# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 1n99A 166 1.78e-02 b.36.1.1 85459 b.36.1.1 85460 1vjzA 341 3.23e-02 c.1.8.3 -5318 1q5qA 259 5.67e-02 d.153.1.4 -11433 1fhvA 323 1.28e-01 1fhuA c.1.11.2 29235 d.54.1.1 38879 1emsA 440 1.80e-01 1emsA d.13.1.1 37520 d.160.1.1 42086 1r6wA 322 1.89e-01 c.1.11.2 -5563 d.54.1.1 -9821 1pmaP 211 2.16e-01 1pmaP d.153.1.4 41863 1rypC 244 2.29e-01 1rypC d.153.1.4 41934 1rypG 244 2.31e-01 d.153.1.4 41938 1iakA 199 6.24e-01 1iakA b.1.1.2 21625 d.19.1.1 38199 1e19A 314 6.38e-01 1b7bA c.73.1.1 34967 1ndbA 596 6.84e-01 c.43.1.3 80411 c.43.1.3 80412 1eqcA 394 7.36e-01 1cz1A c.1.8.3 28811 1cz1A 394 7.43e-01 1cz1A c.1.8.3 28839 1q6hA 224 8.31e-01 d.26.1.1 -9487 1hlrA 907 8.56e-01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1nm8A 616 9.18e-01 c.43.1.3 85872 c.43.1.3 85873 1q8iA 783 9.57e-01 c.55.3.5 -7635 e.8.1.1 -11885 1p9rA 418 9.62e-01 c.37.1.11 -7142 1oltA 457 9.62e-01 unknown_sccs -5688 1ev7B 317 9.87e-01 1ev7B c.52.1.9 33316 1iawA 317 1.06e+00 c.52.1.9 62126 1uwvA 433 1.10e+00 unknown_sccs -3950 unknown_sccs -8107 1ub0A 258 1.26e+00 c.72.1.2 88394 1k38A 254 1.49e+00 e.3.1.1 84303 1s72Q 96 1.51e+00 1jj2P 95 1.71e+00 1ffkN b.34.5.1 63101 1pysA 350 1.77e+00 1pysA d.104.1.1 40775 1at3A 247 1.80e+00 1at3A b.57.1.1 27021 1kn0A 212 2.08e+00 d.50.1.3 77444 1odzA 386 2.14e+00 c.1.8.3 86889 1jdfA 447 2.15e+00 c.1.11.2 62897 d.54.1.1 62898 1m6kA 251 2.21e+00 e.3.1.1 78695 1j9yA 385 2.28e+00 1j9yA c.1.8.3 62791 1914 232 2.39e+00 1914 d.49.1.1 83028 d.49.1.1 83029 1pmaA 233 2.59e+00 1pmaA d.153.1.4 41918 1s6yA 450 2.60e+00 1dgjA 907 2.74e+00 1alo a.56.1.1 17909 d.15.4.2 37694 d.41.1.1 38585 d.133.1.1 41415 1k1gA 131 2.79e+00 d.51.1.1 68015 1b7yA 350 2.80e+00 1pysA d.104.1.1 40776 1bqg 451 2.97e+00 1bqg c.1.11.2 29217 d.54.1.1 38861 1fhuA 320 3.08e+00 1fhuA c.1.11.2 29234 d.54.1.1 38878 1aj6 219 3.15e+00 1aj6 d.122.1.2 41106 1te5A 257 3.36e+00 3pmgA 561 3.40e+00 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1gw1A 376 3.79e+00 c.1.8.3 76361 1o6uA 403 3.81e+00 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1bdg 451 3.82e+00 1qhaA c.55.1.3 33461 c.55.1.3 33462 1rr9A 200 3.91e+00 unknown_sccs -9100 1nu5A 370 4.21e+00 c.1.11.2 -5565 d.54.1.1 -9823 1rdzA 337 4.27e+00 1frpA e.7.1.1 42882 1h4pA 408 4.75e+00 c.1.8.3 -5314 1c0pA 363 4.80e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 1lxtA 561 4.99e+00 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1bdo 80 5.32e+00 