# List of top-scoring protein chains for t2k-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 1gz8A 299 1.24e-36 d.144.1.7 83405 1hcl 298 1.42e-36 1hcl d.144.1.7 41593 1e1xA 299 1.72e-36 1hcl d.144.1.7 59157 1jvpP 298 2.02e-36 d.144.1.7 67371 1cmkE 350 2.74e-36 1cdkA d.144.1.7 41623 1cdkA 350 3.16e-36 1cdkA d.144.1.7 41620 1xh9A 350 3.17e-36 1q8uA 350 3.77e-36 d.144.1.7 96230 1apmE 350 8.27e-36 1cdkA d.144.1.7 41628 1o6lA 337 1.11e-35 d.144.1.7 81092 1mq4A 272 1.49e-35 d.144.1.7 91391 1yhvA 297 1.63e-35 2bdwA 362 1.74e-35 2bfxA 284 2.25e-35 1rdqE 350 2.30e-35 d.144.1.7 97314 2f57A 317 2.70e-35 1xjdA 345 2.73e-35 1f3mC 297 9.86e-35 1hcl d.144.1.7 41677 1phk 298 1.15e-34 1cdkA d.144.1.7 41635 2c30A 321 2.50e-34 1zrzA 364 4.86e-34 1h1wA 289 6.91e-34 d.144.1.7 83460 1jksA 294 9.65e-34 d.144.1.7 71710 1uu3A 310 1.28e-33 d.144.1.7 99999 1kobA 387 2.62e-33 1tkiA d.144.1.7 41640 1blxA 326 4.78e-33 1hcl d.144.1.7 41596 2b9hA 353 9.15e-33 1tvoA 368 1.00e-32 3erk 364 1.32e-32 1hcl d.144.1.7 41654 1p4fA 293 1.34e-32 d.144.1.7 104063 1wbsA 360 1.87e-32 1r3cA 366 2.89e-32 d.144.1.7 96906 1pmnA 364 3.55e-32 d.144.1.7 94907 1vzoA 355 4.47e-32 d.144.1.7 108971 1ia8A 289 4.53e-32 1ia8A d.144.1.7 62112 2eueA 279 6.11e-32 1zz2A 360 6.17e-32 1zzlA 351 6.63e-32 1pme 380 7.24e-32 1hcl d.144.1.7 41653 1ywrA 360 1.51e-31 1s9jA 341 2.32e-31 2gfsA 372 2.89e-31 1t4hA 290 4.76e-31 d.144.1.7 106420 1o6yA 299 5.52e-31 d.144.1.7 81106 1q41A 424 8.89e-31 d.144.1.7 95774 1j1bA 420 9.11e-31 d.144.1.7 90758 1omwA 689 1.28e-30 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 2ac5A 316 4.90e-30 2bvaA 292 8.42e-30 2evaA 307 1.05e-29 1tkiA 321 1.22e-29 1tkiA d.144.1.7 41638 1ymiA 334 1.66e-29 1opjA 293 2.01e-29 d.144.1.7 87230 1zy4A 303 2.26e-29 2ac3A 316 2.40e-29 3lck 271 2.50e-29 1fmk d.144.1.7 41686 1qpcA 279 2.67e-29 1fgkA d.144.1.7 41685 2bikB 313 3.02e-29 1xwsA 313 3.18e-29 1fmk 452 1.00e-28 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1lpuA 332 1.04e-28 d.144.1.7 74177 1lp4A 332 1.08e-28 d.144.1.7 74170 1m2rA 327 1.13e-28 d.144.1.7 84760 1om1A 332 1.77e-28 d.144.1.7 93347 1lufA 343 2.34e-28 d.144.1.7 78223 1a6o 332 2.48e-28 1a6o 2a19B 284 2.75e-28 1mp8A 281 3.84e-28 d.144.1.7 91384 1jpaA 312 5.64e-28 d.144.1.7 67011 2b7aA 293 6.48e-28 1fvrA 327 8.94e-28 d.144.1.7 60047 1z57A 339 1.15e-27 1ir3A 306 1.24e-27 1fmk d.144.1.7 41702 1t46A 313 1.56e-27 d.144.1.7 106397 1xbbA 291 2.72e-27 1irk 