# List of top-scoring protein chains for T0373.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 2a61A 145 4.62e-16 2fbhA 146 2.09e-15 1jgsA 138 2.80e-15 a.4.5.28 66683 2fbiA 142 3.33e-15 1z91A 147 6.01e-15 2ethA 154 1.21e-14 1lnwA 147 7.16e-14 a.4.5.28 78104 1s3jA 155 2.38e-13 a.4.5.28 98437 1lj9A 144 5.24e-13 a.4.5.28 78035 2fxaA 207 1.85e-09 1hsjA 487 8.72e-07 4mbp a.4.5.28,c.94.1.1 61237,61238 1p4xA 250 4.58e-06 a.4.5.28,a.4.5.28 87784,87785 1ku9A 152 5.86e-06 a.4.5.36 77544 1ub9A 100 1.10e-05 a.4.5.28 99159 2fnpA 124 2.16e-05 2frhA 127 4.75e-05 1fzpB 123 5.04e-05 1fznD a.4.5.28 19008 1on2A 142 6.22e-05 a.4.5.24,a.76.1.1 87103,87104 2ev0A 142 8.28e-05 1b1bA 140 4.71e-04 1bi0 a.4.5.24,a.76.1.1 16215,18421 1fx7A 230 4.94e-04 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1sfxA 109 6.69e-04 a.4.5.50 105505 1mkmA 249 1.01e-03 a.4.5.33,d.110.2.2 79242,79243 1f5tA 121 1.55e-03 1bi0 a.4.5.24,a.76.1.1 16203,18409 1c0wA 225 1.62e-03 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 2tdx 226 1.72e-03 1bi0 a.4.5.24,a.76.1.1 16201,18407 1g3tA 226 1.76e-03 a.4.5.24,a.76.1.1,b.34.1.2 65127,65128,65129 2dtr 226 1.77e-03 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1fwzA 226 1.96e-03 a.4.5.24,a.76.1.1,b.34.1.2 60077,60078,60079 1g3yA 226 2.07e-03 a.4.5.24,a.76.1.1,b.34.1.2 65136,65137,65138 1z7uA 112 2.61e-03 1xcvA 139 3.33e-03 1p92A 226 3.66e-03 a.4.5.24,a.76.1.1,b.34.1.2 104085,104086,104087 2cfxA 144 4.85e-03 1okrA 123 5.58e-03 a.4.5.39 93269 1sd6A 123 7.73e-03 a.4.5.39 98803 2b0lA 102 9.33e-03 1ulyA 192 1.69e-02 2dbbA 151 1.79e-02 1r22A 122 1.96e-02 a.4.5.5 104777 1yyvA 131 2.22e-02 1i1gA 141 3.31e-02 a.4.5.32,d.58.4.2 65982,65983 1dpuA 99 3.38e-02 1dpuA a.4.5.16 16150 1z1dA 103 3.44e-02 1xnpA 202 3.60e-02 1sd4A 126 3.97e-02 a.4.5.39 105428 1r1tA 122 4.19e-02 a.4.5.5 104769 2co5A 99 4.46e-02 1ft9A 222 5.90e-02 1ft9A a.4.5.4,b.82.3.1 16107,28131 1xmaA 145 6.87e-02 1o3sA 200 7.65e-02 a.4.5.4,b.82.3.2 86609,86610 2fswA 107 8.08e-02 2g7uA 257 9.04e-02 1o5lA 213 9.98e-02 b.82.3.2 92506 1j75A 67 1.06e-01 a.4.5.19 62673 1hw5A 210 1.12e-01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1o3tA 200 1.13e-01 a.4.5.4,b.82.3.2 86611,86612 2f2eA 146 1.14e-01 1i6xA 209 1.18e-01 a.4.5.4,b.82.3.2 83673,83674 1i5zA 209 1.18e-01 a.4.5.4,b.82.3.2 83669,83670 1g6nA 210 