# List of top-scoring protein chains for T0222.t2k-w0.5 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 1pe1A 267 6.43e-10 1lroA 267 2.10e-09 c.1.10.4 78161 1o60A 292 4.11e-07 1d9eA 284 6.25e-07 1d9eA c.1.10.4 29195 1g7uA 284 6.35e-07 1d9eA c.1.10.4 60334 1a53 247 8.42e-02 1a53 c.1.2.4 28564 1jul 248 8.42e-02 1a53 c.1.2.4 28566 1of8A 370 1.17e-01 1og0A 370 1.22e-01 1c89A 134 2.22e-01 1msi b.85.1.1 28314 b.85.1.1 28315 3nla 74 2.62e-01 1msi b.85.1.1 28316 1i5gA 144 2.72e-01 1ewxA c.47.1.10 61784 1fg4A 149 2.85e-01 1ewxA c.47.1.10 59814 1o6jA 150 2.86e-01 c.47.1.10 81089 1o81A 152 2.89e-01 c.47.1.10 81175 1oc9A 152 3.00e-01 c.47.1.10 86797 1ops 64 4.24e-01 1msi b.85.1.1 28302 1ucsA 64 5.86e-01 b.85.1.1 88466 9ameA 66 7.14e-01 1msi b.85.1.1 28294 1kp8A 547 7.33e-01 a.129.1.1 84414 c.8.5.1 84415 d.56.1.1 84416 1oelA 547 7.52e-01 1derA a.129.1.1 19452 c.8.5.1 30781 d.56.1.1 38900 1grlA 548 7.53e-01 1pcqA 524 7.57e-01 1mnfA 547 7.61e-01 1gr5A 547 7.68e-01 i.16.1.1 65478 1j4zA 547 7.74e-01 1j4aA 333 8.43e-01 c.2.1.4 71502 c.23.12.1 71503 1j49A 333 8.48e-01 c.2.1.4 71498 c.23.12.1 71499 1a6dB 543 1.37e+00 1a6dA a.129.1.2 19489 c.8.5.2 30820 d.56.1.2 38937 1j5tA 242 1.38e+00 c.1.2.4 71583 1mxsA 225 1.51e+00 1i4nA 251 1.52e+00 c.1.2.4 71114 1ub3A 220 1.61e+00 c.1.10.1 88395 1p4cA 380 1.94e+00 4pgaA 337 2.01e+00 4pgaA c.88.1.1 35565 1djpA 330 2.02e+00 4pgaA c.88.1.1 35567 1i2mB 402 2.04e+00 1a12A b.69.5.1 61569 1a12A 413 2.17e+00 1a12A b.69.5.1 27663 1h1dA 221 2.26e+00 c.66.1.1 83452 3pga1 337 2.28e+00 4pgaA 2dldA 337 2.53e+00 1dxy c.2.1.4 30099 c.23.12.1 31359 1mzhA 225 2.85e+00 c.1.10.1 79698 1pdo 135 2.89e+00 1pdo c.54.1.1 33376 1l4uA 176 2.91e+00 c.37.1.2 73568 1jf8A 131 3.09e+00 c.44.1.1 66621 1b7jA 66 3.17e+00 1msi b.85.1.1 28283 1tfaA 329 3.19e+00 1nnt c.94.1.2 35880 1me8A 503 3.39e+00 c.1.5.1 79028 1iejA 332 3.48e+00 1nnt c.94.1.2 62328 1e0rB 159 3.56e+00 1a6dA c.8.5.2 30824 1j7hA 130 3.57e+00 d.79.1.1 77097 1erzA 303 3.57e+00 1erzA d.160.1.2 59498 1nnt 328 3.76e+00 1nnt c.94.1.2 35884 1mq9A 180 3.87e+00 c.62.1.1 79411 1ox6A 555 4.07e+00 c.1.2.1 87505 c.23.16.1 87506 1jvnA 554 4.09e+00 c.1.2.1 67355 c.23.16.1 67356 1g8mA 593 4.19e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1qgeD 