 a.133.1.2 -1971 1tj9A 121 3.71e+00 1tk4A 121 3.71e+00 1sx5A 244 3.95e+00 c.52.1.2 -7551 1igd 61 3.98e+00 2igd d.15.7.1 37822 2igd 61 3.98e+00 2igd d.15.7.1 37821 1jae 471 4.14e+00 1smd b.71.1.1 27773 c.1.8.1 28760 1rvaA 244 4.17e+00 1rvaA c.52.1.2 33240 1ezwA 349 4.33e+00 1ezwA c.1.16.3 29558 2reb 352 4.41e+00 2reb c.37.1.11 32282 d.48.1.1 38767 1pbuA 162 4.50e+00 d.58.46.1 88030 1bxrA 1073 4.60e+00 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1fv0A 121 4.86e+00 a.133.1.2 70147 1kpmA 121 5.04e+00 a.133.1.2 72844 1keeE 1073 5.15e+00 a.92.1.1 68508 c.24.1.1 68509 c.30.1.1 68510 c.30.1.1 68511 d.142.1.2 68512 d.142.1.2 68513 1eonA 245 5.20e+00 1rvaA c.52.1.2 33238 1kczA 413 5.33e+00 c.1.11.2 68451 d.54.1.1 68452 1g291 372 5.48e+00 1g291 1f1xA 322 5.71e+00 d.32.1.3 83208 d.32.1.3 83209 1c3oG 1073 5.76e+00 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1vhh 162 5.95e+00 1vhh d.65.1.2 39550 1jdbB 1073 5.96e+00 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1p9oA 313 6.19e+00 unknown_sccs -8423 1tljA 213 6.23e+00 1f1uA 323 6.46e+00 d.32.1.3 83200 d.32.1.3 83201 1eulA 994 6.49e+00 1eulA 1no5A 114 6.68e+00 unknown_sccs -9785 1a3gA 308 6.69e+00 1daaA e.17.1.1 43286 1vizA 240 6.73e+00 c.1.4.1 -5212 2rveA 244 6.76e+00 1rvaA c.52.1.2 33283 1lshA 1056 6.77e+00 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1qm9A 198 6.81e+00 1qm9A d.58.7.1 39207 d.58.7.1 39208 1keeG 1073 6.87e+00 a.92.1.1 68516 c.24.1.1 68517 c.30.1.1 68518 c.30.1.1 68519 d.142.1.2 68520 d.142.1.2 68521 1hx0A 496 7.29e+00 b.71.1.1 61346 c.1.8.1 61347 1pkoA 139 7.93e+00 b.1.1.1 88147 1cxvA 164 8.04e+00 1ck7A d.92.1.11 40404 1h8uA 117 8.15e+00 1h8uA d.169.1.1 60793 1iwgA 1053 8.15e+00 d.58.44.1 76874 d.58.44.1 76875 d.58.44.1 76876 d.58.44.1 76877 d.225.1.1 76878 d.225.1.1 76879 f.35.1.1 76880 f.35.1.1 76881 1hnoA 280 8.24e+00 1hnoA c.14.1.3 61095 1su4A 994 8.43e+00 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1b25A 619 8.66e+00 1b25A a.110.1.1 19044 d.152.1.1 41796 1bxdA 161 8.69e+00 1bxdA d.122.1.3 41111 1l2tA 235 8.73e+00 c.37.1.12 73514 1oyeA 1049 8.77e+00 d.58.44.1 87587 d.58.44.1 87588 d.58.44.1 87589 d.58.44.1 87590 d.225.1.1 87591 d.225.1.1 87592 f.35.1.1 87593 f.35.1.1 87594 1hh1A 143 9.23e+00 1gefA c.52.1.18 61036 1mvfD 82 9.44e+00 b.129.1.1 85143 1ck7A 631 9.68e+00 1ck7A a.20.1.2 58969 b.66.1.1 27538 d.92.1.11 58970 g.14.1.2 44674 g.14.1.2 44675 g.14.1.2 44676 1iyeA 309 1.01e+01 e.17.1.1 83786 8ohm 435 1.02e+01 1heiA c.37.1.14 32469 c.37.1.14 32470 1egzA 291 1.03e+01 7a3hA c.1.8.3 28828 1cs0C 1073 1.05e+01 