# List of top-scoring protein chains for t2k-100-30-alpha 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 1pw4A 451 4.41e-02 1hmcA 148 2.86e-01 1hmcB a.26.1.2 16867 1cjaA 342 4.25e-01 1cjaA d.144.1.3 41708 1odoA 408 5.55e-01 1ah7 245 5.89e-01 1ah7 a.124.1.1 19339 1hmcB 148 6.14e-01 1hmcB a.26.1.2 16868 1fkmA 396 1.04e+00 1fkmA a.69.2.1 18315 a.69.2.1 18316 1l9hA 349 1.05e+00 f.13.1.2 73720 1ppjC 379 1.11e+00 1u19A 349 1.20e+00 1hzxA 349 1.57e+00 1f88A f.13.1.2 61466 1j5sA 463 1.58e+00 c.1.9.8 71580 1lkxA 697 1.59e+00 c.37.1.9 73981 1h2vC 771 1.59e+00 a.118.1.2 76592 a.118.1.2 76593 a.118.1.2 76594 1qjbA 245 1.78e+00 1qjaA a.118.7.1 19202 1n1bA 549 1.97e+00 a.102.4.1 79799 a.128.1.3 79800 1g71A 347 2.04e+00 1g71A e.16.1.1 43268 1mhyB 395 2.28e+00 1mtyB a.25.1.2 16781 1h6kA 757 2.32e+00 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 1qcrC 378 2.32e+00 1be3C f.32.1.1 75931 f.21.1.2 75932 1kb9C 385 2.43e+00 f.32.1.1 77315 f.21.1.2 77316 1ezvC 385 2.61e+00 1be3C f.32.1.1 75833 f.21.1.2 75834 1ezfA 340 2.78e+00 1ezfA a.128.1.2 19440 1f88A 348 3.33e+00 1f88A f.13.1.2 43429 1mhyG 169 3.42e+00 1mtyG a.23.3.1 16518 1fqiA 147 3.62e+00 1agrE a.91.1.1 18542 1lla 628 3.66e+00 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1ajqB 557 3.68e+00 1ajqB 1j4nA 271 3.69e+00 f.19.1.1 71510 1gm9B 557 3.69e+00 1gm7B 557 4.54e+00 1ifa 158 4.56e+00 1ifa a.26.1.3 16892 1gk9B 557 4.68e+00 3crxA 343 5.03e+00 4crxA a.60.9.1 18101 d.163.1.1 42161 1ihgA 370 5.07e+00 2cpl a.118.8.1 62380 b.62.1.1 62381 1gkfB 557 5.10e+00 1be3C 379 5.52e+00 1be3C f.32.1.1 75805 f.21.1.2 75806 1crxA 322 5.58e+00 4crxA a.60.9.1 18097 d.163.1.1 42157 1qbkB 890 5.78e+00 1qbkB a.118.1.1 19127 1e3aB 560 6.30e+00 1ajqB 1r1mA 164 6.33e+00 2pgd 482 6.53e+00 2pgd a.100.1.1 18778 c.2.1.6 30190 1ouoA 210 6.55e+00 1uk8A 282 6.71e+00 1s2xA 206 6.75e+00 1amz 435 6.78e+00 1csh a.103.1.1 18884 1j99A 293 7.08e+00 c.37.1.5 71618 1i36A 264 7.11e+00 a.100.1.8 71108 c.2.1.6 71109 1keyA 235 7.31e+00 a.118.16.1 72389 1c17M 177 7.47e+00 1c17M f.18.1.1 43648 1tbmA 326 7.49e+00 1ku1A 230 7.70e+00 a.118.3.1 72996 1pnkB 557 7.82e+00 1ajqB 1olrA 224 7.97e+00 1jipA 403 7.99e+00 a.104.1.1 66748 1a76 326 8.33e+00 1a76 a.60.7.1 18091 c.120.1.2 33361 1iapA 211 8.34e+00 a.91.1.1 62119 1ll1 590 8.79e+00 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.18.3 21864 1kqfC 217 8.83e+00 f.21.1.1 72874 1b5l 172 9.47e+00 1b5l a.26.1.3 16900 2dri 271 9.73e+00 2dri c.93.1.1 35637 1kbuA 349 9.89e+00 a.60.9.1 72284 d.163.1.1 72285 1hg4A 279 1.03e+01 1lbd a.123.1.1 19333 1dugA 234 1.05e+01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1ichA 112 1.07e+01 a.77.1.2 71182 1gw5B 591 1.08e+01 a.118.1.10 70630 1fo3A 460 1.10e+01 1dl2A a.102.2.1 18845 1b9zA 516 1.10e+01 1b9zA b.3.1.1 22528 c.1.8.1 28798 1eupA 403 1.11e+01 1rom a.104.1.1 