222 4.26e+00 1cvl c.69.1.18 34773 1rvkA 382 4.44e+00 1m9nA 613 4.58e+00 c.24.1.3 78870 c.97.2.1 78871 1fo6A 304 4.72e+00 1erzA d.160.1.2 59923 1rd4A 191 4.76e+00 2msi 66 4.81e+00 1msi b.85.1.1 28297 7msi 66 4.88e+00 1msi b.85.1.1 28290 1lfaA 187 4.89e+00 1ido c.62.1.1 34122 1dgqA 188 4.98e+00 1ido c.62.1.1 34131 1cqpA 182 4.99e+00 1ido c.62.1.1 34127 1pvnA 376 5.16e+00 c.1.5.1 88312 1msi 70 5.23e+00 1msi b.85.1.1 28281 1ktnA 250 5.30e+00 c.1.10.1 72988 1ljuA 130 5.30e+00 c.44.1.1 73944 1ljlA 131 5.40e+00 c.44.1.1 73939 1lrtA 376 5.41e+00 c.1.5.1 84685 1p1xA 260 5.43e+00 1np6A 174 5.45e+00 c.37.1.10 85954 1uf5A 303 5.46e+00 1vjrA 271 5.58e+00 1rxiA 131 5.59e+00 1rvgA 305 5.84e+00 1kde 70 5.84e+00 1msi b.85.1.1 28310 1pw5A 253 5.85e+00 1eklA 66 6.00e+00 1msi b.85.1.1 28289 1jcjA 260 6.04e+00 c.1.10.1 66499 1cvl 319 6.05e+00 1cvl c.69.1.18 34786 1tahA 318 6.25e+00 1cvl c.69.1.18 34775 5msi 66 6.29e+00 1msi b.85.1.1 28293 1p9nA 170 6.59e+00 c.37.1.10 87997 4msi 66 6.64e+00 1msi b.85.1.1 28292 1p0kA 349 6.65e+00 c.1.4.1 87648 1o5kA 305 6.69e+00 1ea9C 583 6.79e+00 b.1.18.2 70087 b.71.1.1 70088 c.1.8.1 70089 3msi 66 6.87e+00 1msi b.85.1.1 28282 1ame 67 7.16e+00 1msi b.85.1.1 28285 1hg7A 66 7.21e+00 1msi b.85.1.1 28280 2msjA 66 7.55e+00 1msi b.85.1.1 28303 3ameA 66 7.58e+00 1msi b.85.1.1 28304 2spgA 66 7.61e+00 1msi b.85.1.1 28291 1gzi 65 7.71e+00 1msi b.85.1.1 28295 1lk0A 131 7.72e+00 c.44.1.1 73948 1jr2A 286 7.93e+00 c.113.1.1 67111 6msi 66 7.95e+00 1msi b.85.1.1 28296 1g69A 228 8.40e+00 c.1.3.1 60313 1g6cA 227 8.42e+00 c.1.3.1 60315 1g4sA 226 8.44e+00 c.1.3.1 60247 1g67A 225 8.46e+00 c.1.3.1 60311 1ass 159 8.47e+00 1a6dA c.8.5.2 30818 8msiA 66 8.49e+00 1msi b.85.1.1 28308 1ovt 686 8.61e+00 1nnt c.94.1.2 35882 c.94.1.2 35883 1f1uA 323 8.78e+00 d.32.1.3 83200 d.32.1.3 83201 1b7iA 66 9.01e+00 1msi b.85.1.1 28288 1m5wA 243 9.09e+00 c.1.24.1 84836 1ho1A 242 9.12e+00 1ho1A c.1.24.1 61097 1jabA 66 9.18e+00 1msi b.85.1.1 28284 1gkpA 458 9.22e+00 b.92.1.3 70231 c.1.9.6 70232 1mh6A 125 9.34e+00 d.32.1.2 79116 1ewjA 126 9.36e+00 1ecsA d.32.1.2 59526 1qu9A 128 9.42e+00 1qu9A d.79.1.1 39755 4lipD 320 9.49e+00 1cvl c.69.1.18 34783 2jiaA 66 9.60e+00 1msi b.85.1.1 28286 1ypn 313 9.74e+00 1pda c.94.1.1 35754 