306 3.98e-27 1fmk d.144.1.7 41703 1p4oA 322 5.46e-27 d.144.1.7 87775 1u59A 287 6.01e-27 d.144.1.7 107681 1jqhA 308 8.93e-27 d.144.1.7 71793 1r0pA 312 1.27e-26 d.144.1.7 96734 1x8bA 289 1.72e-26 2eu9A 355 1.87e-26 1fgkA 310 2.00e-26 1fgkA d.144.1.7 41693 1u46A 291 2.04e-26 d.144.1.7 107656 1jwhA 337 2.28e-26 d.144.1.7 71913 1howA 373 7.69e-26 1hcl d.144.1.7 41679 1ywnA 316 1.17e-25 1q8yA 373 1.71e-25 d.144.1.7 96234 1wbpA 397 1.74e-24 1vjyA 303 1.49e-22 d.144.1.7 108633 1b6cB 342 2.55e-22 1b6cB d.144.1.7 41673 1py5A 326 3.20e-22 d.144.1.7 104389 1ckiA 317 7.78e-20 1csn d.144.1.7 41660 1csn 298 6.73e-19 1csn d.144.1.7 41664 1tqmA 282 1.84e-07 a.4.5.56,d.144.1.9 107236,107237 1zarA 282 1.98e-07 1zthA 258 5.61e-05 1e7uA 961 1.28e-03 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1e8xA 961 2.03e-03 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1e8yA 966 2.77e-03 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1j7lA 264 2.03e-02 d.144.1.6 62697 1nd4A 264 2.34e-02 d.144.1.6 91815 2bkkA 264 1.47e-01 1f2hA 169 3.49e-01 1f3vA d.58.22.1 59612 1f3vA 179 3.97e-01 1f3vA d.58.22.1 39382 1b24A 188 4.58e-01 1b24A d.95.2.1,d.95.2.1 40573,40574 1j7iA 264 4.78e-01 1j7iA d.144.1.6 62694 2exrA 524 5.27e-01 1vzyA 291 6.27e-01 1i50K 120 7.33e-01 d.74.3.2 61765 2ghpA 292 7.53e-01 2av5A 120 9.06e-01 2a6mA 155 1.01e+00 1ifqA 138 1.17e+00 1ifqA d.110.4.1 62350 1kcfA 258 1.35e+00 a.140.2.1,c.55.3.7 68434,68435 1vgjA 184 1.55e+00 1z5oA 242 1.65e+00 2bfdA 400 1.78e+00 1gw5S 142 1.82e+00 d.110.4.2 70633 1coy 507 1.92e+00 1b8sA c.3.1.2,d.16.1.1 30333,37864 1cjaA 342 1.97e+00 1cjaA d.144.1.3 41708 1txqA 93 1.98e+00 2ap1A 327 2.05e+00 1twfK 120 2.07e+00 2fb0A 94 2.11e+00 3cox 507 2.25e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 1r89A 437 2.26e+00 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 2b7oA 464 2.60e+00 1uebA 184 2.64e+00 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1uetA 437 2.66e+00 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1b8sA 504 2.74e+00 1b8sA c.3.1.2,d.16.1.1 30335,37866 1b4vA 504 2.84e+00 1b8sA c.3.1.2,d.16.1.1 30334,37865 1ijhA 504 2.89e+00 c.3.1.2,d.16.1.1 66161,66162 2bfgA 503 3.04e+00 1wf3A 301 3.16e+00 1mxtA 504 3.18e+00 c.3.1.2,d.16.1.1 79671,79672 1aipC 196 3.18e+00 1tfe a.5.2.2,d.43.1.1 58930,58931 1xwyA 264 3.18e+00 1n1pA 504 3.20e+00 c.3.1.2,d.16.1.1 91546,91547 1n4wA 504 3.20e+00 c.3.1.2,d.16.1.1 91676,91677 1vdxA 184 