# List of top-scoring protein chains for t04-100-30-str2 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 1jogA 146 1.78e-28 a.24.16.2 77142 1dk8A 147 7.13e-02 1agrE a.91.1.1 18548 1aua 296 8.33e-02 1aua a.5.3.1 16290 c.13.1.1 30882 1rx0A 393 1.09e-01 a.29.3.1 -742 e.6.1.1 -11858 1i50B 1224 1.17e-01 e.29.1.1 61755 1or7A 194 1.71e-01 a.4.13.2 87332 a.177.1.1 87333 1b8dA 164 2.26e-01 1cpcA a.1.1.3 15665 1js8A 394 2.41e-01 a.86.1.1 67219 b.112.1.1 67220 1buoA 121 2.96e-01 1buoA d.42.1.1 38631 1mojA 182 3.23e-01 a.25.1.1 -669 2cxbA 124 3.35e-01 1ycc a.3.1.1 15891 1cxc 124 3.38e-01 1ycc a.3.1.1 15890 1h16A 759 3.99e-01 c.7.1.1 76462 1mb3A 124 4.77e-01 c.23.1.1 78907 1s7zA 117 6.03e-01 unknown_sccs -344 1cm5A 759 7.01e-01 1cm5A c.7.1.1 30671 1n3kA 130 8.00e-01 a.77.1.4 79965 1icrA 217 8.18e-01 1vfrA d.90.1.1 62274 1o3uA 135 9.38e-01 a.24.16.3 86615 1iw7C 1119 1.13e+00 e.29.1.1 71474 1su8A 636 1.53e+00 e.26.1.2 -12015 1jjyA 636 1.53e+00 1jjyA 1cxzB 86 1.60e+00 1cxzB a.2.6.1 15705 1pa7A 130 1.68e+00 a.40.1.1 -896 1l3lA 234 1.75e+00 a.4.6.2 73541 d.110.5.1 73542 1nksA 194 1.83e+00 1nksA c.37.1.1 31886 3lynA 136 1.89e+00 1lis a.19.1.1 16413 1k04A 162 1.90e+00 a.24.14.1 67904 1ir6A 424 1.95e+00 c.107.1.2 71342 1q08A 99 2.03e+00 a.6.1.3 -381 1mvoA 136 2.07e+00 c.23.1.1 79513 1rkeA 262 2.17e+00 a.24.9.1 -582 a.24.9.1 -583 1bhdA 118 2.20e+00 1bkrA a.40.1.1 17398 1ah7 245 2.25e+00 1ah7 a.124.1.1 19339 1e4yA 214 2.28e+00 1zin c.37.1.1 31901 g.41.2.1 45181 1rfzA 168 2.48e+00 unknown_sccs -1206 1uzbA 516 2.51e+00 c.82.1.1 -8552 1nznA 126 2.53e+00 a.118.8.1 -1616 1rktA 205 2.59e+00 a.4.1.9 -210 a.121.1.1 -1663 1fpoA 171 2.59e+00 1fpoA a.2.3.1 15693 a.23.1.1 16487 1teaA 299 2.77e+00 1qh8A 478 2.85e+00 1qguA c.92.2.3 35633 1k4nA 192 2.88e+00 d.32.1.5 72059 1miwA 404 2.94e+00 a.173.1.1 79162 d.218.1.4 79163 1amf 233 3.02e+00 1wod c.94.1.1 35833 2gdm 153 3.04e+00 2gdm a.1.1.2 15212 1ockA 412 3.42e+00 c.117.1.1 86802 1h6pA 203 3.58e+00 a.146.1.1 60690 1nu7D 282 3.69e+00 unknown_sccs -433 unknown_sccs -434 1qmyA 167 3.76e+00 1qmyA d.3.1.2 37094 1dcs 311 3.84e+00 1dcs b.82.2.1 28124 2igd 61 3.85e+00 2igd d.15.7.1 37821 1sqsA 242 3.87e+00 unknown_sccs -6433 1rkpA 326 3.90e+00 a.125.1.1 -1729 1qq5A 253 3.95e+00 1qq5A c.108.1.1 43327 1o98A 511 3.99e+00 c.105.1.1 86684 