# 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 1ef8A 261 1.19e-02 1ef8A c.14.1.3 30921 1hzdA 272 1.28e-02 c.14.1.3 65969 1eudA 311 2.16e-02 2scuA c.2.1.8 30312 c.23.4.1 31140 1jx2B 315 3.81e-02 c.37.1.8 67404 1b57A 358 3.85e-02 1dosA c.1.10.2 29177 7odcA 424 4.62e-02 7odcA b.49.2.1 26488 c.1.6.1 28650 1dosA 358 5.36e-02 1dosA c.1.10.2 29175 3pnp 289 1.08e-01 1b8oA c.56.2.1 33763 1pbn 289 1.16e-01 1b8oA c.56.2.1 33771 1nzyA 269 1.22e-01 1nzyA c.14.1.3 30903 1b8oA 284 1.30e-01 1b8oA c.56.2.1 33762 1e5xA 486 2.04e-01 c.79.1.1 59283 1qumA 285 2.14e-01 1qumA c.1.15.1 29393 1qtwA 285 2.30e-01 1qumA c.1.15.1 29392 1dciA 275 2.66e-01 1dciA c.14.1.3 30918 1qo7A 394 2.82e-01 1qo7A c.69.1.11 34697 1d7kA 421 2.88e-01 7odcA b.49.2.1 26486 c.1.6.1 28648 1tyfA 193 3.82e-01 1tyfA c.14.1.1 30885 1exmA 405 4.70e-01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1aipE 405 4.84e-01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1d2nA 272 4.93e-01 1d2nA c.37.1.13 32428 1ecpA 238 5.02e-01 1ecpA c.56.2.1 33775 1e1oA 504 5.32e-01 1lylA b.40.4.1 25258 d.104.1.1 40714 1f2dA 341 5.69e-01 1f2dA c.79.1.1 35298 1j9yA 385 6.40e-01 1j9yA c.1.8.3 62791 1k9sA 237 6.45e-01 c.56.2.1 68359 1c3qA 272 6.86e-01 1c3qA c.72.1.2 34948 1ekqA 272 7.17e-01 1c3qA c.72.1.2 34941 1d3hA 367 7.45e-01 1d3gA c.1.4.1 28601 1qe3A 489 8.75e-01 2bce c.69.1.1 34630 1c7sA 858 9.15e-01 1qba b.1.1.5 21812 b.2.2.3 22408 c.1.8.6 29011 d.92.2.1 40410 1lylA 504 1.04e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 1nsf 273 1.09e+00 1d2nA c.37.1.13 32429 1fxjA 331 1.19e+00 1fwyA b.81.1.4 28062 c.68.1.5 34520 1ecxA 384 1.24e+00 1ecxA c.67.1.3 34431 2scuB 388 1.25e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1gjwA 637 1.31e+00 b.71.1.1 60582 c.1.8.1 60583 1etu 394 1.31e+00 1efcA c.37.1.8 64737 1gjuA 637 1.31e+00 b.71.1.1 60580 c.1.8.1 60581 1eg5A 384 1.31e+00 1ecxA c.67.1.3 34429 2dubE 261 1.35e+00 1nzyA c.14.1.3 30916 1a0cA 438 1.36e+00 1a0cA c.1.15.3 29529 1gs5A 258 1.42e+00 1hv9A 456 1.43e+00 1fwyA b.81.1.4 28060 c.68.1.5 34518 1k3fA 253 1.44e+00 c.56.2.1 68105 1d3gA 367 1.45e+00 1d3gA c.1.4.1 28600 1d2eA 397 1.50e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1wetA 340 1.52e+00 1qpzA a.35.1.5 17093 c.93.1.1 35670 1qpzA 340 1.71e+00 1qpzA a.35.1.5 17097 c.93.1.1 35673 1qba 858 1.78e+00 1qba b.1.1.5 21810 b.2.2.3 22406 c.1.8.6 29009 d.92.2.1 40408 1hnuA 280 1.83e+00 1hnoA c.14.1.3 61096 1lx7A 253 2.01e+00 6ldh 330 2.34e+00 3ldh c.2.1.5 30161 