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1o50A 157 1.06e+01 d.37.1.1 -9604 d.37.1.1 -9605 1hnuA 280 1.08e+01 1hnoA c.14.1.3 61096 1edt 271 1.13e+01 2ebn c.1.8.5 28993 1c3oE 1073 1.14e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1oi7A 288 1.15e+01 c.2.1.8 87049 c.23.4.1 87050 1bglA 1023 1.16e+01 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.5.1 24358 c.1.8.3 28857 830cA 168 1.16e+01 1ck7A d.92.1.11 40400 1psuA 140 1.19e+01 d.38.1.5 88285 1a9xA 1058 1.19e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 2bifA 469 1.20e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1bif 469 1.20e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1n91A 108 1.23e+01 d.206.1.1 80326 1o5zA 442 1.26e+01 c.59.1.2 -7939 c.72.2.2 -8418 1c3oA 1073 1.26e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1qgwA 76 1.30e+01 1qgwA d.184.1.1 42616 1m2rA 327 1.31e+01 d.144.1.7 84760 1r89A 437 1.33e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1i1kA 309 1.35e+01 1daaA e.17.1.1 61533 1pvmA 184 1.36e+01 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1juk 248 1.37e+01 1a53 c.1.2.4 28567 1mhxA 65 1.38e+01 d.15.7.1 79134 3bifA 468 1.39e+01 1bif c.37.1.7 31962 c.60.1.4 34008 1gd1O 334 1.41e+01 1dssG c.2.1.3 29962 d.81.1.1 39877 1c3oC 1073 1.43e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1t6aA 126 1.44e+01 1keeC 1073 1.44e+01 a.92.1.1 68500 c.24.1.1 68501 c.30.1.1 68502 c.30.1.1 68503 d.142.1.2 68504 d.142.1.2 68505 1cnv 299 1.49e+01 1cnv c.1.8.5 28989 1heiA 451 1.49e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 1g94A 448 1.52e+01 b.71.1.1 65169 c.1.8.1 65170 1fm0E 150 1.58e+01 1fmaE d.41.5.1 38629 1igs 248 1.59e+01 1a53 c.1.2.4 28565 1erzA 303 1.60e+01 1erzA d.160.1.2 59498 1jxpA 186 1.63e+01 1jxpA b.47.1.3 26402 1nf3C 128 1.63e+01 b.36.1.1 85596 1aqm 453 1.64e+01 1smd b.71.1.1 27717 c.1.8.1 28704 1nfkA 325 1.67e+01 1a3qA b.1.18.1 21929 b.2.5.3 22444 1b88A 114 1.67e+01 1tcrA b.1.1.1 20608 1uf5A 303 1.68e+01 1dp0A 1023 1.69e+01 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1keeA 1073 1.71e+01 a.92.1.1 68492 c.24.1.1 68493 c.30.1.1 68494 c.30.1.1 68495 d.142.1.2 68496 d.142.1.2 68497 1djxA 624 1.73e+01 1djxB a.39.1.7 17342 b.7.1.1 23159 c.1.18.1 29587 1qwgA 251 1.75e+01 unknown_sccs -5678 1nq6A 302 1.77e+01 c.1.8.3 -5332 1fmaE 150 1.78e+01 1fmaE d.41.5.1 38630 1vh5A 148 1.78e+01 d.38.1.5 -9677 1rm4A 337 1.80e+01 2gd1O 334 1.83e+01 1dssG c.2.1.3 29978 d.81.1.1 39893 1qatB 622 1.91e+01 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 1smd 496 2.01e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1djxB 