3.25e+00 1t9bA 677 3.36e+00 2bs9A 503 3.36e+00 1ttwA 138 3.40e+00 d.198.1.1 107308 1hh2P 344 3.50e+00 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1v1rA 400 3.50e+00 c.36.1.11 108272 1lci 550 3.55e+00 1lci e.23.1.1 43349 1jysA 242 3.59e+00 c.56.2.1 77216 1i50C 318 3.63e+00 d.74.3.1,d.181.1.1 61756,61757 1x7yA 400 3.67e+00 1tcoA 375 3.73e+00 1auiA d.159.1.3 42084 1k3eA 156 3.74e+00 d.198.1.1 68103 1z5nA 242 3.79e+00 1josA 128 4.31e+00 d.52.7.1 84191 1xkpC 143 4.45e+00 1pixA 587 4.63e+00 c.14.1.4 94708 1vhwA 253 4.69e+00 c.56.2.1 100706 1quqA 129 4.98e+00 1quqA b.40.4.3 25303 1yixA 265 5.10e+00 1jscA 630 5.17e+00 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1szhA 161 5.33e+00 a.226.1.1 106157 1auiA 521 5.51e+00 1auiA d.159.1.3 42085 1c9bB 180 5.64e+00 1ytbA d.129.1.1,d.129.1.1 41216,41217 1q8bA 105 6.14e+00 d.58.4.6 96201 1ncx 162 6.35e+00 1ncx a.39.1.5 17222 1zbfA 142 6.41e+00 1vlyA 338 6.75e+00 b.44.2.1,d.250.1.1 108871,108872 2cb2A 318 6.76e+00 1twfC 318 6.80e+00 1hw8A 467 6.83e+00 1dqaA d.58.20.1,d.179.1.1 61298,61299 1rpuA 172 6.96e+00 d.255.1.1 97716 1o97C 264 7.09e+00 c.26.2.3 81232 1k38A 254 7.21e+00 e.3.1.1 84303 1dy9A 187 7.34e+00 1jxpA b.47.1.3 26400 1i58A 189 7.55e+00 1b3qA d.122.1.3 61773 2fyxA 143 7.68e+00 1olsA 400 7.78e+00 c.36.1.11 93331 1n9bA 265 7.94e+00 e.3.1.1 85463 1a99A 344 8.07e+00 1pot c.94.1.1 35812 1x7vA 99 8.34e+00 d.58.4.11 109501 1gyxA 76 8.42e+00 d.80.1.1 76387 1itwA 741 8.65e+00 c.77.1.2 76793 1wchA 315 8.72e+00 1iuhA 198 8.82e+00 d.61.1.2 83711 1prtA 234 8.90e+00 1bcpA d.166.1.1 42253 1btkA 169 8.96e+00 1btkA b.55.1.1 26959 2b3hA 329 9.17e+00 1chuA 540 9.43e+00 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1xfsA 178 9.45e+00 d.129.3.5 109589 1yqyA 523 9.52e+00 1top 162 9.54e+00 1ncx a.39.1.5 17223 1e4fT 419 9.63e+00 1e4fT c.55.1.1,c.55.1.1 33453,33454 1ifrA 121 9.86e+00 b.1.16.1 71203 1dqaA 467 9.93e+00 1dqaA d.58.20.1,d.179.1.1 39364,42585 1jzuA 157 1.04e+01 b.60.1.1 84271 1ia9A 280 1.04e+01 1ia9A d.144.1.5 62113 1j6oA 268 1.05e+01 c.1.9.12 77088 1w6uA 302 1.06e+01 1b55A 169 1.08e+01 1btkA b.55.1.1 26963 1seiA 130 1.08e+01 1seiA d.140.1.1 41463 1jyoA 130 1.10e+01 d.198.1.1 67483 1vjhA 122 1.11e+01 d.129.3.1 100811 1em2A 229 1.12e+01 1em2A d.129.3.2 41321 1j7nA 776 1.18e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1y0hA 105 1.19e+01 1ptoA 244 1.22e+01 1bcpA d.166.1.1 42257 1cdwA 179 1.22e+01 1ytbA d.129.1.1,d.129.1.1 