# 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 1ii5A 233 2.83e-02 c.94.1.1 62412 1iiwA 232 3.29e-02 c.94.1.1 62461 1kq3A 376 4.73e-01 e.22.1.2 68790 1e5dA 402 4.73e-01 1e5dA c.23.5.1 31208 d.157.1.3 42061 2ts1 419 5.79e-01 2ts1 c.26.1.1 31564 4ts1A 319 6.25e-01 2ts1 c.26.1.1 31565 1wdnA 226 6.77e-01 1lst c.94.1.1 35816 1qo7A 394 7.55e-01 1qo7A c.69.1.11 34697 1al3 324 8.07e-01 1al3 c.94.1.1 35835 1ccwA 137 9.20e-01 1be1 c.23.6.1 31238 1sbp 310 1.22e+00 1sbp c.94.1.1 35760 1gggB 226 1.23e+00 1lst c.94.1.1 35818 1c7nA 399 1.54e+00 1d2fA c.67.1.3 34413 1ezm 301 1.68e+00 1hyt d.92.1.2 58980 1i40A 175 1.78e+00 b.40.5.1 66024 1irxA 523 1.86e+00 1ftkA 279 1.99e+00 1gr2A c.94.1.1 35819 1d2fA 390 2.01e+00 1d2fA c.67.1.3 34411 1ipwA 175 2.55e+00 2prd b.40.5.1 25427 1bmqA 167 2.64e+00 1pauA c.17.1.1 30998 1sig 339 2.88e+00 1sig a.112.1.1 19068 1qjdA 571 2.97e+00 1qjdA a.138.1.3 19695 c.3.1.4 30432 d.168.1.1 42315 1gr2A 279 3.11e+00 1gr2A c.94.1.1 35825 1h75A 81 3.32e+00 1h75A c.47.1.1 60716 1obwA 175 3.35e+00 2prd b.40.5.1 25416 1cl1A 395 3.54e+00 1cl2A c.67.1.3 34395 1joa 447 3.57e+00 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1amf 233 3.64e+00 1wod c.94.1.1 35833 1qfmA 710 3.80e+00 1qfmA b.69.7.1 27673 c.69.1.4 34641 1aerA 205 3.80e+00 1aerA d.166.1.1 42249 1bqcA 302 3.84e+00 1bqcA c.1.8.3 28831 1ibcA 194 3.85e+00 1pauA c.17.1.1 30997 1nhp 447 3.85e+00 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1j4aA 333 3.87e+00 1hslA 238 3.95e+00 1lst c.94.1.1 35804 1nhs 447 4.09e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1gx3A 284 4.20e+00 1wod 233 4.48e+00 1wod c.94.1.1 35832 1e3dB 542 4.58e+00 1h2rL e.18.1.1 59189 1jdc 429 4.97e+00 1jdc b.71.1.1 27789 c.1.8.1 28776 1dtwB 342 5.02e+00 1qs0B c.36.1.3 31828 c.48.1.2 33102 16pk 415 5.30e+00 16pk c.86.1.1 35454 3adk 195 5.31e+00 1zin c.37.1.1 31885 1cl2A 395 5.40e+00 1cl2A c.67.1.3 34397 1e39A 571 5.47e+00 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1gcyA 527 5.78e+00 1jdc b.71.1.1 27788 c.1.8.1 28775 1pot 325 5.91e+00 1pot c.94.1.1 35807 1f2vA 219 6.18e+00 1f2vA c.23.17.1 59627 1qsdA 106 6.23e+00 1qsdA a.7.5.1 16335 1kgsA 225 6.41e+00 a.4.6.1 68596 c.23.1.1 68597 1jr2A 286 6.53e+00 c.113.1.1 67111 1gpjA 404 6.78e+00 a.151.1.1 65451 c.2.1.10 65452 d.58.39.1 65453 1ej1A 190 6.88e+00 1ejhA d.86.1.1 40144 1mldA 314 7.18e+00 2cmd c.2.1.5 30122 d.162.1.1 42089 1tmy 120 7.24e+00 1dbwA c.23.1.1 31083 1jcqA 382 7.50e+00 a.118.6.1 66504 1onrA 316 7.52e+00 1onrA c.1.10.1 29169 1ld8A 382 7.55e+00 1aky 221 7.81e+00 1zin c.37.1.1 31896 g.41.2.1 45197 1lucA 355 7.87e+00 1lucA c.1.16.1 29547 1add 349 7.91e+00 1a4mA c.1.9.1 29020 1jcrA 377 7.91e+00 a.118.6.1 66506 1a4mA 349 8.09e+00 1a4mA c.1.9.1 29014 1chuA 540 8.09e+00 