c.76.1.3 86685 1f74A 293 3.99e+00 1nal3 c.1.10.1 29079 1eqjA 511 4.07e+00 1ejjA c.105.1.1 59495 c.76.1.3 59496 1i58A 189 4.38e+00 1b3qA d.122.1.3 61773 1v4eA 299 4.38e+00 a.128.1.1 -1781 1m6kA 251 4.47e+00 e.3.1.1 78695 1izmA 184 4.64e+00 unknown_sccs -1233 1ov2A 99 4.71e+00 a.13.1.1 -457 1mp4A 292 4.74e+00 c.68.1.6 79376 1wod 233 4.80e+00 1wod c.94.1.1 35832 1uqvA 85 5.09e+00 a.60.1.2 -1010 1q02A 52 5.21e+00 a.5.2.1 -351 4crxA 322 5.36e+00 4crxA a.60.9.1 18095 d.163.1.1 42155 2nacA 393 5.38e+00 2nadA c.2.1.4 30088 c.23.12.1 31348 1i39A 225 5.81e+00 1ekeA c.55.3.1 61585 1ld8A 382 5.85e+00 a.118.6.1 73838 1p9bA 442 6.01e+00 c.37.1.10 -7115 1lvaA 258 6.08e+00 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1pq9A 253 6.15e+00 a.123.1.1 -1687 1i8jA 323 6.23e+00 1b4kA c.1.10.3 61968 2tct 207 6.54e+00 2tct a.4.1.9 16063 a.121.1.1 19240 1l6sA 323 6.66e+00 c.1.10.3 73627 2occE 109 6.75e+00 2occE a.118.11.1 19224 1ebmA 317 6.77e+00 1ebmA a.96.1.3 18751 d.129.1.2 41300 1oxkB 134 6.87e+00 c.23.1.1 -6411 1lis 136 6.93e+00 1lis a.19.1.1 16406 2lisA 136 6.93e+00 1lis a.19.1.1 16405 1o5hA 214 6.96e+00 unknown_sccs -1078 1ukz 203 7.21e+00 1zin c.37.1.1 31840 7a3hA 303 7.33e+00 7a3hA c.1.8.3 28817 1qgtA 149 7.65e+00 1qgtA a.62.1.1 18135 1g60A 260 7.65e+00 c.66.1.11 70151 1dgfA 497 7.65e+00 1cf9A e.5.1.1 42782 1jvsA 400 7.70e+00 a.69.3.1 77187 c.2.1.3 77188 d.81.1.3 77189 1v4vA 376 7.76e+00 c.87.1.3 -8583 1tmy 120 7.81e+00 1dbwA c.23.1.1 31083 1q0qA 406 7.81e+00 1at3A 247 8.00e+00 1at3A b.57.1.1 27021 1jipA 403 8.00e+00 a.104.1.1 66748 1v54E 109 8.02e+00 a.118.11.1 -1652 1qq7A 253 8.10e+00 1qq5A c.108.1.1 43329 1b5tA 275 8.16e+00 1b5tA c.1.23.1 29676 1ki1B 352 8.25e+00 a.87.1.1 72497 b.55.1.1 72498 1p32A 209 8.35e+00 1p32A d.25.1.1 38379 1sqgA 429 8.35e+00 1mi3A 322 8.85e+00 c.1.7.1 -5257 1h8uA 117 8.93e+00 1h8uA d.169.1.1 60793 1mjhA 162 9.03e+00 1mjhA c.26.2.4 31639 1fjgD 209 9.12e+00 1c05A d.66.1.2 39553 1a0p 290 9.13e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 1jj2L 194 9.19e+00 1ffkI d.12.1.2 63097 1o4sA 389 9.19e+00 c.67.1.1 86620 1f44A 324 9.23e+00 a.60.9.1 64982 d.163.1.1 64983 1csn 298 9.30e+00 1csn d.144.1.7 41664 1au1A 166 9.53e+00 1ifa a.26.1.3 16889 1cjcA 460 9.65e+00 1cjcA c.3.1.1 30319 c.4.1.1 30604 1wdgA 94 9.72e+00 1q0gA 117 9.77e+00 