18967 1j1jA 240 1.11e+01 1csh 435 1.13e+01 1csh a.103.1.1 18880 4crxA 322 1.14e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1dq3A 454 1.14e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1gx3A 284 1.17e+01 d.3.1.5 70678 1l0lA 446 1.18e+01 d.185.1.1 84482 d.185.1.1 84483 1rr7A 129 1.18e+01 1qlaC 256 1.19e+01 1qlaC f.21.2.1 43722 1a0rP 245 1.20e+01 1b9yC c.47.1.6 33054 1b43A 340 1.21e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1e9lA 377 1.22e+01 1e9lA c.1.8.5 59395 d.26.3.1 59396 2ran 316 1.24e+01 1avc a.65.1.1 18170 1ea3A 164 1.25e+01 1aa7A a.95.1.1 59398 1a8b 318 1.31e+01 1avc a.65.1.1 18171 1xyzA 347 1.31e+01 1taxA c.1.8.3 28804 2bidA 197 1.31e+01 2bidA f.1.4.1 43398 1bib 321 1.32e+01 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1iupA 282 1.33e+01 c.69.1.10 76815 1a8a 318 1.35e+01 1avc a.65.1.1 18169 1ltm 320 1.36e+01 1ltm d.2.1.6 36992 1tljA 213 1.36e+01 1mtyG 162 1.37e+01 1mtyG a.23.3.1 16498 1ehkA 562 1.37e+01 1ehkA f.24.1.1 43624 1s7zA 117 1.38e+01 1ecrA 309 1.38e+01 1ecrA e.2.1.1 42678 1qusA 322 1.38e+01 1ltm d.2.1.6 36991 1ldfA 281 1.40e+01 f.19.1.1 73845 1xsvA 113 1.42e+01 5bcaA 516 1.44e+01 1b9zA b.3.1.1 22529 c.1.8.1 28799 1dofA 403 1.44e+01 1c3cA a.127.1.1 19429 1bp3A 191 1.47e+01 1huw a.26.1.1 16838 1fjgD 209 1.51e+01 1c05A d.66.1.2 39553 1jk0B 345 1.52e+01 a.25.1.2 63143 1pu6A 218 1.52e+01 1gnlA 544 1.52e+01 e.26.1.1 70287 1anxA 319 1.53e+01 1avc a.65.1.1 18161 1ofcX 304 1.54e+01 1tw9A 206 1.54e+01 1qjaA 245 1.55e+01 1qjaA a.118.7.1 19204 1nc5A 373 1.59e+01 a.102.1.6 85548 1eqfA 280 1.60e+01 1eqfA a.29.2.1 16972 a.29.2.1 16973 1n83A 270 1.61e+01 a.123.1.1 80276 1be3A 446 1.62e+01 1be3A d.185.1.1 58950 d.185.1.1 58951 1b77A 228 1.63e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1lvoA 302 1.63e+01 b.47.1.4 74284 1uedA 406 1.64e+01 1qfjA 232 1.69e+01 1qfjA b.43.4.2 25655 c.25.1.1 31545 1f6bA 198 1.69e+01 c.37.1.8 64986 1s6bB 119 1.72e+01 3fapB 94 1.75e+01 1nsgB a.24.7.1 16612 1h5vA 304 1.78e+01 c.1.8.3 70898 1e5rA 290 1.81e+01 1e5rA b.82.2.4 59276 1ib2A 349 1.81e+01 1ib2A a.118.1.8 62141 1t8qA 336 1.83e+01 1r0vA 305 1.86e+01 1pme 380 1.87e+01 1hcl d.144.1.7 41653 1bia 321 1.91e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1so2A 420 1.95e+01 1tn6A 382 1.96e+01 1h7eA 245 1.96e+01 c.68.1.13 60717 1v33A 366 1.99e+01 1aa7A 158 2.03e+01 1aa7A a.95.1.1 18741 1ht6A 405 2.06e+01 b.71.1.1 83629 c.1.8.1 83630 1j8rA 196 2.08e+01 1j8rA b.2.3.3 62745 7a3hA 303 2.09e+01 7a3hA c.1.8.3 28817 1tbfA 347 2.09e+01 1qgrA 876 2.10e+01 1qgrA a.118.1.1 19119 1by2 119 2.14e+01 1by2 d.170.1.1 42452 1wer 334 2.17e+01 1wer a.116.1.2 19108 1h68A 239 2.17e+01 f.13.1.1 60664 1q8yA 373 2.18e+01 1ornA 226 2.19e+01 a.96.1.1 87342 1ld8A 382 2.21e+01 a.118.6.1 73838 1jetA 517 2.23e+01 1jevA c.94.1.1 35718 1q5zA 177 2.25e+01 1utg 70 