1bdo b.84.1.1 28214 1fmk 452 5.80e+00 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.7 41690 1spuB 727 5.84e+00 1oacA b.30.2.1 24399 d.17.2.1 38025 d.17.2.1 38026 d.82.1.1 40012 1l3lA 234 5.85e+00 a.4.6.2 73541 d.110.5.1 73542 2scuB 388 6.10e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1kxrA 339 6.12e+00 d.3.1.3 73175 1frpA 335 6.28e+00 1frpA e.7.1.1 42875 1o12A 376 6.35e+00 b.92.1.5 80758 c.1.9.10 80759 1q0bA 367 6.39e+00 c.37.1.9 -7105 1eceA 358 6.45e+00 1eceA c.1.8.3 28813 1c0dA 358 6.46e+00 1eceA c.1.8.3 28815 1b4kA 337 6.53e+00 1b4kA c.1.10.3 29184 1r6jA 82 6.58e+00 b.36.1.1 -3732 1ev7A 317 6.77e+00 1ev7B c.52.1.9 33315 1nteA 82 6.79e+00 b.36.1.1 86163 1vypX 364 6.82e+00 1nfkA 325 7.17e+00 1a3qA b.1.18.1 21929 b.2.5.3 22444 1vyrA 364 7.20e+00 1gvoA 364 7.21e+00 c.1.4.1 76357 1h61A 364 7.31e+00 1oyc c.1.4.1 60657 1oyeA 1049 7.34e+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 1inp 400 7.36e+00 1inp e.7.1.1 42972 1ffkN 95 7.54e+00 1ffkN b.34.5.1 24606 1dmuA 299 7.56e+00 1dmuA c.52.1.4 33294 1js8A 394 7.79e+00 a.86.1.1 67219 b.112.1.1 67220 1qm4A 396 7.84e+00 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 2phh 394 7.86e+00 1pbe c.3.1.2 30353 d.16.1.2 37884 1gzgA 337 8.12e+00 c.1.10.3 70805 3cla 213 8.31e+00 3cla c.43.1.1 32610 1rypB 250 8.80e+00 1rypB d.153.1.4 41933 1l7aA 318 9.09e+00 c.69.1.25 77772 1wab 232 9.12e+00 1wab c.23.10.3 31341 1d6zA 727 9.13e+00 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1oacA 727 9.19e+00 1oacA b.30.2.1 24390 d.17.2.1 38007 d.17.2.1 38008 d.82.1.1 40003 1btmA 252 9.97e+00 1amk c.1.1.1 28513 1dkzA 219 1.01e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1oo2A 119 1.03e+01 b.3.4.1 -2925 1g65K 211 1.03e+01 d.153.1.4 41907 1mrj 247 1.04e+01 1mrj d.165.1.1 42177 1s3iA 310 1.06e+01 b.46.1.1 -4111 c.65.1.1 -8042 1mzeA 351 1.07e+01 b.82.2.6 79694 1dkxA 219 1.08e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 1nbaA 264 1.10e+01 1nbaA unknown_sccs 31753 1iwgA 1053 1.12e+01 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 1jihA 531 1.14e+01 unknown_sccs -10212 unknown_sccs -11922 1daaA 282 1.15e+01 1daaA e.17.1.1 43270 1nar 290 1.15e+01 1nar c.1.8.5 28988 3daaA 277 1.16e+01 1daaA e.17.1.1 43272 1theB 260 1.17e+01 1theB d.3.1.1 37057 1rypL 212 1.22e+01 d.153.1.4 41880 1qu6A 179 1.22e+01 1qu6A d.50.1.1 38784 d.50.1.1 38785 1bak 119 1.23e+01 1bak b.55.1.1 26973 1rvkA 382 1.23e+01 c.1.11.2 -5568 d.54.1.1 -9826 1es9A 232 1.24e+01 1wab c.23.10.3 