# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1g9oA 91 2.51e-20 1pdr b.36.1.1 60400 1i92A 91 1.37e-19 1pdr b.36.1.1 61990 1tp5A 119 2.12e-18 1bfeA 119 2.15e-18 1pdr b.36.1.1 24775 2fe5A 94 2.60e-18 1be9A 119 3.15e-18 1pdr b.36.1.1 24774 2fneA 117 3.16e-18 1pdr 99 5.20e-18 1pdr b.36.1.1 24771 1n7eA 97 8.24e-17 b.36.1.1 91691 2fcfA 103 2.14e-16 1q3oA 109 4.45e-16 b.36.1.1 95700 1wf7A 103 6.02e-16 2f5yA 91 7.05e-16 1n7fA 97 9.82e-16 b.36.1.1 91692 1ihjA 98 1.14e-15 1pdr b.36.1.1 62382 1qavA 90 1.31e-15 1qauA b.36.1.1 24777 1mfgA 95 2.00e-15 b.36.1.1 79043 1n99A 166 2.46e-15 b.36.1.1,b.36.1.1 85459,85460 1m5zA 91 7.51e-15 b.36.1.1 78676 1v5lA 103 3.26e-14 b.36.1.1 108378 1l6oA 95 3.27e-14 b.36.1.1 84534 1kwaA 88 6.46e-14 1kwaA b.36.1.1 24772 2f0aA 98 6.71e-13 1nf3C 128 8.48e-13 b.36.1.1 85596 1kwaB 88 4.75e-12 1kwaA b.36.1.1 24773 1nteA 82 6.55e-12 b.36.1.1 86163 1qauA 112 8.18e-12 1qauA b.36.1.1 24779 1i16 130 9.06e-12 1i16 b.36.1.2 24787 1r6jA 82 1.05e-11 b.36.1.1 97151 1qavB 115 1.34e-11 1qauA b.36.1.1 24780 1b8qA 127 5.64e-11 1qauA b.36.1.1 24781 1fc6A 388 1.30e-10 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 2.73e-09 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 3.30e-08 1ky9B 448 2.02e-07 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1y8tA 324 5.20e-06 1ky9A 448 7.74e-05 b.36.1.4,b.47.1.1 73198,73199 1sotA 320 1.28e-03 b.36.1.4,b.47.1.1 105852,105853 1fxlA 167 3.24e-02 1b7fA d.58.7.1,d.58.7.1 39183,39184 1y9wA 140 5.56e-02 1cof 143 8.90e-02 1cof d.109.1.2 40860 1db3A 372 9.12e-02 1db3A c.2.1.2 29813 1vc3B 97 1.02e-01 1cfyA 143 1.77e-01 1cof d.109.1.2 40858 1se8A 301 2.44e-01 b.40.4.3 105448 1xk5A 204 3.77e-01 1ti6A 875 5.90e-01 b.52.2.2,c.81.1.1 106974,106975 1cvjA 190 5.95e-01 1cvjB d.58.7.1,d.58.7.1 39191,39192 1qw2A 102 6.52e-01 d.249.1.1 96456 1skyB 502 6.64e-01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1kw4A 89 6.88e-01 a.60.1.2 73077 1r13A 148 7.53e-01 d.169.1.1,h.1.1.1 96782,96783 1yvkA 163 7.76e-01 2ck3A 510 9.10e-01 1x67A 146 9.29e-01 1ugmA 125 9.32e-01 d.15.1.3 107827 1lci 550 9.43e-01 1lci e.23.1.1 43349 2aexA 346 1.02e+00 1bx4A 345 1.04e+00 1bx4A c.72.1.1 34935 1bmfA 510 1.43e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1e79A 510 1.57e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1xebA 150 1.59e+00 1cis 66 1.62e+00 2sniI k.1.1.1 46375 2fl4A 149 1.72e+00 1h8eA 510 1.82e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 