1.18e-01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1cgpA 205 1.20e-01 a.4.5.4,b.82.3.2 16096,28135 1bw6A 56 1.60e-01 1bw6A a.4.1.7 16052 1u2wA 122 1.82e-01 1ruoA 209 2.03e-01 2cgpA a.4.5.4,b.82.3.2 16105,28144 1tbxA 99 2.29e-01 a.4.5.48 106748 1hlvA 131 2.53e-01 a.4.1.7,a.4.1.7 65854,65855 2acjA 66 2.94e-01 1q1hA 110 3.07e-01 a.4.5.41 95580 1qgpA 77 3.23e-01 1qbjA a.4.5.19 16158 1ri7A 171 3.47e-01 a.4.5.32,d.58.4.2 97504,97505 1qbjA 81 3.56e-01 1qbjA a.4.5.19 16155 1xn7A 78 3.84e-01 1r1uA 106 4.45e-01 a.4.5.5 104771 1zljA 78 5.21e-01 1zybA 232 5.53e-01 1wdvA 152 6.40e-01 1zlkA 95 8.06e-01 1ixcA 294 8.23e-01 a.4.5.37,c.94.1.1 83764,83765 1je8A 82 8.26e-01 a.4.6.2 77108 2cg4A 152 9.89e-01 1wucA 250 1.05e+00 1wsuA 124 1.10e+00 1v4rA 102 1.21e+00 1p6rA 82 1.31e+00 a.4.5.39 94187 1yg2A 179 1.38e+00 1bjaA 95 1.42e+00 1bjaA a.4.5.9 16122 1i1sA 96 1.42e+00 1bjaA a.4.5.9 16124 1lvaA 258 1.48e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1sgoA 139 1.57e+00 d.82.3.1 98857 1q2lA 939 1.65e+00 1mzbA 136 1.85e+00 a.4.5.42 91497 1t6sA 162 1.94e+00 2fu4A 83 2.19e+00 6paxA 133 2.21e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 1lccA 51 2.31e+00 1pru a.35.1.5 17110 1wi9A 72 2.39e+00 1lqc 56 2.48e+00 1pru a.35.1.5 17109 1z6rA 406 2.62e+00 1cjgA 62 2.73e+00 1pru a.35.1.5 17112 1l1mA 62 2.76e+00 a.35.1.5 73474 2eshA 118 2.84e+00 1pdnC 128 2.84e+00 6paxA a.4.1.5 16047 1z05A 429 3.09e+00 1c8bA 371 3.18e+00 1c8bA c.56.1.2 59082 1s7oA 113 3.43e+00 a.4.13.3 105354 1e2xA 243 3.49e+00 1e2xA a.4.5.6,a.78.1.1 16113,18443 1hw1A 239 3.67e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 2bjcA 62 3.75e+00 1k78A 149 3.86e+00 a.4.1.5,a.4.1.5 68255,68256 1yqyA 523 4.02e+00 1utxA 66 4.23e+00 a.35.1.3 108034 1ge9A 184 4.60e+00 1dd5A d.67.3.1 60463 2givA 295 4.68e+00 2bx9A 53 4.68e+00 1tw3A 360 4.73e+00 a.4.5.29,c.66.1.12 107373,107374 2a2jA 246 5.70e+00 1pwuA 776 5.72e+00 d.92.1.14,d.92.1.14,d.166.1.1 95244,95245,95246 1j7nA 776 5.83e+00 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1zx4A 192 6.14e+00 2bgsA 344 6.55e+00 1p5fA 189 6.71e+00 c.23.16.2 94142 1pdvA 197 6.73e+00 c.23.16.2 88036 1pe0A 197 6.89e+00 c.23.16.2 88045 1al3 324 6.90e+00 1al3 c.94.1.1 35835 1j42A 189 6.93e+00 c.23.16.2 90837 1zcoA 262 7.56e+00 1ka2A 499 8.05e+00 d.92.1.5 77305 1lea 84 8.37e+00 1lea