31340 1fr2B 134 1.24e+01 d.4.1.1 83257 1theA 260 1.25e+01 1theB d.3.1.1 37056 1jssA 224 1.30e+01 d.129.3.2 71844 1nuyA 337 1.30e+01 e.7.1.1 86213 1nfp 228 1.32e+01 1nfp c.1.16.2 29555 1ec7A 446 1.32e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 2bpa1 426 1.32e+01 2bpa1 1azpA 66 1.40e+01 1azpA b.34.13.1 37467 1rbp 182 1.41e+01 1aqb b.60.1.1 27085 5fbpA 335 1.41e+01 1frpA e.7.1.1 42873 1emvB 134 1.42e+01 1bxiB d.4.1.1 37135 1nox 205 1.43e+01 1nox d.90.1.1 40242 1hi0P 664 1.43e+01 1hi0P e.8.1.6 61051 1ro2A 216 1.49e+01 unknown_sccs -11391 1guzA 310 1.50e+01 c.2.1.5 65586 d.162.1.1 65587 1f4tA 368 1.51e+01 1f4tA a.104.1.1 18973 1v97A 1332 1.51e+01 1kijA 390 1.53e+01 d.14.1.3 72514 d.122.1.2 72515 1bxiB 134 1.54e+01 1bxiB d.4.1.1 37136 1rypH 205 1.54e+01 d.153.1.4 41876 1r3cA 366 1.55e+01 d.144.1.7 -11296 1azqA 66 1.58e+01 1azpA b.34.13.1 37469 1jm4B 118 1.59e+01 a.29.2.1 71746 1io7A 368 1.62e+01 1f4tA a.104.1.1 18971 1pz1A 333 1.62e+01 c.1.7.1 -5255 1gmyA 261 1.66e+01 d.3.1.1 76236 1pieA 419 1.67e+01 d.14.1.5 -9075 unknown_sccs -10120 1hbq 183 1.68e+01 1aqb b.60.1.1 27078 1ton 235 1.71e+01 5ptp b.47.1.2 26307 1g9oA 91 1.72e+01 1pdr b.36.1.1 60400 2shpA 525 1.73e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 2prd 174 1.74e+01 2prd b.40.5.1 25435 1h2kA 349 1.76e+01 b.82.2.6 76572 1b25A 619 1.78e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1jx4A 352 1.79e+01 unknown_sccs -10188 unknown_sccs -11898 1k7kA 221 1.79e+01 c.51.4.1 72104 1mkmA 249 1.82e+01 a.4.5.33 79242 d.110.2.2 79243 1bfi 112 1.86e+01 1qadA d.93.1.1 40499 1kjkA 64 1.87e+01 d.10.1.4 72613 1mk4A 157 1.87e+01 d.108.1.1 84979 1ts3A 194 1.89e+01 1aw7A b.40.2.2 25168 d.15.6.1 37757 1hbp 183 1.97e+01 1aqb b.60.1.1 27079 3fruA 269 1.99e+01 1agdA b.1.1.2 20657 d.19.1.1 38150 1g4uS 383 1.99e+01 1g4uS a.24.11.1 16643 c.45.1.2 32691 1e1hA 287 2.00e+01 d.92.1.7 83167 1mdwA 328 2.00e+01 d.3.1.3 84934 1dar 691 2.01e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1oi2A 366 2.01e+01 c.32.1.2 87039 d.79.2.2 87040 1fiqC 763 2.02e+01 1fiqC d.41.1.1 38588 d.133.1.1 41418 1ceo 343 2.05e+01 1ceo c.1.8.3 28808 1jobA 162 2.08e+01 1f35A b.94.1.1 63207 1f35A 162 2.08e+01 1f35A b.94.1.1 59628 1kz8A 337 2.09e+01 e.7.1.1 77633 1gw5M 435 2.11e+01 b.2.7.1 70631 d.110.4.2 70632 1mo7A 213 2.14e+01 d.220.1.1 85028 1rg9A 383 2.16e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 2cro 71 2.17e+01 1r69 a.35.1.2 17038 1zug 71 2.18e+01 1r69 a.35.1.2 17041 1im8A 244 