41212,41213 1umgA 362 1.22e+01 d.280.1.1 107956 1f8rA 498 1.22e+01 1f8rA c.3.1.2,d.16.1.5 30410,37974 1ki9A 192 1.23e+01 c.37.1.1 84404 1gifA 115 1.26e+01 1dptA d.80.1.3 39837 1vheA 373 1.27e+01 b.49.3.1,c.56.5.4 100669,100670 1m2oA 768 1.28e+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 1ln1A 214 1.28e+01 d.129.3.2 74038 1jmvA 141 1.35e+01 c.26.2.4 66897 1m0qA 433 1.36e+01 c.67.1.4 78350 1f4qA 165 1.38e+01 1alvA a.39.1.8 17360 1souA 194 1.39e+01 c.124.1.6 105858 1dqaC 467 1.43e+01 1dqaA d.58.20.1,d.179.1.1 39366,42587 2ch4A 320 1.44e+01 1bcpA 235 1.46e+01 1bcpA d.166.1.1 42255 1nw1A 429 1.46e+01 d.144.1.8 86286 1e7rA 321 1.47e+01 1bsvA c.2.1.2 29808 1zynA 202 1.50e+01 1vr4A 103 1.54e+01 1auvA 311 1.56e+01 1auvA c.30.1.5,d.142.1.3 31723,41558 1b8aA 438 1.56e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1i27A 73 1.58e+01 1i27A a.4.5.30 61555 2bvwA 362 1.60e+01 1bvwA c.6.1.1 30666 1j7nB 776 1.62e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 1r5mA 425 1.62e+01 1w85A 368 1.64e+01 1ocnA 362 1.65e+01 c.6.1.1 86808 1booA 323 1.68e+01 1booA c.66.1.11 34248 1bvwA 360 1.70e+01 1bvwA c.6.1.1 30668 2as0A 396 1.71e+01 1oc7A 364 1.73e+01 c.6.1.1 86794 1k94A 165 1.79e+01 a.39.1.8 68333 1k0dA 260 1.83e+01 a.45.1.1,c.47.1.5 67930,67931 1qs0A 407 1.83e+01 1qs0A c.36.1.11 31829 1fqgA 263 1.84e+01 1btl e.3.1.1 42699 1zuwA 272 1.89e+01 1lp8A 254 1.90e+01 d.165.1.1 91082 2ebn 289 1.92e+01 2ebn c.1.8.5 28990 1gd0A 122 1.92e+01 1dptA d.80.1.3 39834 1b4cA 92 1.94e+01 1b4cA a.39.1.2 17169 1on3A 523 1.95e+01 c.14.1.4,c.14.1.4 87107,87108 1dzkA 157 1.99e+01 1obpA b.60.1.1 27096 1xgsA 295 2.00e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1g6wA 261 2.01e+01 1hqoA a.45.1.1,c.47.1.5 17751,33045 1rl0A 255 2.01e+01 1btkB 169 2.01e+01 1btkA b.55.1.1 26960 2acvA 463 2.02e+01 1ry9A 145 2.03e+01 d.198.1.1 98094 1xkpB 124 2.06e+01 1l1qA 186 2.07e+01 c.61.1.1 77653 1ermA 263 2.08e+01 1btl e.3.1.1 42690 1ax0 239 2.08e+01 1led b.29.1.1 24042 1btl 263 2.10e+01 1btl e.3.1.1 42691 1reoA 486 2.11e+01 c.3.1.2,d.16.1.5 97325,97326 1io2A 213 2.11e+01 1ekeA c.55.3.1 62612 1zwyA 185 2.12e+01 1k6zA 141 2.12e+01 d.198.1.1 68247 1lenA 181 2.14e+01 1led b.29.1.1 24032 1k6wA 426 2.15e+01 b.92.1.2,c.1.9.5 68236,68237 2ddrA 306 2.17e+01 1s3aA 102 2.17e+01 1a3yA 149 2.18e+01 1obpA b.60.1.1 27110 2fpnA 216 2.20e+01 1jl2A 156 2.21e+01 c.55.3.1 66822 1nykA 165 2.21e+01 b.33.1.1 86408 1w1oA 534 