a.4.5.2 16085 1rr7A 129 9.95e+00 a.4.1.14 105075 1y56B 382 1.03e+01 1j5yA 187 1.07e+01 a.4.5.1,d.94.2.1 71592,71593 1ev7A 317 1.10e+01 1ev7B c.52.1.9 33315 1in6A 334 1.15e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1puoA 170 1.23e+01 a.101.1.1,a.101.1.1 95134,95135 1jhhA 202 1.25e+01 a.4.5.2,b.87.1.1 63060,63061 1y0uA 96 1.25e+01 1jhfA 202 1.27e+01 a.4.5.2,b.87.1.1 63057,63058 1j7kA 334 1.33e+01 1hqcA a.4.5.11,c.37.1.20 62695,62696 2bj4A 252 1.34e+01 1r71A 178 1.35e+01 a.4.14.1 104823 1in8A 334 1.37e+01 1hqcA a.4.5.11,c.37.1.20 62605,62606 1in4A 334 1.37e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1in5A 334 1.37e+01 1hqcA a.4.5.11,c.37.1.20 62599,62600 1in7A 334 1.38e+01 1hqcA a.4.5.11,c.37.1.20 62603,62604 1x7rA 245 1.39e+01 1gwqA 248 1.40e+01 a.123.1.1 76366 1gwrA 245 1.40e+01 a.123.1.1 76368 1g50A 247 1.40e+01 a.123.1.1 65149 2b1vA 257 1.41e+01 1qkuA 250 1.41e+01 3erdA a.123.1.1 19306 1xpcA 248 1.42e+01 1errA 253 1.42e+01 3erdA a.123.1.1 19298 1a52A 258 1.42e+01 3erdA a.123.1.1 19296 3ertA 261 1.43e+01 3erdA a.123.1.1 19292 1onkA 254 1.47e+01 d.165.1.1 93359 1pcgA 244 1.56e+01 a.123.1.1 94432 2ayrA 248 1.59e+01 1xqcA 254 1.60e+01 1m2tA 254 1.66e+01 d.165.1.1 84761 1l2iA 261 1.68e+01 a.123.1.1 73503 1b0nA 111 1.69e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 2a33A 215 1.71e+01 1kyzA 365 1.84e+01 a.4.5.29,c.66.1.12 73312,73313 1puzA 82 1.86e+01 a.218.1.1 104320 1iyxA 432 1.92e+01 c.1.11.1,d.54.1.1 83815,83816 2g7gA 213 1.94e+01 1v88A 130 1.95e+01 b.55.1.1 108423 1efaA 333 2.00e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1jyfA 349 2.05e+01 c.93.1.1 67456 2b5aA 77 2.06e+01 1jyeA 349 2.06e+01 c.93.1.1 67455 2bgcA 238 2.07e+01 2beoA 236 2.08e+01 1xdpA 687 2.13e+01 1pru 56 2.14e+01 1pru a.35.1.5 17104 1lbiA 360 2.15e+01 1tlfA c.93.1.1 35694 1omiA 248 2.24e+01 b.82.3.3,a.4.5.4 87079,87080 1zncA 266 2.24e+01 2cba b.74.1.1 27955 1g91A 77 2.24e+01 1b3aA d.9.1.1 60389 1p3y1 194 2.28e+01 1pumA 249 2.28e+01 d.165.1.1 104314 1jhgA 101 2.36e+01 1jhgA a.4.12.1 19009 1a04A 215 2.39e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1kn6A 90 2.44e+01 d.58.3.3 72770 1s1iQ 100 2.49e+01 i.1.1.1 105191 2hcc 66 2.54e+01 1b3aA d.9.1.1 37457 2a6cA 83 2.55e+01 1erg 70 2.55e+01 1cds g.7.1.3 44462 1mt0A 241 2.57e+01 c.37.1.12 85096 1xefA 241 2.57e+01 