d.162.1.1 42128 1bi5A 389 2.34e+00 1bi5A c.95.1.2 35985 c.95.1.2 35986 1hzgA 295 2.45e+00 1hzgA d.194.1.1 61436 1evyA 366 2.47e+00 1evyA a.100.1.6 18811 c.2.1.6 30215 1efcA 393 2.50e+00 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1ha3A 405 2.73e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1bfd 528 2.96e+00 1bfd c.31.1.3 31745 c.36.1.1 31801 c.36.1.1 31802 3fruA 269 2.99e+00 1agdA b.1.1.2 20657 d.19.1.1 38150 1gewA 356 3.08e+00 1gewA c.67.1.1 60470 1pmi 440 3.10e+00 1pmi b.82.1.3 28114 1ekjA 221 3.23e+00 1ekjB c.53.2.1 33364 1a3h 300 3.25e+00 7a3hA c.1.8.3 28819 1hnoA 280 3.28e+00 1hnoA c.14.1.3 61095 1fwyA 331 3.32e+00 1fwyA b.81.1.4 28064 c.68.1.5 34522 1a8h 500 3.36e+00 1a8h a.27.1.1 16922 c.26.1.1 31589 1hq0A 295 3.47e+00 1hzgA d.194.1.1 61122 1d3yA 301 3.49e+00 1d3yA e.12.1.1 43252 1fm0E 150 3.54e+00 1fmaE d.41.5.1 38629 1lvl 458 3.58e+00 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1rpxA 230 3.67e+00 1rpxA c.1.2.2 28536 1dar 691 3.67e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1eg7A 557 3.70e+00 1eg7A c.37.1.10 32241 1am2 199 3.87e+00 1am2 b.86.1.2 28381 1fg7A 356 3.92e+00 1gewA c.67.1.1 59819 7a3hA 303 3.98e+00 7a3hA c.1.8.3 28817 1g4uS 383 4.06e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1ii7A 333 4.33e+00 1ii7A d.159.1.4 62415 1ryc 294 4.34e+00 1ryc a.93.1.1 18601 3mhtA 327 4.38e+00 6mhtA c.66.1.10 34234 1gtmA 419 4.61e+00 1hwyA c.2.1.7 30223 c.58.1.1 33871 1i86A 389 4.64e+00 c.95.1.2 66068 c.95.1.2 66069 1in4A 334 4.72e+00 1hqcA a.4.5.11 62597 c.37.1.13 62598 1fmaE 150 4.89e+00 1fmaE d.41.5.1 38630 1lam 484 4.91e+00 1lam c.50.1.1 33166 c.56.5.3 33829 1lap 488 4.93e+00 1lam c.50.1.1 33171 c.56.5.3 33834 1tplA 426 4.94e+00 1ax4A c.67.1.2 34387 1ekjB 221 4.97e+00 1ekjB c.53.2.1 33365 1e0tA 470 5.19e+00 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 2scuA 288 5.27e+00 2scuA c.2.1.8 30303 c.23.4.1 31131 1scuA 288 5.50e+00 2scuA c.2.1.8 30307 c.23.4.1 31135 2napA 723 5.67e+00 2napA b.52.2.2 26926 c.81.1.1 35334 6mhtA 327 5.76e+00 6mhtA c.66.1.10 34226 1ivyA 452 5.81e+00 1ivyA c.69.1.5 34654 1bw0A 416 5.84e+00 1bw0A c.67.1.1 34385 1ckmA 330 5.89e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1kq3A 376 6.40e+00 e.22.1.2 68790 1ig8A 486 6.40e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1k4gA 386 6.49e+00 1eudB 396 7.03e+00 2scuB c.23.4.1 31150 d.142.1.4 41571 1pamA 686 7.05e+00 1cxlA b.1.1.5 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1cx8B 639 