2gw6A 123 1.86e+00 1widA 130 2.04e+00 3lck 271 2.19e+00 1fmk d.144.1.7 41686 2c5qA 240 2.31e+00 1n6eA 1071 2.33e+00 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1cvjB 190 2.38e+00 1cvjB d.58.7.1,d.58.7.1 39193,39194 2cwaA 263 2.41e+00 2b4aA 138 2.43e+00 3sxlA 184 2.49e+00 1b7fA d.58.7.1,d.58.7.1 39173,39174 2d4pA 141 2.63e+00 1h9mA 145 2.84e+00 1h9jA b.40.6.2,b.40.6.2 60833,60834 1y9kA 157 2.94e+00 1b7fA 168 2.94e+00 1b7fA d.58.7.1,d.58.7.1 39169,39170 1o8bA 219 3.00e+00 c.124.1.4,d.58.40.1 81180,81181 1k32A 1045 3.12e+00 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1h9jA 145 3.22e+00 1h9jA b.40.6.2,b.40.6.2 60829,60830 1wznA 252 3.27e+00 1i18A 97 3.30e+00 b.43.4.3 61520 1uc2A 481 3.38e+00 d.261.1.1 99161 1jt8A 102 3.59e+00 b.40.4.5 63279 2bfxA 284 3.63e+00 1lkzA 219 3.98e+00 c.124.1.4,d.58.40.1 73991,73992 1ia8A 289 4.05e+00 1ia8A d.144.1.7 62112 2g3aA 152 4.10e+00 1ipiA 123 4.49e+00 c.52.1.18 66255 1dfd 64 4.54e+00 1fxd d.58.1.4 38995 1v7wA 807 4.67e+00 a.102.1.4,b.30.5.3 108411,108412 1zm8A 259 4.72e+00 1ygs 234 4.74e+00 1ygs b.26.1.1 23907 1mek 120 4.83e+00 1erv c.47.1.2 32775 1t3qB 788 5.09e+00 d.41.1.1,d.133.1.1 106369,106370 1um0A 365 5.23e+00 d.258.1.1 107942 1qpcA 279 5.50e+00 1fgkA d.144.1.7 41685 1ylxA 103 5.94e+00 1t6t1 118 5.95e+00 1g8aA 227 6.42e+00 c.66.1.3 90506 1ks2A 219 6.47e+00 c.124.1.4,d.58.40.1 72908,72909 1dax 64 6.49e+00 1fxd d.58.1.4 38996 1v70A 105 6.82e+00 1uheA 97 6.84e+00 1iyhA 198 7.04e+00 a.45.1.1,c.47.1.5 83790,83791 1wmiA 90 7.24e+00 1ebfA 358 7.72e+00 1ebuA c.2.1.3,d.81.1.2 30033,39948 1zhhB 242 8.31e+00 1louA 101 8.48e+00 1ris d.58.14.1 39323 2cqsA 842 8.70e+00 2a19B 284 8.72e+00 1jj2D 176 8.75e+00 1ffkD d.77.1.1 63088 1j1bA 420 8.76e+00 d.144.1.7 90758 2fsxA 148 8.84e+00 1fxrA 64 8.91e+00 1fxd d.58.1.4 38993 1yz7A 188 9.09e+00 1cqmA 101 9.11e+00 1ris d.58.14.1 39321 1hl6A 165 9.96e+00 d.58.7.1 83609 1fl0A 171 1.00e+01 1eujA b.40.4.4 25315 1u4nA 310 1.01e+01 2cvdA 198 1.03e+01 2fsp 124 1.06e+01 1dz3A c.23.1.1 31119 1ifyA 49 1.07e+01 a.5.2.1 71207 2bw3A 534 1.08e+01 2sxl 88 1.13e+01 1b7fA d.58.7.1 39179 1zh2A 121 1.14e+01 1vjuA 309 1.14e+01 d.248.1.1 100835 1vllA 334 1.14e+01 c.2.1.13 108834 1xwsA 313 1.17e+01 1f7sA 139 1.22e+01 1cof d.109.1.2 40857 1eujA 166 1.24e+01 1eujA b.40.4.4 25316 1f60B 94 1.24e+01 1b64 d.58.12.1 39307 1pyoA 167 1.24e+01 c.17.1.1 95370 1wmhB 86 1.25e+01 1mt6A 280 1.32e+01 b.76.2.1,b.85.7.1 79446,79447 2bkfA 87 