1ldkB 366 2.63e+01 a.4.5.34,e.40.1.1 73852,73853 1cdq 77 2.77e+01 1cds g.7.1.3 44459 1uirA 314 2.78e+01 c.66.1.17 99429 1fehA 574 2.83e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1res 43 2.84e+01 1ret a.4.1.2 16023 1qzzA 374 3.03e+01 a.4.5.29,c.66.1.12 96719,96720 1xsvA 113 3.05e+01 1i6uA 130 3.23e+01 d.140.1.1 61850 1sz6A 249 3.23e+01 1mgtA 174 3.36e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1c75A 71 3.38e+01 451c a.3.1.1 15796 2csbA 519 3.54e+01 1zk8A 183 3.55e+01 1a6i 217 3.77e+01 2tct a.4.1.9,a.121.1.1 16066,19243 1qpiA 203 3.90e+01 2tct a.4.1.9,a.121.1.1 16072,19249 1z67A 135 3.92e+01 2tct 207 3.97e+01 2tct a.4.1.9,a.121.1.1 16063,19240 1bjz 207 3.97e+01 2tct a.4.1.9,a.121.1.1 16065,19242 1r7jA 95 3.98e+01 a.4.5.49 104836 1wmhA 89 4.22e+01 1dl5A 317 4.23e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1g82A 160 4.40e+01 1bfg b.42.1.1 60337 2cohA 202 4.49e+01 1rcsA 105 4.51e+01 1jhgA a.4.12.1 19025 1uthA 315 4.52e+01 c.94.1.1 108032 1uthB 315 4.53e+01 c.94.1.1 108033 2trt 217 4.54e+01 2tct a.4.1.9,a.121.1.1 16064,19241 1utbA 315 4.54e+01 c.94.1.1 108030 2wrpR 107 4.57e+01 1jhgA a.4.12.1 19010 3wrp 108 4.60e+01 1jhgA a.4.12.1 19015 1trrA 107 4.60e+01 1jhgA a.4.12.1 19017 1utbB 315 4.62e+01 c.94.1.1 108031 1troA 108 4.66e+01 1jhgA a.4.12.1 19011 1sfuA 75 4.66e+01 a.4.5.19 105503 1vie 62 4.68e+01 1vie b.34.4.1 24592 1b24A 188 4.83e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1ihkA 174 4.90e+01 1bfg b.42.1.1 62384 1squA 155 4.92e+01 d.252.1.1 98971 1ul1X 379 4.93e+01 2f4iA 197 4.96e+01 1p99A 295 5.01e+01 c.94.1.1 94384 1xkoA 159 5.09e+01 2hdhA 293 5.13e+01 2hdhA a.100.1.3,c.2.1.6 18795,30199 1svdA 473 5.20e+01 1lsjA 302 5.25e+01 a.100.1.3,c.2.1.6 91116,91117 1kjlA 146 5.27e+01 1y0yA 353 5.35e+01 1bdg 451 5.36e+01 1qhaA c.55.1.3,c.55.1.3 33461,33462 2axlA 144 5.37e+01 1xfoA 357 5.40e+01 1il0A 302 5.40e+01 a.100.1.3,c.2.1.6 66189,66190 1f0yA 302 5.45e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 3hadA 308 5.45e+01 2hdhA a.100.1.3,c.2.1.6 18799,30203 1f17A 310 5.45e+01 2hdhA a.100.1.3,c.2.1.6 18797,30201 1lsoA 302 5.46e+01 a.100.1.3,c.2.1.6 91120,91121 1m76A 302 5.48e+01 a.100.1.3,c.2.1.6 91216,91217 1q4rA 112 5.53e+01 d.58.4.4 95823 1dhjA 159 5.54e+01 1vdrA c.71.1.1 34833 1nnwA 252 5.60e+01 d.159.1.5 80674 1uxc 65 5.60e+01 1uxc