7.16e+00 1cx8B a.48.2.1 17783 c.8.4.1 30764 c.56.5.5 33852 1gjnA 153 7.27e+00 1j5eB 256 7.54e+00 1dbqA 289 7.58e+00 1qpzA c.93.1.1 35666 1kfiA 572 7.58e+00 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1yasA 257 7.66e+00 1qj4A c.69.1.20 34801 1cec 343 7.67e+00 1ceo c.1.8.3 28809 1gr8A 412 8.30e+00 1ceo 343 8.44e+00 1ceo c.1.8.3 28808 1qpsA 261 8.44e+00 1ckqA c.52.1.1 33234 3pfk 319 8.48e+00 3pfk c.89.1.1 35581 1crl 534 8.59e+00 1thg c.69.1.17 34765 1theB 260 8.81e+00 1theB d.3.1.1 37057 9ldtA 332 9.02e+00 3ldh c.2.1.5 30154 d.162.1.1 42121 1e1aA 314 9.05e+00 1e1aA b.68.6.1 59155 1skyB 502 9.27e+00 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1i88A 389 9.37e+00 c.95.1.2 66070 c.95.1.2 66071 1lxtA 561 9.44e+00 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1mil 104 9.67e+00 1d4tA d.93.1.1 40496 1tfr 305 9.84e+00 1tfr a.60.7.1 18081 c.53.1.2 33351 1hgxA 183 1.01e+01 1tc1A c.61.1.1 34027 1theA 260 1.01e+01 1theB d.3.1.1 37056 1kid 203 1.03e+01 1derA c.8.5.1 30771 1qidA 537 1.05e+01 2bce c.69.1.1 34593 1qj4A 257 1.05e+01 1qj4A c.69.1.20 34796 1vxrA 537 1.06e+01 2bce c.69.1.1 34595 1dt6A 473 1.06e+01 1dt6A a.104.1.1 18977 1a36A 592 1.07e+01 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1aq0A 306 1.08e+01 1aq0A c.1.8.3 28842 1jjfA 268 1.08e+01 c.69.1.2 66765 3pmgA 561 1.09e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1ehaA 558 1.09e+01 1ehaA b.1.1.5 21859 b.71.1.1 27786 c.1.8.1 28773 1cleA 534 1.13e+01 1thg c.69.1.17 34771 8rucA 475 1.16e+01 1burA c.1.14.1 29339 d.58.9.1 39245 1jg8A 347 1.18e+01 1jg8A c.67.1.1 62946 1aqzA 149 1.21e+01 1aqzA d.1.1.1 36238 2cyp 294 1.21e+01 1ryc a.93.1.1 18600 4pfk 319 1.23e+01 3pfk c.89.1.1 35582 1c4oA 664 1.23e+01 1d2mA c.37.1.13 32415 c.37.1.13 32416 1cr1A 296 1.23e+01 1cr1A c.37.1.11 32286 7taa 478 1.23e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1csbB 205 1.24e+01 1theB 1cknA 330 1.24e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1kamA 194 1.24e+01 1qi9A 556 1.24e+01 1qhbA a.111.1.2 19053 1cx8A 639 1.24e+01 1cx8B a.48.2.1 17782 c.8.4.1 30763 c.56.5.5 33851 1f6dA 376 1.27e+01 1f6dA c.87.1.3 35467 1f2tB 148 1.29e+01 1f2tB 1j8mF 297 1.30e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1ea5A 537 1.34e+01 2bce c.69.1.1 34592 1d4oA 184 1.35e+01 1d4oA c.31.1.4 31748 1tib 269 1.36e+01 3tgl c.69.1.17 34738 1i1qB 192 1.37e+01 1qdlB c.23.16.1 61544 1oaa 259 1.41e+01 1oaa c.2.1.2 29829 1srvA 145 1.42e+01 1derA c.8.5.1 30817 1g4wR 383 