1.36e+01 1q41A 424 1.37e+01 d.144.1.7 95774 1rwzA 245 1.44e+01 d.131.1.2,d.131.1.2 98005,98006 2ciaA 102 1.45e+01 1m0uA 249 1.49e+01 a.45.1.1,c.47.1.5 78359,78360 1svy 114 1.52e+01 1svy d.109.1.1 40831 1ris 101 1.54e+01 1ris d.58.14.1 39314 2ffjA 300 1.55e+01 1j8fA 323 1.61e+01 1j8fA c.31.1.5 62738 1coaI 64 1.63e+01 2sniI d.40.1.1 38574 1howA 373 1.64e+01 1hcl d.144.1.7 41679 1rqpA 299 1.67e+01 b.141.1.1,c.132.1.1 97754,97755 1mo1A 87 1.68e+01 d.94.1.1 91363 1cozA 129 1.70e+01 1cozA c.26.1.2 31598 1u4cA 349 1.71e+01 b.69.4.2 107666 1qlpA 394 1.72e+01 1ovaA e.1.1.1 42628 1j24A 143 1.73e+01 c.52.1.20 84008 1sfp 114 1.73e+01 1sfp b.23.1.1 23895 1b43A 340 1.73e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 2cc0A 195 1.75e+01 1vqoM 195 1.76e+01 1fr3A 67 1.77e+01 1fr3A b.40.6.1 25436 1mq4A 272 1.78e+01 d.144.1.7 91391 1bcsB 160 1.78e+01 1whtB 1cyx 205 1.78e+01 1cyx b.6.1.2 23023 1evlA 401 1.78e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1q7rA 219 1.80e+01 c.23.16.1 96054 1xjdA 345 1.81e+01 1a62 130 1.83e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1rxwA 336 1.85e+01 a.60.7.1,c.120.1.2 98059,98060 2ew8A 249 1.94e+01 1bo4B 168 1.95e+01 1bo4A d.108.1.1 40799 1vr9A 213 1.97e+01 1ckmA 330 1.98e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 2b7aA 293 1.99e+01 1uzcA 71 2.00e+01 a.159.2.1 100222 1wjuA 100 2.01e+01 1yqbA 100 2.03e+01 1vcoA 550 2.06e+01 c.23.16.1,c.37.1.10 108508,108509 1l0wA 580 2.06e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1qhlA 227 2.07e+01 1qhlA c.37.1.12 32382 1p27B 106 2.08e+01 d.58.7.1 93908 1x47A 98 2.13e+01 1lybA 97 2.15e+01 1smrA b.50.1.2 26857 1ccwB 483 2.17e+01 1cb7B c.1.19.2 29646 2brfA 110 2.17e+01 1uh5A 329 2.19e+01 c.2.1.2 107840 1aiqA 264 2.20e+01 1bkpA d.117.1.1 40967 1s72M 194 2.20e+01 d.12.1.2 105332 1q92A 197 2.22e+01 c.108.1.8 96250 1vctA 205 2.23e+01 1yfqA 342 2.27e+01 1b9mA 265 2.27e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1ymiA 334 2.27e+01 1fx3A 169 2.27e+01 1fx3B d.33.1.1 38524 1qapA 296 2.28e+01 1qpoA c.1.17.1,d.41.2.1 29559,38595 1whsB 153 2.30e+01 1whtB 1gweA 503 2.30e+01 e.5.1.1 70667 1khxA 227 2.31e+01 b.26.1.1 68631 1jzxK 205 2.34e+01 i.1.1.2 67885 1whi 122 2.34e+01 1whi b.39.1.1 24810 1vheA 373 2.40e+01 b.49.3.1,c.56.5.4 100669,100670 2sniI 83 2.41e+01 2sniI d.40.1.1 38573 1whtB 153 2.42e+01 1whtB 1koe 172 2.44e+01 1koe d.169.1.5 42448 1hbzA 498 2.46e+01 1cf9A e.5.1.1 60937 2fvgA 340 2.46e+01 1j2gA 319 