# List of top-scoring protein chains for t2k-100-30-o_notor2-scores 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 1rfeA 162 2.58e-11 2asfA 137 7.30e-10 2fg9A 178 3.10e-08 1xxoA 147 8.42e-08 1w9aA 147 9.21e-08 2aq6A 147 1.02e-07 2fhqA 141 3.04e-07 2furA 209 8.50e-07 1dnlA 199 1.04e-05 1ci0A b.45.1.1 25753 1g79A 218 1.09e-05 1ci0A b.45.1.1 25752 1w3oA 216 2.44e-05 1nrgA 261 6.99e-05 b.45.1.1 80694 1t9mA 214 1.24e-04 1vl7A 157 2.99e-04 b.45.1.1 108732 2arzA 247 5.35e-04 1ty9A 222 8.45e-04 1flmA 122 5.37e-03 1axj b.45.1.1 25747 1axj 122 7.33e-03 1axj b.45.1.1 25749 1ejeA 192 2.35e-02 1ejeA b.45.1.2 25757 1ci0A 228 8.48e-02 1ci0A b.45.1.1 25750 1xhnA 184 4.30e-01 1pvtA 238 9.87e-01 c.74.1.1 95189 1qyaA 307 1.20e+00 d.21.1.2,d.21.1.2 104653,104654 1ko3A 230 1.33e+00 d.157.1.1 90974 1tr8A 102 1.50e+00 1sdjA 310 1.61e+00 d.21.1.2,d.21.1.2 98807,98808 1pysA 350 1.97e+00 1pysA d.104.1.1 40775 1d7pM 159 3.64e+00 1cztA b.18.1.2 23718 1b7yA 350 3.83e+00 1pysA d.104.1.1 40776 1tuaA 191 4.14e+00 d.51.1.1,d.51.1.1 107321,107322 1udzA 182 4.42e+00 b.51.1.1 99239 1qmyA 167 4.67e+00 1qmyA d.3.1.2 37094 1azpA 66 4.67e+00 1azpA b.34.13.1 37467 1h91A 180 4.83e+00 b.60.1.1 60805 1jkmB 361 5.34e+00 1jkmA c.69.1.2 34634 1wnyA 186 5.57e+00 1wk8A 194 5.70e+00 1gr3A 160 5.71e+00 b.22.1.1 65476 1i4uA 181 5.88e+00 b.60.1.1 61732 2cxaA 256 6.07e+00 1obpA 159 6.89e+00 1obpA b.60.1.1 27092 1ob8A 135 7.03e+00 1ew3A 159 7.05e+00 1mup b.60.1.1 27114 1xyiA 66 7.33e+00 1azqA 66 7.40e+00 1azpA b.34.13.1 37469 1tikA 213 7.70e+00 c.23.5.3 107003 1k3eA 156 7.83e+00 d.198.1.1 68103 2fcpA 723 7.86e+00 1by5A f.4.3.3 43802 1lfdA 87 8.47e+00 1lfdA d.15.1.5 37622 2bgiA 272 8.60e+00 1jkmA 358 9.03e+00 1jkmA c.69.1.2 34633 1e88A 160 9.45e+00 g.14.1.2,g.14.1.2,g.27.1.1 44669,44670,44950 1qxrA 189 9.85e+00 b.82.1.7 96552 1dgrN 79 9.91e+00 1caxB 1qfgA 725 1.03e+01 1by5A f.4.3.3 43803 2bjrA 368 1.04e+01 2agyA 361 1.13e+01 1dgrV 79 1.14e+01 1caxB b.82.1.2 28099 1wmmA 145 1.15e+01 1smlA 269 1.21e+01 1smlA d.157.1.1 42053 1vk8A 106 1.21e+01 d.58.48.1 108636 1x82A 190 1.24e+01 1aqb 183 1.25e+01 1aqb b.60.1.1 27084 1r5mA 425 1.26e+01 1lzlA 323 1.30e+01 c.69.1.2 78306 1j1lA 290 