1q6hA 224 9.82e+00 d.26.1.1 -9487 1q1aA 289 1.03e+01 c.31.1.5 -6781 1qgrA 876 1.07e+01 1qgrA a.118.1.1 19119 1ur3M 319 1.08e+01 c.1.7.1 -5248 1jigA 146 1.09e+01 a.25.1.1 71685 1k38A 254 1.13e+01 e.3.1.1 84303 1umdA 367 1.18e+01 c.36.1.11 -6969 1us6A 102 1.19e+01 2a0b 125 1.20e+01 2a0b a.24.10.1 16630 1oj7A 408 1.23e+01 1uzcA 71 1.23e+01 a.159.2.1 -339 1ui8A 638 1.24e+01 b.30.2.1 -3525 d.17.2.1 -9272 d.17.2.1 -9273 1r8iA 213 1.25e+01 unknown_sccs -411 1hlvA 131 1.26e+01 a.4.1.7 65854 a.4.1.7 65855 1knqA 175 1.27e+01 c.37.1.17 72786 1j09A 468 1.27e+01 a.97.1.1 77025 c.26.1.1 77026 1ccwA 137 1.27e+01 1be1 c.23.6.1 31238 1a6m 151 1.28e+01 1a6m a.1.1.2 15018 1k6wA 426 1.34e+01 b.92.1.2 68236 c.1.9.5 68237 1e7uA 961 1.35e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1p4oA 322 1.35e+01 d.144.1.7 87775 1jsxA 207 1.36e+01 c.66.1.20 71846 1vkeA 133 1.37e+01 1ail 73 1.38e+01 1ail a.16.1.1 16381 1a32 88 1.40e+01 1a32 a.16.1.2 16384 1eexA 554 1.46e+01 1dioA c.1.19.3 29650 1g03A 134 1.47e+01 1qrjB a.73.1.1 60162 1m1nA 491 1.49e+01 c.92.2.3 78417 1iqyA 638 1.50e+01 b.30.2.1 76763 d.17.2.1 76764 d.17.2.1 76765 1r5lA 262 1.50e+01 a.5.3.1 -360 c.13.1.1 -6215 1jnyA 435 1.50e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1pvyA 227 1.52e+01 d.115.1.2 -10937 1hrkA 359 1.53e+01 1hrkA c.92.1.1 61228 1dg9A 157 1.54e+01 1dg9A c.44.1.1 32637 1j4nA 271 1.57e+01 f.19.1.1 71510 1t7pA 698 1.61e+01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1d1qA 161 1.63e+01 1dg9A c.44.1.1 32642 1snnA 227 1.66e+01 1w2wA 211 1.66e+01 1bh9B 89 1.67e+01 1bh9B a.22.1.3 16485 1k3yA 221 1.67e+01 a.45.1.1 77245 c.47.1.5 77246 1rxqA 178 1.67e+01 1hwxA 501 1.68e+01 1hwyA c.2.1.7 30250 c.58.1.1 33898 1ciy 590 1.69e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1dat 174 1.70e+01 2fha a.25.1.1 16677 1ui7A 638 1.71e+01 b.30.2.1 -3523 d.17.2.1 -9268 d.17.2.1 -9269 1jk0A 419 1.78e+01 a.25.1.2 63142 1ihgA 370 1.81e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1qwgA 251 1.84e+01 unknown_sccs -5678 2lbp 346 1.87e+01 2liv c.93.1.1 35709 1n40A 396 1.87e+01 a.104.1.1 79977 1udxA 416 1.88e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1pjr 724 1.89e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 1ozjA 144 1.92e+01 d.164.1.1 -11537 1m3qA 317 1.96e+01 a.96.1.3 -1288 