2.47e+01 d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4 103824,103825,103826,103827,103828 1rl2A 137 2.47e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1lngA 87 2.47e+01 d.201.1.1 74045 1vs0A 310 2.49e+01 2bolA 314 2.53e+01 2g8mA 264 2.54e+01 2beiA 170 2.55e+01 2b9hA 353 2.57e+01 1fx3B 169 2.58e+01 1fx3B d.33.1.1 38525 1eu1A 780 2.59e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1omoA 322 2.60e+01 c.2.1.13 104017 1cyw 205 2.66e+01 1cyx b.6.1.2 23024 1tzjA 338 2.69e+01 1i6uA 130 2.73e+01 d.140.1.1 61850 1bi0 226 2.74e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16202,18408,24453 1fmk 452 2.75e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1vkcA 158 2.77e+01 1h6kA 757 2.77e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1zh5A 195 2.80e+01 1rxdA 159 2.81e+01 1qo0D 196 2.83e+01 1qo0D c.23.1.3 31125 1vpqA 273 2.83e+01 1r0uA 148 2.85e+01 b.60.1.5 96741 1y1oA 203 2.86e+01 1evfA 264 2.89e+01 1bkpA d.117.1.1 40932 1iukA 140 2.90e+01 c.2.1.8 83712 2bikB 313 2.90e+01 1f1zA 273 2.90e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 2czrA 226 2.95e+01 1gutA 68 2.96e+01 b.40.6.1 65576 1zsyA 357 3.03e+01 1cvrA 435 3.08e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1rutX 188 3.11e+01 1ftkA 279 3.12e+01 1gr2A c.94.1.1 35819 1x3mA 415 3.12e+01 1vj0A 380 3.14e+01 b.35.1.2,c.2.1.1 100786,100787 1dioA 554 3.15e+01 1dioA c.1.19.3 29656 1vr3A 191 3.16e+01 1mtpB 43 3.21e+01 1mh9A 197 3.22e+01 c.108.1.8 79118 2aefA 234 3.22e+01 1h80A 464 3.24e+01 b.80.1.8 65714 1cknA 330 3.26e+01 1ckmA b.40.4.6,d.142.2.3 25360,41587 1vhxA 150 3.28e+01 c.55.3.8 100712 1qf6A 642 3.31e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1yloA 348 3.31e+01 1f5nA 592 3.32e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 2mysC 149 3.35e+01 1wdcC a.39.1.5 17323 1ab7 89 3.36e+01 1ay7B c.9.1.1 30835 1ptf 88 3.37e+01 1ptf d.94.1.1 40549 1bo4A 168 3.45e+01 1bo4A d.108.1.1 40798 1q8uA 350 3.46e+01 d.144.1.7 96230 1hnuA 280 3.49e+01 1hnoA c.14.1.3 61096 1b48A 221 3.50e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1hw7A 255 3.51e+01 1i7fA d.193.1.1 61297 1g7rA 594 3.55e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1g6gA 127 3.55e+01 1g6gA b.26.1.2 23916 1o7iA 119 3.58e+01 b.40.4.3 86642 1vbwA 68 3.63e+01 1zy4A 303 3.64e+01 1l2tA 235 3.64e+01 c.37.1.12 73514 1gr2A 279 3.65e+01 1gr2A c.94.1.1 35825 1zclA 180 3.69e+01 1t5hX 504 3.70e+01 e.23.1.1 106449 1qqqA 264 3.71e+01 1bkpA