2.22e+01 d.58.32.4,d.145.1.1 109071,109072 1bwsA 321 2.23e+01 1bsvA c.2.1.2 29812 1t71A 281 2.27e+01 2bw3A 534 2.29e+01 1ru0A 105 2.29e+01 1nrkA 328 2.30e+01 b.44.2.1,d.250.1.1 92089,92090 1sviA 195 2.30e+01 c.37.1.8 106048 1hyuA 521 2.31e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1nu0A 138 2.32e+01 c.55.3.8 92165 1a2xA 159 2.34e+01 1ncx a.39.1.5 17251 1uwsA 489 2.35e+01 c.1.8.4 108073 1qksA 567 2.37e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 2bzlA 325 2.38e+01 1o20A 427 2.38e+01 c.82.1.1 86556 1i8dA 213 2.40e+01 b.43.4.3,b.43.4.3 61953,61954 1kyqA 274 2.40e+01 c.2.1.11,e.37.1.1 73281,73282 1twdA 256 2.42e+01 c.1.30.1 107397 1vrpA 381 2.43e+01 1mfiA 114 2.43e+01 1dptA d.80.1.3 39856 1qm4A 396 2.43e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1gfsA 321 2.44e+01 c.2.1.2 29811 2a9sA 171 2.45e+01 1yb3A 175 2.45e+01 1ecpA 238 2.46e+01 1ecpA c.56.2.1 33775 1bsvA 321 2.46e+01 1bsvA c.2.1.2 29809 1ra0A 430 2.47e+01 1hqoA 258 2.47e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1oygA 447 2.49e+01 b.67.2.2 93726 1sffA 426 2.49e+01 c.67.1.4 105482 1vjeA 166 2.49e+01 d.185.1.2 100807 1wluA 136 2.49e+01 1f93A 104 2.50e+01 1dcpA d.74.1.1 39688 1gtdA 85 2.50e+01 d.284.1.1 76344 2ey4C 82 2.57e+01 1aoqA 567 2.58e+01 1qksA a.3.1.2,b.70.2.1 15934,27692 1s28A 132 2.58e+01 d.198.1.1 105223 1dcpA 104 2.59e+01 1dcpA d.74.1.1 39672 1larA 575 2.65e+01 1larA c.45.1.2,c.45.1.2 32693,32694 4ts1A 319 2.66e+01 2ts1 c.26.1.1 31565 1ng1 294 2.68e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 2aq5A 402 2.68e+01 1t0fA 276 2.68e+01 1regX 122 2.70e+01 1regX d.58.27.1 39406 1drqA 131 2.71e+01 1drmA 1vk8A 106 2.71e+01 d.58.48.1 108636 1rybA 212 2.71e+01 c.56.3.1 98098 1evhA 112 2.71e+01 1evhA b.55.1.4 26997 1e6uA 321 2.72e+01 1bsvA c.2.1.2 29805 1gowA 489 2.73e+01 1qvbA c.1.8.4 28981 1uaaA 673 2.74e+01 1pjr c.37.1.19,c.37.1.19 32401,32402 1nvpD 108 2.76e+01 a.32.1.1,b.56.1.1 92213,92214 1ffh 294 2.76e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1bjt 793 2.77e+01 1bjt e.11.1.1 43249 1t17A 148 2.78e+01 1kutA 230 2.79e+01 d.143.1.1 73017 1jpnA 296 2.79e+01 a.24.13.1,c.37.1.10 67039,67040 1f07A 321 2.80e+01 1ezwA c.1.16.3 59560 2ki5A 366 2.80e+01 1qhiA c.37.1.1 31862 1ls1A 295 2.80e+01 a.24.13.1,c.37.1.10 78170,78171 1g7rA 594 2.82e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1eudA 311 2.82e+01 2scuA 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