d.129.1.2 -11006 1rwhA 757 1.97e+01 a.102.3.2 -1340 b.24.1.1 -3300 b.30.5.2 -3508 1ntyA 311 1.99e+01 1r6rA 100 1.99e+01 unknown_sccs -1071 1go3F 107 1.99e+01 a.60.8.2 65407 1eupA 403 2.00e+01 1rom a.104.1.1 18967 1jalA 363 2.01e+01 c.37.1.8 84138 d.15.10.2 84139 1rxxA 421 2.02e+01 unknown_sccs -10982 1c0eA 157 2.02e+01 1dg9A c.44.1.1 32638 1im8A 244 2.03e+01 c.66.1.14 66212 1g4yR 148 2.06e+01 1cll a.39.1.5 60252 1q5zA 177 2.07e+01 unknown_sccs -1215 1vhnA 318 2.07e+01 c.1.4.1 -5209 1d8wA 426 2.09e+01 1de5A c.1.15.2 29394 1bykA 255 2.09e+01 1bykA c.93.1.1 35706 1a76 326 2.09e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1apyA 162 2.11e+01 1apyA d.153.1.5 42004 1qgoA 264 2.13e+01 1qgoA c.92.1.2 35596 1tdhA 364 2.14e+01 1hw1A 239 2.14e+01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1n1fA 159 2.15e+01 a.26.1.3 79803 1gk9B 557 2.19e+01 2gsq 202 2.20e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1vhzA 198 2.20e+01 d.113.1.1 -10897 1no7A 604 2.24e+01 unknown_sccs -12043 1usgA 346 2.24e+01 c.93.1.1 -8635 1iybA 208 2.25e+01 d.124.1.1 -10977 1chkA 238 2.27e+01 1chkA d.2.1.7 36999 1ls1A 295 2.29e+01 a.24.13.1 78170 c.37.1.10 78171 2sqcA 631 2.30e+01 2sqcA a.102.4.2 18854 a.102.4.2 18855 1b0b 142 2.32e+01 2fal a.1.1.2 15010 1l3pA 102 2.35e+01 a.24.17.1 84520 1k20A 310 2.36e+01 c.107.1.1 68027 1k0wA 231 2.39e+01 c.74.1.1 77220 1qflA 389 2.43e+01 1afwA c.95.1.1 35908 c.95.1.1 35909 1e6yB 433 2.44e+01 1mroB a.89.1.1 18535 d.58.31.2 39453 1wdcB 156 2.47e+01 1wdcB a.39.1.5 17302 1p3jA 217 2.48e+01 c.37.1.1 -6996 g.41.2.1 -12769 1m3kA 392 2.49e+01 c.95.1.1 78565 c.95.1.1 78566 1viuA 203 2.50e+01 d.113.1.1 -10889 1r5zA 323 2.51e+01 unknown_sccs -12289 1pu6A 218 2.51e+01 unknown_sccs -1282 1hvvA 75 2.52e+01 1hvvA h.1.15.1 45639 1l9lA 74 2.54e+01 a.64.1.1 77827 1o9rA 162 2.54e+01 a.25.1.1 86706 1m4tA 392 2.57e+01 c.95.1.1 78617 c.95.1.1 78618 1ax4A 467 2.58e+01 1ax4A c.67.1.2 34391 1mh1 186 2.59e+01 1eesA c.37.1.8 32002 1gxyA 226 2.64e+01 d.166.1.3 76380 1f8mA 429 2.65e+01 1dquA c.1.12.7 29315 1c7gA 456 2.68e+01 c.67.1.2 -8153 1hq0A 295 2.71e+01 1hzgA d.194.1.1 61122 1t7sA 137 2.75e+01 1kk8B 139 2.76e+01 a.39.1.5 77430 1ojrA 274 2.77e+01 c.74.1.1 -8441 1lb2B 84 2.79e+01 a.60.3.1 77871 1anv 356 2.82e+01 1anv a.54.1.1 17890 g.51.1.1 45365 g.51.1.1 