d.50.2.1 38797 1ecsA 126 9.79e+00 1ecsA d.32.1.2 59407 1gtkA 313 9.82e+00 c.94.1.1 76346 d.50.2.1 76347 1v02A 565 9.94e+00 1e4iA 447 1.00e+01 1e70M c.1.8.4 59225 1m3uA 264 1.01e+01 c.1.12.8 84784 1tr1A 447 1.01e+01 1e70M c.1.8.4 28957 1gzgA 337 1.02e+01 c.1.10.3 70805 1b4kA 337 1.12e+01 1b4kA c.1.10.3 29184 9msiA 66 1.13e+01 1msi b.85.1.1 28307 1km5A 247 1.13e+01 c.1.2.3 72741 1bgaA 447 1.14e+01 1e70M c.1.8.4 28961 1bggA 448 1.14e+01 1e70M c.1.8.4 28953 1gvcA 157 1.16e+01 c.94.1.2 65607 8ameA 66 1.16e+01 1msi b.85.1.1 28301 1gv8A 159 1.16e+01 c.94.1.2 65606 1j6oA 268 1.16e+01 c.1.9.12 77088 1v02E 565 1.17e+01 1mjnA 179 1.18e+01 c.62.1.1 79210 1pkxA 592 1.18e+01 1ovb 159 1.18e+01 1nnt c.94.1.2 35875 1uufA 369 1.19e+01 1mq8B 177 1.19e+01 c.62.1.1 79407 1j08A 226 1.19e+01 c.47.1.2 83855 c.47.1.2 83856 1h5yA 253 1.22e+01 c.1.2.1 65638 1vpe 398 1.24e+01 16pk c.86.1.1 35453 7ameA 66 1.24e+01 1msi b.85.1.1 28287 1plq 258 1.25e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1eiwA 111 1.30e+01 1eiwA c.23.3.1 31130 1ojxA 263 1.35e+01 1v03A 565 1.37e+01 1ad1A 266 1.38e+01 1aj2 c.1.21.1 29668 1klyA 247 1.40e+01 c.1.2.3 72730 2tpsA 227 1.40e+01 2tpsA c.1.3.1 28591 6ameA 66 1.44e+01 1msi b.85.1.1 28299 2ameA 66 1.53e+01 1msi b.85.1.1 28300 1pda 313 1.54e+01 1pda c.94.1.1 35751 d.50.2.1 38794 1qoxA 449 1.57e+01 c.1.8.4 28965 1msjA 66 1.62e+01 1msi b.85.1.1 28305 1losA 224 1.63e+01 c.1.2.3 74157 1dtlA 161 1.64e+01 1ncx a.39.1.5 17229 1ile 821 1.65e+01 1ile a.27.1.1 16924 b.51.1.1 26889 c.26.1.1 31591 1f74A 293 1.67e+01 1nal3 c.1.10.1 29079 1aj4 161 1.69e+01 1ncx a.39.1.5 17244 1uyrA 737 1.73e+01 1klzA 247 1.73e+01 c.1.2.3 72731 1uyvA 737 1.74e+01 1km4A 247 1.75e+01 c.1.2.3 72740 1lp6A 229 1.79e+01 c.1.2.3 74171 1dvjA 246 1.80e+01 1dvjA c.1.2.3 28546 1loqA 228 1.81e+01 c.1.2.3 74155 1km2A 247 1.82e+01 c.1.2.3 72738 1km0A 247 1.82e+01 c.1.2.3 72732 1dv7A 227 1.83e+01 1dvjA c.1.2.3 28550 1dot 686 1.88e+01 1nnt c.94.1.2 35876 c.94.1.2 35877 1e5dA 402 1.88e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 1km6A 247 1.89e+01 c.1.2.3 72742 1la0A 161 1.89e+01 a.39.1.5 77864 1od2A 805 1.90e+01 c.14.1.4 86821 c.14.1.4 86822 1km1A 247 1.91e+01 c.1.2.3 72736 1agx 331 1.92e+01 4pgaA c.88.1.1 35564 1b7kA 66 