d.117.1.1 40931 1g65K 211 3.72e+01 d.153.1.4 41907 1g6hA 257 3.73e+01 1gajA c.37.1.12 60318 1zuoA 186 3.78e+01 2d1pC 95 3.79e+01 1z4rA 168 3.80e+01 2ghjA 118 3.82e+01 1y51A 88 3.86e+01 1dazC 99 3.94e+01 1hvc b.50.1.1 26501 1vmeA 410 3.95e+01 c.23.5.1,d.157.1.3 108893,108894 1qfhA 212 3.95e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1d4xG 126 3.96e+01 1d0nA d.109.1.1 59109 1b0fA 218 4.03e+01 1a7s b.47.1.2 26237 1lw6I 64 4.03e+01 d.40.1.1 74294 1oapA 109 4.05e+01 d.79.7.1 92706 1dvh 79 4.05e+01 1c53 a.3.1.1 15802 1to2I 64 4.08e+01 1pcl 355 4.08e+01 1pcl b.80.1.1 28021 1vqoD 177 4.09e+01 1vkkA 154 4.09e+01 d.109.1.2 108669 1imjA 210 4.13e+01 c.69.1.23 71246 1sfjA 238 4.17e+01 1sflA 238 4.19e+01 1ezvE 185 4.20e+01 1rie b.33.1.1,f.23.12.1 59548,59549 1pb1A 416 4.21e+01 c.77.1.1 88014 1x8bA 289 4.24e+01 1vybA 238 4.26e+01 d.151.1.1 108897 1ut7A 171 4.27e+01 b.143.1.1 99906 1r0pA 312 4.27e+01 d.144.1.7 96734 1axwA 265 4.27e+01 1bkpA d.117.1.1 40938 1qgdA 662 4.28e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1pk1B 89 4.28e+01 1scmB 145 4.29e+01 1wdcB a.39.1.5 17304 1dmr 823 4.31e+01 1dmr b.52.2.2,c.81.1.1 26904,35312 2ci9A 102 4.34e+01 1ha1 184 4.35e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 2gcuA 245 4.37e+01 1h72C 296 4.38e+01 d.14.1.5,d.58.26.1 60712,60713 2g1lA 104 4.39e+01 1tin 69 4.40e+01 2sniI d.40.1.1 38580 1jqhA 308 4.40e+01 d.144.1.7 71793 1ybvA 283 4.43e+01 1ybvA c.2.1.2 29948 1pyp 285 4.43e+01 1wgjA b.40.5.1 25409 2a6hA 315 4.44e+01 2g8oA 264 4.46e+01 1h2bA 359 4.46e+01 b.35.1.2,c.2.1.1 90543,90544 2f57A 317 4.46e+01 2cfxA 144 4.48e+01 1s8fA 177 4.49e+01 c.37.1.8 105370 1gmxA 108 4.50e+01 c.46.1.3 65355 1ebuA 358 4.54e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1k1tA 99 4.60e+01 b.50.1.1 71995 1txyA 104 4.61e+01 1y96A 86 4.62e+01 1aba 87 4.63e+01 1aba c.47.1.1 32760 1zoyA 622 4.64e+01 1ztdA 133 4.64e+01 1nmeA 146 4.68e+01 c.17.1.1 85874 2b8wA 328 4.69e+01 1hnoA 280 4.69e+01 1hnoA c.14.1.3 61095 1mjhA 162 4.71e+01 1mjhA c.26.2.4 31639 1pauA 147 4.71e+01 1pauA c.17.1.1 30994 2fclA 169 4.72e+01 1n26A 325 4.73e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1euvA 221 4.74e+01 1euvA d.3.1.7 37133 1xhfA 123 4.74e+01 1iso 416 4.75e+01 1iso c.77.1.1 35065 9apiA 347 4.78e+01 1ovaA e.1.1.1 42630 1n0qA 93 4.78e+01 k.37.1.1 79754 1cb7B 483 4.78e+01 1cb7B c.1.19.2 29648 1hvyA 288 4.78e+01 1bkpA d.117.1.1 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