1.43e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 2tpsA 227 1.43e+01 2tpsA c.1.3.1 28591 1et0A 269 1.47e+01 1et0A e.17.1.1 43289 3ldh 330 1.51e+01 3ldh i.12.1.1 46015 1eq2A 310 1.51e+01 1eq2A c.2.1.2 29814 2cy3 118 1.52e+01 3cyr a.138.1.1 19649 1ejjA 511 1.52e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1pfkA 320 1.53e+01 3pfk c.89.1.1 35575 1kgnA 329 1.53e+01 a.25.1.2 68584 1ghr 306 1.57e+01 1aq0A c.1.8.3 28844 1eqjA 511 1.57e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ccwB 483 1.65e+01 1cb7B c.1.19.2 29646 1cl1A 395 1.66e+01 1cl2A c.67.1.3 34395 1nbaA 264 1.67e+01 1nbaA c.33.1.1 31753 1d2fA 390 1.68e+01 1d2fA c.67.1.3 34411 1f5mA 180 1.73e+01 1f5mB d.110.2.1 40895 1cseE 274 1.75e+01 1gci c.41.1.1 32481 1dttA 560 1.76e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1inlA 296 1.77e+01 c.66.1.17 66220 1f5mB 180 1.77e+01 1f5mB d.110.2.1 40896 1llp 343 1.77e+01 1arv a.93.1.1 18578 1ab4 477 1.79e+01 1ab4 e.11.1.1 43251 1iibA 106 1.81e+01 1iibA c.44.2.1 32648 1gvfA 286 1.83e+01 1nfp 228 1.87e+01 1nfp c.1.16.2 29555 1cbg 490 1.89e+01 1e70M c.1.8.4 28933 1zpdA 568 1.94e+01 1zpdA c.31.1.3 31741 c.36.1.1 31785 c.36.1.1 31786 1j7lA 264 1.95e+01 d.144.1.6 62697 1ihcA 188 1.97e+01 1di6A c.57.1.1 62379 1g41A 444 1.99e+01 1do0A c.37.1.13 32450 1fjgB 256 2.03e+01 1fjfB c.23.15.1 31400 1gw5B 591 2.04e+01 1jq3A 296 2.05e+01 c.66.1.17 67079 1b0pA 1231 2.07e+01 c.36.1.4 31831 c.36.1.4 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1sup 275 2.20e+01 1gci c.41.1.1 32510 1dqwA 267 2.24e+01 1dqwA c.1.2.3 28551 1eyqA 222 2.37e+01 1eypA d.36.1.1 38534 1thg 544 2.39e+01 1thg c.69.1.17 34763 1f0kA 364 2.40e+01 1f0kA c.87.1.2 35465 1cl2A 395 2.42e+01 1cl2A c.67.1.3 34397 1fn9A 365 2.44e+01 1fn9A d.196.1.1 59894 2mbr 340 2.46e+01 2mbr d.145.1.2 41749 d.146.1.1 41762 1pytA 94 2.48e+01 1pytA d.58.3.1 39064 1uxy 340 2.49e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1lucB 324 2.55e+01 1lucA c.1.16.1 29548 1tig 94 2.57e+01 1tig d.68.1.1 39566 1ihuA 589 2.58e+01 c.37.1.10 62394 c.37.1.10 62395 1fcdA 401 2.59e+01 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1dwtA 153 2.62e+01 1a6m a.1.1.2 15190 1ktbA 405 2.64e+01 1f60A 458 2.67e+01 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1bqcA 302 2.69e+01 1bqcA c.1.8.3 28831 1eypA 222 2.73e+01 1eypA d.36.1.1 38536 1qb7A 236 2.73e+01 1qb7A c.61.1.1 34087 1aqzB 149 2.78e+01 1aqzA d.1.1.1 36239 1eh2 106 2.79e+01 1eh2 a.39.1.6 17339 1dguA 183 2.85e+01 1dguA a.39.1.5 