624 2.02e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1o5hA 214 2.11e+01 unknown_sccs -1078 1qfoC 119 2.11e+01 1qfoA b.1.1.1 19710 1f07A 321 2.13e+01 1ezwA c.1.16.3 59560 1mngA 203 2.16e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 1rpxA 230 2.17e+01 1rpxA c.1.2.2 28536 1a79A 171 2.29e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1bzsA 165 2.30e+01 1hfc d.92.1.11 40348 1cjaA 342 2.41e+01 1cjaA d.144.1.3 41708 1oa8A 133 2.41e+01 unknown_sccs -5142 1ac5 483 2.53e+01 1ac5 c.69.1.5 34653 1ujxA 119 2.54e+01 b.26.1.2 -3325 1dysA 348 2.54e+01 1bvwA c.6.1.1 30669 1kb5A 115 2.57e+01 1tvdA b.1.1.1 20611 1qfoA 119 2.60e+01 1qfoA b.1.1.1 19708 1mnmA 100 2.66e+01 1mnmA d.88.1.1 40232 1auiB 169 2.67e+01 1auiB a.39.1.5 17325 1dekA 241 2.69e+01 1dekA c.37.1.1 31842 3proD 166 2.70e+01 3proC d.52.1.1 38814 d.52.1.1 38815 1dj8A 89 2.77e+01 1bg8A a.57.1.1 17919 1byrA 155 2.80e+01 1byrA d.136.1.1 41450 1a53 247 2.83e+01 1a53 c.1.2.4 28564 1j31A 262 2.86e+01 d.160.1.2 -11473 1rj9A 304 2.90e+01 a.24.13.1 -631 c.37.1.10 -7129 1un7A 400 2.92e+01 b.92.1.5 -5077 c.1.9.10 -5429 1pbjA 125 2.98e+01 d.37.1.1 -9608 d.37.1.1 -9609 1o12A 376 3.02e+01 b.92.1.5 80758 c.1.9.10 80759 1gvfA 286 3.03e+01 c.1.10.2 70599 1f4lA 551 3.08e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1iq6A 134 3.09e+01 d.38.1.4 76755 1g55A 343 3.21e+01 1g55A c.66.1.26 34247 1bzyA 217 3.23e+01 1qk3A c.61.1.1 34071 1gvmA 136 3.27e+01 b.109.1.1 70612 1i76A 163 3.28e+01 1hfc d.92.1.11 61877 1exbA 332 3.29e+01 1qrqA c.1.7.1 28666 1dm0A 287 3.30e+01 1dm0A d.165.1.2 42227 1qrqA 325 3.30e+01 1qrqA c.1.7.1 28667 1qvzA 237 3.32e+01 c.23.16.2 -6537 1gv3A 248 3.35e+01 a.2.11.1 70585 d.44.1.1 70586 3proC 166 3.37e+01 3proC d.52.1.1 38812 d.52.1.1 38813 2ucz 165 3.46e+01 1u9aA d.20.1.1 38330 1rw7A 243 3.48e+01 c.23.16.2 -6530 1xxcA 78 3.49e+01 1xxaA d.74.2.1 39712 1v93A 296 3.52e+01 c.1.23.1 -5654 1bncB 449 3.53e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1dv1A 449 3.55e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1s2wA 295 3.59e+01 c.1.12.7 -5577 2ifeA 100 3.61e+01 1tig d.68.1.1 39567 1imoA 88 3.66e+01 1imoA c.15.1.2 62590 1jslA 327 3.69e+01 c.88.1.1 67233 2pii 112 3.69e+01 2pii d.58.5.1 39071 1nls 237 3.71e+01 1nls b.29.1.1 23928 1jysA 242 3.77e+01 c.56.2.1 77216 1j3wA 163 3.80e+01 unknown_sccs -10870 1jsrA 327 3.80e+01 c.88.1.1 67237 1b5tA 275 3.81e+01 1b5tA c.1.23.1 29676 1eq6A 189 3.95e+01 1eq6A d.107.1.1 40796 1gypA 358 3.97e+01 1dssG c.2.1.3 30004 d.81.1.1 39919 1mxgA 435 4.00e+01 b.71.1.1 85193 c.1.8.1 85194