2.25e+01 1utg a.101.1.1 18813 1jcqA 382 2.26e+01 a.118.6.1 66504 1u4qA 322 2.28e+01 1h2kA 349 2.28e+01 b.82.2.6 76572 1sftA 388 2.35e+01 1bd0A b.49.2.2 26482 c.1.6.1 28644 1rkpA 326 2.38e+01 1rztA 331 2.38e+01 1gkxA 388 2.38e+01 a.29.5.1 65266 d.122.1.4 65267 1howA 373 2.39e+01 1hcl d.144.1.7 41679 1hfoA 113 2.40e+01 d.80.1.3 61006 1fx8A 281 2.45e+01 f.19.1.1 43651 1ppjA 446 2.45e+01 1hqvA 191 2.49e+01 1hqvA a.39.1.8 61160 1n40A 396 2.55e+01 a.104.1.1 79977 2olbA 517 2.59e+01 1jevA c.94.1.1 35721 3erk 364 2.60e+01 1hcl d.144.1.7 41654 1h2sA 225 2.62e+01 f.13.1.1 76578 1qcrA 446 2.65e+01 1be3A d.185.1.1 59025 d.185.1.1 59026 1g2nA 264 2.66e+01 1lbd a.123.1.1 60227 2at9 247 2.67e+01 1c3wA f.13.1.1 43427 1mjgM 729 2.67e+01 e.26.1.3 79204 1bd0A 388 2.69e+01 1bd0A b.49.2.2 26480 c.1.6.1 28642 1b3qA 379 2.71e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 5csmA 256 2.75e+01 5csmA a.130.1.2 19494 1va6A 518 2.76e+01 1mmoG 162 2.77e+01 1mtyG a.23.3.1 16512 1u5pA 216 2.78e+01 1aueA 100 2.79e+01 1nsgB a.24.7.1 16615 1oxa 403 2.79e+01 1f4tA a.104.1.1 18965 1a3h 300 2.80e+01 7a3hA c.1.8.3 28819 1l2tA 235 2.81e+01 c.37.1.12 73514 1pxfA 111 2.86e+01 b.40.4.4 88341 821p 166 2.86e+01 1ctqA c.37.1.8 31969 1jgjA 217 2.87e+01 1c3wA f.13.1.1 62952 1ofv 169 2.89e+01 1rcf c.23.5.1 31184 1qceA 123 2.95e+01 1qbzC h.3.2.1 45750 5p21 166 2.96e+01 1ctqA c.37.1.8 31966 1v5xA 203 2.98e+01 1nsgB 94 2.98e+01 1nsgB a.24.7.1 16613 1ctqA 166 3.02e+01 1ctqA c.37.1.8 31965 1itcA 516 3.06e+01 b.3.1.1 83705 c.1.8.1 83706 2utgA 70 3.07e+01 1utg a.101.1.1 18814 1cznA 169 3.07e+01 1rcf c.23.5.1 31181 1gcvA 140 3.08e+01 1cg5B a.1.1.2 15410 1p9uA 302 3.11e+01 b.47.1.4 88001 1brlA 355 3.11e+01 1lucA c.1.16.1 29553 1ls6A 295 3.17e+01 1rykA 69 3.19e+01 1h1yA 228 3.21e+01 c.1.2.2 76506 1oa4A 222 3.27e+01 b.29.1.11 86731 1elwA 118 3.29e+01 1a17 a.118.8.1 19207 1oaoC 729 3.32e+01 e.26.1.3 86746 1tllA 688 3.38e+01 1gvhA 396 3.45e+01 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1dnpA 471 3.47e+01 1qnf a.99.1.1 18775 c.28.1.1 31630 1hvd 319 3.48e+01 1avc a.65.1.1 18154 1csmA 256 3.48e+01 5csmA a.130.1.2 19495 1kyoC 385 3.52e+01 f.32.1.1 75904 f.21.1.2 75905 1pot 325 3.54e+01 1pot c.94.1.1 35807 1jfaA 374 3.59e+01 a.128.1.5 66622 1wmuA 141 3.60e+01 1aisB 200 3.61e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 2ts1 419 3.62e+01 2ts1 c.26.1.1 31564 1pzlA 237 3.65e+01 1iqrA 420 3.66e+01 a.99.1.1 66275 c.28.1.1 66276 1np7A 489 3.67e+01 a.99.1.1 80677 c.28.1.1 80678 1m1hA 248 3.69e+01 b.114.1.1 78415 d.58.42.1 78416 1envA 123 3.74e+01 1envA h.3.2.1 45726 1k0iA 394 3.75e+01 c.3.1.2 67942 d.16.1.2 67943 1qpaA 345 3.76e+01 1arv a.93.1.1 18585 1rec 201 3.88e+01 1rec a.39.1.5 17326 1e3oC 160 3.93e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 2phh 394 4.00e+01 1pbe c.3.1.2 30353 d.16.1.2 37884