1.92e+01 1msi b.85.1.1 28306 4ameA 66 1.93e+01 1msi b.85.1.1 28298 1vhcA 224 1.94e+01 1uasA 362 1.98e+01 b.71.1.1 88388 c.1.8.1 88389 1uf3A 228 2.03e+01 1ml9A 302 2.07e+01 b.85.7.1 79282 1k8yA 268 2.08e+01 c.1.2.4 72183 1kfbA 268 2.11e+01 c.1.2.4 77369 1f1xA 322 2.13e+01 d.32.1.3 83208 d.32.1.3 83209 1h0pA 182 2.21e+01 b.62.1.1 76450 1iirA 415 2.23e+01 1iirA c.87.1.5 62453 1beuA 268 2.24e+01 2tysA c.1.2.4 28574 1r30A 369 2.35e+01 1m54A 363 2.37e+01 c.79.1.1 74463 1p50A 356 2.47e+01 a.83.1.1 87786 d.128.1.2 87787 1qopA 268 2.50e+01 2tysA c.1.2.4 28570 1l5zA 155 2.50e+01 c.23.1.1 77722 1kfcA 268 2.52e+01 c.1.2.4 77371 1q3sA 548 2.53e+01 1gydB 315 2.55e+01 b.67.2.1 70751 1bg0 356 2.56e+01 1qh4A a.83.1.1 18476 d.128.1.2 41211 1m15A 357 2.57e+01 a.83.1.1 78368 d.128.1.2 78369 1qkkA 155 2.59e+01 1dbwA c.23.1.1 31104 1nkwS 115 2.60e+01 i.1.1.2 80604 1q3qA 548 2.61e+01 1rl1A 114 2.66e+01 1p5dX 463 2.67e+01 1f9aA 168 2.70e+01 1f9aA c.26.1.3 31602 1oe9B 151 2.71e+01 1o1zA 234 2.71e+01 c.1.18.3 86555 1jbqA 435 2.73e+01 1oasA c.79.1.1 62850 1km3A 247 2.77e+01 c.1.2.3 72739 1o99A 511 2.77e+01 c.105.1.1 81235 c.76.1.3 81236 1o73A 144 2.79e+01 c.47.1.10 86638 1j1lA 290 2.86e+01 1od0A 468 2.88e+01 c.1.8.4 86818 1o98A 511 2.89e+01 c.105.1.1 86684 c.76.1.3 86685 1io2A 213 2.90e+01 1ekeA c.55.3.1 62612 1s5pA 235 2.93e+01 1ovgA 238 3.00e+01 1fa2A 498 3.02e+01 1byb c.1.8.1 28797 1pk9A 237 3.06e+01 1ecpA 238 3.07e+01 1ecpA c.56.2.1 33775 1pw7A 239 3.08e+01 1brt 277 3.10e+01 1brt c.69.1.12 34699 1d4xA 375 3.15e+01 1yagA c.55.1.1 59107 c.55.1.1 59108 1e19A 314 3.16e+01 1b7bA c.73.1.1 34967 1pnuS 113 3.27e+01 i.1.1.1 88216 1kq1A 77 3.35e+01 b.38.1.2 72848 1q0cA 365 3.40e+01 d.32.1.3 88343 d.32.1.3 88344 1p9qC 256 3.43e+01 1nzoA 363 3.43e+01 1pzgA 331 3.49e+01 1k2yX 463 3.52e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1q3rA 548 3.56e+01 1d6sA 322 3.66e+01 1oasA c.79.1.1 35295 1viaA 175 3.67e+01 1lte 239 3.67e+01 1led b.29.1.1 24047 1fcjA 322 3.69e+01 1oasA c.79.1.1 35289 1nj4A 363 3.78e+01 b.105.1.1 80545 e.3.1.1 80546 1gdhA 320 3.88e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1p52A 357 3.88e+01 a.83.1.1 87792 d.128.1.2 87793 1ka9F 252 3.95e+01 c.1.2.1 77307 1fiuA 286 3.96e+01 1fiuA c.52.1.10 33317