a.35.1.5 17119 1wxqA 397 5.61e+01 2cu6A 103 5.68e+01 1lqtA 456 5.77e+01 c.3.1.1,c.4.1.1 74198,74199 1orjA 130 5.84e+01 a.24.19.1 93456 1oryA 130 5.85e+01 a.24.19.1 93466 1yf8A 240 5.98e+01 1vj2A 126 5.99e+01 b.82.1.10 100796 1p4wA 99 6.00e+01 a.4.6.2 87783 1nc2B 221 6.02e+01 b.1.1.1,b.1.1.2 91783,91784 1m75A 302 6.03e+01 a.100.1.3,c.2.1.6 91212,91213 1xiqA 157 6.07e+01 3hdhA 302 6.16e+01 2hdhA a.100.1.3,c.2.1.6 18805,30209 2fztA 79 6.29e+01 2lfb 100 6.39e+01 1lfb a.4.1.1 15990 1cqjB 385 6.40e+01 2scuB c.23.4.1,d.142.1.4 31143,41564 2scuB 388 6.45e+01 2scuB c.23.4.1,d.142.1.4 31141,41562 1jllB 388 6.46e+01 c.23.4.1,d.142.1.4 66853,66854 1tcf 159 6.48e+01 1ncx a.39.1.5 17250 1gotB 340 6.59e+01 1tbgA b.69.4.1 27648 1a0rB 340 6.60e+01 1tbgA b.69.4.1 27658 1tbgA 340 6.66e+01 1tbgA b.69.4.1 27649 1zakA 222 6.67e+01 1zin c.37.1.1,g.41.2.1 31913,45202 2bcjB 340 6.67e+01 1g6uA 48 6.69e+01 1g6uA k.9.1.1 46425 1mspA 126 6.74e+01 1mspA b.1.11.2 22333 1ce7A 241 6.78e+01 1mrj d.165.1.1 42194 2mllA 241 6.80e+01 1mrj d.165.1.1 42195 1vgqA 427 6.97e+01 c.123.1.1 108623 1wwlA 312 7.00e+01 1t4cB 427 7.00e+01 c.123.1.1 106411 1vgrA 427 7.00e+01 c.123.1.1 108625 1t3zA 427 7.03e+01 c.123.1.1 106388 1t4cA 427 7.04e+01 c.123.1.1 106410 1p5hA 428 7.06e+01 c.123.1.1 87802 1ldjA 760 7.08e+01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1lfb 99 7.13e+01 1lfb a.4.1.1 15989 1e19A 314 7.14e+01 1b7bA c.73.1.1 34967 1oqlA 249 7.17e+01 d.165.1.1 87306 2axoA 270 7.25e+01 1u6gA 776 7.30e+01 1iab 200 7.45e+01 1iae d.92.1.8 40312 1ddsA 159 7.99e+01 1vdrA c.71.1.1 34858 1jpdX 324 8.02e+01 c.1.11.2,d.54.1.1 67014,67015 1le8A 53 8.10e+01 a.4.1.1 73867 4dfrA 159 8.12e+01 1vdrA c.71.1.1 34822 1draA 159 8.27e+01 1vdrA c.71.1.1 34831 1ra9 159 8.31e+01 1vdrA c.71.1.1 34820 2drcA 159 8.33e+01 1vdrA c.71.1.1 34848 1dhiA 159 8.40e+01 1vdrA c.71.1.1 34844 1sq8A 64 8.41e+01 a.35.1.2 105888 2dc3A 193 8.44e+01 1f3lA 321 8.46e+01 1g6q2 c.66.1.6 59630 1drbA 159 8.63e+01 1vdrA c.71.1.1 34828 1b9mA 265 8.66e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1hfgA 71 8.67e+01 1b3aA d.9.1.1 37409 1s1iB 253 8.68e+01 i.1.1.1 105176 1yrnA 61 8.74e+01 1akhA a.4.1.1 15981 1akhA 61 8.77e+01 1akhA a.4.1.1 15980 1i60A 278 8.87e+01 c.1.15.4 71118 2g7rA 117 8.95e+01 1o7lA 262 9.00e+01 a.4.5.8,b.40.6.2,b.40.6.2 81147,81148,81149