45371 1oi7A 288 2.83e+01 c.2.1.8 87049 c.23.4.1 87050 1f61A 429 2.85e+01 1dquA c.1.12.7 29319 1ift 263 2.88e+01 1mrj d.165.1.1 42211 1v9mA 323 2.90e+01 unknown_sccs -12292 1n7sB 68 2.92e+01 h.1.15.1 80272 1oniA 137 2.96e+01 d.79.1.1 87144 1ej0A 180 2.98e+01 1ej0A c.66.1.2 34179 1k94A 165 2.98e+01 a.39.1.8 68333 2abk 211 2.98e+01 2abk a.96.1.1 18743 1itcA 516 3.01e+01 b.3.1.1 83705 c.1.8.1 83706 1e8yA 966 3.03e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1jdw 423 3.03e+01 1jdw d.126.1.2 41129 1s5aA 150 3.06e+01 unknown_sccs -9300 1dmhA 311 3.09e+01 1dmhA b.3.6.1 22633 1uxoA 192 3.10e+01 1n1bA 549 3.21e+01 a.102.4.1 79799 a.128.1.3 79800 1mo0A 275 3.27e+01 c.1.1.1 79329 1e3aB 560 3.28e+01 1ajqB 1ib3A 349 3.29e+01 1ib2A 1oshA 232 3.30e+01 a.123.1.1 -1697 1jdpA 441 3.30e+01 c.93.1.1 62906 1dceA 567 3.30e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1oi6A 205 3.33e+01 1ofnA 205 3.33e+01 b.82.1.1 -4830 1qlaA 656 3.33e+01 1qlaA a.7.3.1 16328 c.3.1.4 30427 d.168.1.1 42310 1a9xA 1058 3.36e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1q1fA 151 3.38e+01 1ee4A 423 3.41e+01 1ee4A a.118.1.1 19128 1d9cA 121 3.46e+01 1d9cA a.26.1.3 16901 1i1nA 226 3.48e+01 c.66.1.7 71102 1gzsB 165 3.48e+01 a.168.1.1 76425 1m0uA 249 3.49e+01 a.45.1.1 78359 c.47.1.5 78360 1e3mA 800 3.52e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1lj2A 110 3.53e+01 h.1.13.2 73926 1fftC 204 3.56e+01 1fftC f.25.1.1 43629 1fmjA 351 3.59e+01 c.37.1.5 59879 1gjnA 153 3.60e+01 a.1.1.2 70191 1d8dA 377 3.63e+01 1ft1A a.118.6.1 19185 1dy5A 124 3.63e+01 7rsa d.5.1.1 37163 1fcjA 322 3.67e+01 1oasA c.79.1.1 35289 1p9qC 256 3.69e+01 1isiA 265 3.69e+01 e.4.1.1 71394 1dwtA 153 3.69e+01 1a6m a.1.1.2 15190 1ib2A 349 3.71e+01 1ib2A a.118.1.8 62141 1r5pA 108 3.75e+01 unknown_sccs -7487 1avk 638 3.81e+01 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1qahA 136 3.84e+01 d.79.1.1 -10377 1ks9A 291 3.84e+01 a.100.1.7 68857 c.2.1.6 68858 1pvaA 110 3.88e+01 1a75A a.39.1.4 17207 1ufyA 122 3.90e+01 d.79.1.2 88489 1ehkA 562 3.91e+01 1ehkA f.24.1.1 43624 1dzaA 129 3.92e+01 7rsa d.5.1.1 37275 1rlr 761 3.92e+01 1rlr a.98.1.1 18753 c.7.1.2 30679 1mhdA 132 3.94e+01 1mhdA d.164.1.1 42175 1lssA 140 3.96e+01 c.2.1.9 74246 1brwA 433 3.98e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626