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1ft1A 377 8.15e+00 1ft1A a.118.6.1 19186 1ihoA 283 8.15e+00 1ihoA c.26.1.4 62390 1a62 130 8.15e+00 1a62 a.140.3.1 64708 b.40.4.5 64709 1i1hA 219 8.16e+00 1f2vA c.23.17.1 61530 1ejhA 190 8.47e+00 1ejhA d.86.1.1 40147 1azwA 313 8.52e+00 1qtrA c.69.1.7 34658 1k78A 149 8.56e+00 a.4.1.5 68255 a.4.1.5 68256 1jilA 420 8.61e+00 c.26.1.1 66745 1fehA 574 8.72e+00 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1a8vA 121 8.78e+00 1a62 a.140.3.1 64712 b.40.4.5 64713 1i6aA 219 8.90e+00 c.94.1.1 61827 1kzhA 555 8.90e+00 1qf9A 194 9.03e+00 1zin c.37.1.1 31848 1broA 277 9.12e+00 1brt c.69.1.12 34700 1frvB 536 9.20e+00 1h2rL e.18.1.1 43296 5ukdA 194 9.22e+00 1zin c.37.1.1 31851 1edg 380 9.54e+00 1edg c.1.8.3 28807 1d8dA 377 9.68e+00 1ft1A a.118.6.1 19185 1cpcA 162 9.70e+00 1cpcA a.1.1.3 15643 1sqc 631 9.86e+00 2sqcA a.102.4.2 18858 a.102.4.2 18859 1cvrA 435 1.02e+01 1cvrA b.1.1.5 21949 c.17.1.2 31006 1jeoA 180 1.02e+01 c.80.1.3 66611 1hrdA 449 1.08e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1pszA 303 1.09e+01 1toaA c.92.2.2 35600 1g2hA 61 1.13e+01 1g2hA a.4.1.10 60224 1f9aA 168 1.14e+01 1f9aA c.26.1.3 31602 1zymA 258 1.14e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1ipcA 217 1.14e+01 1jipA 403 1.14e+01 a.104.1.1 66748 1k89 449 1.17e+01 1k89 c.2.1.7 30218 c.58.1.1 33866 1a8q 274 1.17e+01 1brt c.69.1.12 34702 1im8A 244 1.17e+01 c.66.1.14 66212 2frvB 536 1.18e+01 1h2rL e.18.1.1 43291 2sqcA 631 1.18e+01 2sqcA a.102.4.2 18854 a.102.4.2 18855 1dmaA 214 1.18e+01 1aerA d.166.1.1 42251 2dhqA 146 1.19e+01 2dhqA c.23.13.1 31382 1g5cA 170 1.19e+01 1g5cA c.53.2.1 60264 1a4iA 301 1.20e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1atg 231 1.21e+01 1atg c.94.1.1 35834 1lk5A 229 1.25e+01 1be3A 446 1.27e+01 1be3A d.185.1.1 58950 d.185.1.1 58951 1s01 283 1.28e+01 1gci c.41.1.1 32511 1ikpA 613 1.34e+01 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1jr3E 334 1.35e+01 a.80.1.1 63253 c.37.1.13 63254 1a4iB 301 1.37e+01 1a4iA c.2.1.7 30279 c.58.1.2 33927 1eupA 403 1.37e+01 1rom a.104.1.1 18967 2gsaA 432 1.39e+01 2gsaA c.67.1.4 34446 1a8s 273 1.41e+01 1brt c.69.1.12 34710 1ejbA 168 1.43e+01 1rvv1 c.16.1.1 59417 1bgvA 449 1.44e+01 1k89 c.2.1.7 30217 c.58.1.1 33865 1dkrA 317 1.45e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1dkuA 317 1.45e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1mut 129 1.45e+01 1tum d.113.1.1 40921 1jtkA 136 1.48e+01 1gr0A 367 1.51e+01 1akeA 214 1.51e+01 1zin c.37.1.1 31905 g.41.2.1 45185 1dv0A 47 1.52e+01 1dv0A a.5.2.1 16289 1db3A 372 1.53e+01 1db3A c.2.1.2 29813 1qs0A 407 1.53e+01 1qs0A c.36.1.3 31829 1czaN 917 1.54e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1e4yA 214 1.55e+01 1zin c.37.1.1 31901 