17333 1e32A 458 2.91e+01 1e32A b.52.2.3 59183 c.37.1.13 59184 d.31.1.1 59185 1atg 231 2.96e+01 1atg c.94.1.1 35834 1i7qB 193 2.99e+01 1qdlB c.23.16.1 61902 1qjwA 365 3.02e+01 1bvwA c.6.1.1 30657 2pfkA 320 3.05e+01 3pfk c.89.1.1 35577 1brlA 355 3.05e+01 1lucA c.1.16.1 29553 1hqz9 141 3.05e+01 1ajsA 412 3.06e+01 1ajsA c.67.1.1 34276 1brlB 324 3.09e+01 1lucA c.1.16.1 29554 1iawA 317 3.11e+01 c.52.1.9 62126 1qhtA 775 3.12e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1e39A 571 3.14e+01 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1byrA 155 3.16e+01 1byrA d.136.1.1 41450 1ebfA 358 3.18e+01 1ebuA c.2.1.3 30033 d.81.1.2 39948 1bh9B 89 3.19e+01 1bh9B a.22.1.3 16485 1bc8C 93 3.23e+01 1awcA a.4.5.21 16168 1hxvA 113 3.26e+01 1e79A 510 3.26e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 2hmiA 558 3.27e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1k8tA 510 3.29e+01 e.9.1.4 68316 1c2pA 576 3.34e+01 1quvA e.8.1.4 43117 1irdB 146 3.35e+01 a.1.1.2 66287 5bcaA 516 3.38e+01 1b9zA b.3.1.1 22529 c.1.8.2 28799 1qjdA 571 3.38e+01 1qjdA a.138.1.3 19695 c.3.1.4 30432 d.168.1.1 42315 1fnoA 417 3.41e+01 1ir3A 306 3.41e+01 1fmk d.144.1.2 41702 1augA 215 3.44e+01 1a2zA c.56.4.1 33798 1kekA 1231 3.48e+01 c.36.1.4 68524 c.36.1.4 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1jj2I 145 3.50e+01 1ffkG c.21.1.1 63094 1jepA 222 3.50e+01 d.36.1.1 66612 1b9zA 516 3.53e+01 1b9zA b.3.1.1 22528 c.1.8.2 28798 1din 236 3.53e+01 1din c.69.1.9 34682 1fbaA 361 3.54e+01 1fbaA c.1.10.1 29120 1dkrA 317 3.67e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1skyE 473 3.70e+01 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1cjsA 219 3.70e+01 1cjsA e.24.1.1 43354 1g6q2 328 3.70e+01 1g6q2 1ebuA 358 3.71e+01 1ebuA c.2.1.3 30035 d.81.1.2 39950 1toaA 313 3.73e+01 1toaA c.92.2.2 35598 1cb2A 365 3.73e+01 1bvwA c.6.1.1 30661 1cb7B 483 3.77e+01 1cb7B c.1.19.2 29648 1hwyA 501 3.80e+01 1hwyA c.2.1.7 30262 c.58.1.1 33910 1qnrA 344 3.80e+01 1qnoA c.1.8.3 28834 1qlaC 256 3.83e+01 1qlaC f.2.1.9 43722 1hwxA 501 3.83e+01 1hwyA c.2.1.7 30250 c.58.1.1 33898 1fts 295 3.88e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1irk 306 3.89e+01 1fmk d.144.1.2 41703 1a04A 215 3.89e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1hynP 379 3.94e+01 1hynP d.112.1.2 61408 1cqzA 554 3.95e+01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1h8aC 128 3.95e+01 a.4.1.3 65731 a.4.1.3 65732 1dkgB 197 3.95e+01 1dkgA b.73.1.1 27813 h.1.9.1 45627