2.18e+01 c.66.1.14 66212 1fo4A 1332 2.21e+01 a.56.1.1 17910 d.15.4.2 37695 d.41.1.1 38586 d.87.2.1 40227 d.133.1.1 41416 d.145.1.3 41758 1a0jA 223 2.21e+01 5ptp b.47.1.2 26002 1ajsA 412 2.28e+01 1ajsA c.67.1.1 34276 1p7tA 731 2.33e+01 c.1.13.1 -5600 1lj2A 110 2.34e+01 h.1.13.2 73926 2dabA 282 2.35e+01 1daaA e.17.1.1 43274 1bdfA 235 2.35e+01 1bdfA d.74.3.1 39727 d.181.1.1 42602 1n9bA 265 2.38e+01 e.3.1.1 85463 1fpkA 335 2.38e+01 1frpA e.7.1.1 42930 1pxvA 183 2.41e+01 d.3.1.1 -8881 1uox 296 2.43e+01 1uox 1s72H 171 2.45e+01 1ekfA 365 2.46e+01 1ekfA e.17.1.1 59445 1r4uA 301 2.48e+01 d.96.1.4 -10709 d.96.1.4 -10710 1s14A 194 2.48e+01 d.122.1.2 -10973 1itkA 731 2.48e+01 a.93.1.3 71417 a.93.1.3 71418 1c0eA 157 2.49e+01 1dg9A c.44.1.1 32638 1se9A 126 2.51e+01 d.15.1.1 -9145 1deuA 277 2.52e+01 1theB d.3.1.1 37085 1dlwA 116 2.53e+01 1dlyA a.1.1.1 14982 1btkB 169 2.54e+01 1btkA b.55.1.1 26960 1od2A 805 2.54e+01 c.14.1.4 86821 c.14.1.4 86822 1nvmB 312 2.56e+01 c.2.1.3 86251 d.81.1.1 86252 1cjcA 460 2.56e+01 1cjcA c.3.1.1 30319 c.4.1.1 30604 1tgoA 773 2.60e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1e8oB 106 2.62e+01 1914 d.49.1.1 38775 1sczA 233 2.64e+01 c.43.1.1 -7326 1kanA 253 2.64e+01 1knyA a.24.16.1 75878 d.218.1.1 75879 1fnmA 691 2.65e+01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1kyqA 274 2.66e+01 c.2.1.11 73281 e.37.1.1 73282 1qyaA 307 2.69e+01 7taa 478 2.70e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1bpr 191 2.72e+01 1dkzA unknown_sccs 43319 1o5uA 101 2.74e+01 b.82.1.8 -4845 1auiA 521 2.76e+01 1auiA d.159.1.3 42085 1ly1A 181 2.80e+01 c.37.1.1 74334 1fs0E 138 2.82e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1p9vA 310 2.82e+01 1sdjA 310 2.82e+01 d.21.1.2 -9420 d.21.1.2 -9421 2aaa 484 2.82e+01 7taa b.71.1.1 27777 c.1.8.1 28764 1uvjA 664 2.83e+01 e.8.1.6 -11964 1bbhA 131 2.83e+01 1bbhA a.24.3.2 16546 1ct9A 553 2.84e+01 1ct9A c.26.2.1 31616 d.153.1.1 41834 1kt6A 183 2.84e+01 b.60.1.1 84466 1eaf 243 2.88e+01 1eaf c.43.1.1 32617 1i7qA 519 2.92e+01 1qdlA d.161.1.1 61901 1i92A 91 2.95e+01 1pdr b.36.1.1 61990 1delA 241 2.95e+01 1dekA c.37.1.1 31844 1hhsA 664 2.98e+01 1hi0P e.8.1.6 61045 1d0sA 356 2.98e+01 1d0vA c.39.1.1 32477 1ac5 483 3.01e+01 1ac5 c.69.1.5 34653 1pkp 150 3.01e+01 1pkp d.14.1.1 37551 d.50.1.2 38787 1e79H 146 3.05e+01 1e79H a.2.10.1 15721 b.93.1.1 28438 1jkmB 361 3.07e+01 1jkmA c.69.1.2 34634 1s68A 249 3.08e+01 unknown_sccs -11253 1tkiA 321 3.09e+01 1tkiA d.144.1.7 41638 