g.41.2.1 45181 1qlaC 256 1.58e+01 1qlaC f.2.1.9 43722 1cqxA 403 1.59e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 2cmd 312 1.59e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1ik6A 369 1.60e+01 c.36.1.3 66174 c.48.1.2 66175 1l8bA 190 1.62e+01 1oasA 322 1.63e+01 1oasA c.79.1.1 35293 1oxa 403 1.67e+01 1f4tA a.104.1.1 18965 1dctA 324 1.76e+01 6mhtA c.66.1.10 34244 1bjoA 360 1.77e+01 1bjnA c.67.1.4 34471 1eexA 554 1.80e+01 1dioA c.1.19.3 29650 3chy 128 1.84e+01 3chy c.23.1.1 31038 1cqmA 101 1.84e+01 1ris d.58.14.1 39321 1dgwY 93 1.85e+01 1caxB 1qckA 89 1.87e+01 1qckA a.60.5.1 17976 2ezxA 89 1.87e+01 1qckA a.60.5.1 17978 1zin 217 1.90e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1pytA 94 1.92e+01 1pytA d.58.3.1 39064 1ci4A 89 1.92e+01 1qckA a.60.5.1 17970 1jm6A 407 1.93e+01 a.29.5.1 66876 d.122.1.4 66877 1tx4A 198 1.96e+01 1tx4A a.116.1.1 19098 1fcjA 322 1.96e+01 1oasA c.79.1.1 35289 1howA 373 2.00e+01 1hcl d.144.1.1 41679 1b16A 254 2.02e+01 1b16A c.2.1.2 29875 1vid 221 2.03e+01 1vid c.66.1.1 34178 1aogA 485 2.06e+01 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1e6mA 128 2.08e+01 3chy c.23.1.1 31039 1eyeA 280 2.12e+01 1aj2 c.1.21.1 29672 1qguA 478 2.16e+01 1qguA c.92.2.3 35625 1ciy 590 2.20e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1brlA 355 2.25e+01 1lucA c.1.16.1 29553 1gpiA 431 2.26e+01 b.29.1.10 65450 1ad1A 266 2.28e+01 1aj2 c.1.21.1 29668 1fw9A 164 2.29e+01 1fw9A d.190.1.1 60059 1gnuA 117 2.29e+01 d.15.1.3 65403 1qrqA 325 2.31e+01 1qrqA c.1.7.1 28667 1dgrM 93 2.31e+01 1caxB b.82.1.2 28101 1dgrW 93 2.31e+01 1caxB 1kpf 126 2.33e+01 1kpf d.13.1.1 37507 1dgkN 917 2.34e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1i69A 219 2.35e+01 c.94.1.1 61825 1a4uA 254 2.35e+01 1b16A c.2.1.2 29878 1lxa 262 2.38e+01 1lxa b.81.1.1 28052 1ytbA 180 2.41e+01 1ytbA d.129.1.1 41276 d.129.1.1 41277 1ris 101 2.43e+01 1ris d.58.14.1 39314 1f7uA 607 2.44e+01 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1g59A 468 2.45e+01 a.97.1.1 60257 c.26.1.1 60258 1hx1B 114 2.45e+01 1hx1B a.7.7.1 61350 1jihA 531 2.45e+01 e.8.1.5 66740 1gtzA 156 2.48e+01 1kpeA 126 2.49e+01 1kpf d.13.1.1 37508 1bjt 793 2.54e+01 1bjt e.11.1.1 43249 1akr 147 2.61e+01 1rcf c.23.5.1 31152 1i50F 155 2.62e+01 d.78.1.2 61760 2gar 212 2.62e+01 2gar c.65.1.1 34161 1a04A 215 2.62e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1jevA 517 2.64e+01 1jevA c.94.1.1 35720 1dmtA 696 2.66e+01 1dmtA d.92.1.4 40296 1cv2A 296 2.69e+01 1bn6A c.69.1.8 34680 1hd2A 161 2.70e+01 c.47.1.10 60962 1dd5A 185 2.70e+01 1dd5A d.67.3.1 39564 1c7qA 445 2.71e+01 2pgi c.80.1.2 35307 1eu8A 409 2.75e+01 1eu8A c.94.1.1 59502 1qamA 244 2.75e+01 2ercA c.66.1.9 34220 1cg2A 393 2.76e+01 1cg2A c.56.5.4 33844 d.58.19.1 39360 2ercA 244 2.77e+01 2ercA c.66.1.9 34224 1gg1A 350 2.79e+01 1qr7A c.1.10.4 29187 1jetA 517 2.83e+01 1jevA c.94.1.1 35718 2olbA 517 2.84e+01 1jevA c.94.1.1 35721 1p32A 209 2.85e+01 1p32A d.25.1.1 38379 1cqeA 580 2.85e+01 1cqeA a.93.1.2 18703 g.3.11.1 44246 1c3pA 375 2.86e+01 1c3pA c.42.1.2 32606 1exbA 332 2.87e+01 1qrqA c.1.7.1 28666 2pgi 445 2.92e+01 2pgi c.80.1.2 35308 1qr7A 350 2.93e+01 1qr7A c.1.10.4 29191 1ak7 174 2.96e+01 1cof d.109.1.2 40864 1ggzA 148 2.98e+01 1ftt 68 3.01e+01 2hddA a.4.1.1 15997 1bykA 255 3.04e+01 1bykA c.93.1.1 35706 1c4xA 285 3.05e+01 1c4xA c.69.1.10 34684 1qc9A 276 3.09e+01 1ckqA c.52.1.1 33235 1eudA 311 3.09e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1l1eA 287 3.10e+01 1jscA 630 3.10e+01 c.31.1.3 67224 c.36.1.1 67225 c.36.1.1 67226 1d2eA 397 3.11e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1trb 320 3.11e+01 1trb c.3.1.5 30529 c.3.1.5 30530 1jmrA 249 3.13e+01 1qbqA 333 3.14e+01 1ft1A a.118.6.1 19187 1idrA 136 3.19e+01 1dlyA a.1.1.1 62301 1dioA 554 3.20e+01 1dioA c.1.19.3 29656 1di0A 158 3.21e+01 1di0A c.16.1.1 30957 1k75A 434 3.21e+01 c.82.1.2 68253 2fsp 124 3.22e+01 1dz3A c.23.1.1 31119 1brt 277 3.25e+01 1brt c.69.1.12 34699 1k3kA 158 3.28e+01 3minC 491 3.29e+01 1qguA c.92.2.3 35607 1kbqA 273 3.30e+01 c.23.5.3 68391 1f0kA 364 3.31e+01 1f0kA c.87.1.2 35465 1jbeA 128 3.36e+01 3chy c.23.1.1 62845 1bhe 376 3.37e+01 1bhe b.80.1.3 28030 1bu5A 147 3.42e+01 5nul c.23.5.1 31155 1sup 275 3.44e+01 1gci c.41.1.1 32510 1bjnA 360 3.47e+01 1bjnA c.67.1.4 34469 1huvA 380 3.48e+01 c.1.4.1 61277 1amp 291 3.48e+01 1amp c.56.5.4 33837 1f6dA 376 3.52e+01 1f6dA c.87.1.3 35467 1uroA 367 3.53e+01 1uroA c.1.22.1 29675 1srrA 124 3.55e+01 1dz3A c.23.1.1 31110 1lbeA 258 3.56e+01 1lbeA e.4.1.1 42773 1qh8A 478 3.56e+01 1qguA c.92.2.3 35633 1dlyA 164 3.58e+01 1dlyA a.1.1.1 14983 1qo2A 241 3.63e+01 1qo2A c.1.2.1 28533 1d9eA 284 3.65e+01 1d9eA c.1.10.4 29195 1d4aA 273 3.65e+01 1d4aA c.23.5.3 31219 1p32C 209 3.65e+01 1p32A d.25.1.1 38381 1ef1A 294 3.69e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1b74A 254 3.71e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 1k47A 337 3.77e+01 1bs0A 384 3.79e+01 1bs0A c.67.1.4 34490 1phnA 162 3.80e+01 1cpcA a.1.1.3 15641 1j75A 67 3.82e+01 a.4.5.19 62673 1e5xA 486 3.83e+01 c.79.1.1 59283 1deeG 54 3.84e+01 1fc2C a.8.1.1 16343 1in4A 334 3.84e+01 1hqcA a.4.5.11 62597 c.37.1.13 62598 1ac5 483 3.85e+01 1ac5 c.69.1.5 34653 1kl7A 514 3.87e+01 1e58A 249 3.93e+01 1qhfA c.60.1.1 59262 2liv 344 3.93e+01 2liv c.93.1.1 35708 1ytbB 180 3.94e+01 1ytbA d.129.1.1 41278 d.129.1.1 41279 1maz 221 3.99e+01 1maz f.1.4.1 43393 1f5aA 513 3.99e+01 1fa0B d.58.16.1 39337 e.9.1.2 43231 1h6kA 757 4.00e+01 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677