1mveA 243 3.10e+01 b.29.1.2 85140 1hqz1 141 3.15e+01 1memA 215 3.15e+01 1cs8A d.3.1.1 37069 1dpo 223 3.17e+01 5ptp b.47.1.2 25975 1ilyA 90 3.18e+01 c.55.4.1 71245 1cnv 299 3.18e+01 1cnv c.1.8.5 28989 1kwgA 645 3.23e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1p1lA 102 3.24e+01 d.58.5.2 87695 1jkmA 358 3.25e+01 1jkmA c.69.1.2 34633 1qumA 285 3.26e+01 1qumA c.1.15.1 29393 1lm8V 160 3.27e+01 b.3.3.1 74035 1rreA 200 3.28e+01 unknown_sccs -9106 1i1qA 520 3.28e+01 1qdlA d.161.1.1 61543 1knyA 253 3.28e+01 1knyA a.24.16.1 75896 d.218.1.1 75897 1crzA 403 3.31e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1b6fA 159 3.36e+01 1bv1 d.129.3.1 41316 1fdo 715 3.37e+01 2napA b.52.2.2 26917 c.81.1.1 35325 1lvl 458 3.40e+01 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1j2gA 319 3.41e+01 1ehiA 377 3.44e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1jpmA 366 3.51e+01 c.1.11.2 67031 d.54.1.1 67032 1a05A 358 3.52e+01 1cnzA c.77.1.1 35059 1lqbC 162 3.53e+01 b.3.3.1 74186 1ro0A 216 3.54e+01 unknown_sccs -11390 1mwpA 96 3.60e+01 1mwpA d.170.2.1 42453 1szoA 257 3.63e+01 1nmeA 146 3.64e+01 c.17.1.1 85874 1q3eA 207 3.65e+01 b.82.3.2 -4922 1jj2E 177 3.67e+01 1ffk1 d.141.1.1 63089 d.141.1.1 63090 1c5kA 439 3.68e+01 1crzA b.68.4.1 27630 c.51.2.1 33212 1korA 400 3.69e+01 c.26.2.1 72824 d.210.1.1 72825 1s83A 223 3.70e+01 b.47.1.2 -4178 1nbwA 607 3.71e+01 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1n0uA 842 3.72e+01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1ex2A 189 3.73e+01 1ex2A c.51.4.2 33225 1l2lA 457 3.73e+01 c.72.1.3 77656 1b8dA 164 3.73e+01 1cpcA a.1.1.3 15665 1k51A 72 3.74e+01 d.15.7.1 68147 1oejA 193 3.77e+01 unknown_sccs -4461 1kwhA 492 3.80e+01 c.94.1.1 68876 1j1nA 492 3.81e+01 c.94.1.1 83978 1hl8A 449 3.82e+01 unknown_sccs -4690 unknown_sccs -5361 1bn5 478 3.82e+01 1bn5 a.4.5.25 16224 d.127.1.1 41161 1n6eA 1071 3.83e+01 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1kwkA 645 3.84e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1pujA 282 3.87e+01 c.37.1.8 88294 1fdi 715 3.91e+01 2napA b.52.2.2 26918 c.81.1.1 35326 1ojrA 274 3.93e+01 c.74.1.1 -8441 1h6zA 913 3.94e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1pauA 147 3.94e+01 1pauA c.17.1.1 30994 1ktaA 365 3.94e+01 e.17.1.1 77533 1pcfA 66 3.95e+01 1pcfA d.18.1.1 38142 1nedA 183 3.95e+01 1nedA d.153.1.4 41974 1ad1A 266 3.96e+01 1aj2 c.1.21.1 29668 1frvB 536 3.96e+01 1h2rL e.18.1.1 43296 1o08A 221 3.98e+01 c.108.1.6 86525