1.33e+01 b.82.1.12 90766 1qr4A 186 1.35e+01 1qr4B b.1.2.1,b.1.2.1 21986,21987 1raxA 115 1.36e+01 1lfdA d.15.1.5 37626 1yg9A 330 1.38e+01 1faoA 126 1.40e+01 1faoA b.55.1.1 26974 1b87A 181 1.41e+01 1b87A d.108.1.1 40797 1lxdA 100 1.45e+01 1lfdA d.15.1.5 37624 2fo3A 125 1.46e+01 1dgwX 79 1.57e+01 1caxB b.82.1.2 28091 1s1dA 331 1.57e+01 b.67.3.1 98344 2a4nA 182 1.59e+01 2fsqA 243 1.60e+01 1w98B 283 1.63e+01 1gc1G 321 1.64e+01 1gc1G d.172.1.1 42493 1yemA 179 1.64e+01 1pbn 289 1.81e+01 1b8oA c.56.2.1 33771 1fgyA 127 1.81e+01 1faoA b.55.1.1 26976 1am2 199 1.91e+01 1am2 b.86.1.2 28381 1zy9A 564 1.93e+01 2d93A 134 1.94e+01 1e8bA 160 1.96e+01 1e8bA g.14.1.2,g.14.1.2,g.27.1.1 44671,44672,44951 1j58A 385 1.98e+01 b.82.1.2 71531 1hc7A 477 2.02e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1q2lA 939 2.06e+01 2aioA 269 2.08e+01 1n71A 180 2.09e+01 d.108.1.1 85370 1xcrA 316 2.11e+01 1tqmA 282 2.18e+01 a.4.5.56,d.144.1.9 107236,107237 2faoA 309 2.20e+01 2h0bA 184 2.29e+01 1b00A 127 2.32e+01 3chy c.23.1.1 31122 2cavA 445 2.44e+01 1dgwA b.82.1.2,b.82.1.2 28094,28095 1m2xA 223 2.46e+01 d.157.1.1 84764 2cmwA 310 2.51e+01 1a8rA 221 2.52e+01 1a8rA d.96.1.1 40587 1sap 66 2.54e+01 1azpA b.34.13.1 37472 1rbp 182 2.59e+01 1aqb b.60.1.1 27085 1guiA 155 2.62e+01 b.18.1.14 76351 1t5bA 201 2.64e+01 c.23.5.3 106433 4fiv 113 2.65e+01 1fmb b.50.1.1 26762 2d0oA 610 2.66e+01 1upqA 123 2.75e+01 1zx8A 136 2.78e+01 2cohA 202 2.80e+01 1ofdA 1520 2.89e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 2cwpA 112 2.89e+01 1b8oA 284 2.90e+01 1b8oA c.56.2.1 33762 1hbq 183 2.94e+01 1aqb b.60.1.1 27078 2f15A 96 2.95e+01 1pzsA 208 2.98e+01 b.1.8.1 104397 1widA 130 2.98e+01 1a9t 284 2.99e+01 1b8oA c.56.2.1 33765 1a9cA 221 3.01e+01 1a8rA d.96.1.1 40602 1y8cA 246 3.03e+01 1wd5A 208 3.05e+01 3pnp 289 3.06e+01 1b8oA c.56.2.1 33763 1i9yA 347 3.11e+01 1i9yA d.151.1.2 62101 1vfqA 143 3.14e+01 1fivA 113 3.18e+01 1fmb b.50.1.1 26764 1ecl 597 3.18e+01 1ecl e.10.1.1 43238 1rcqA 357 3.19e+01 b.49.2.2,c.1.6.1 104882,104883 1mjc 69 3.20e+01 1mjc b.40.4.5 25319 1vm6A 228 3.25e+01 c.2.1.3,d.81.1.3 108876,108877 1dxkA 227 3.29e+01 1a7tA d.157.1.1 42036 1xv2A 237 3.30e+01 1tmcA 175 3.35e+01 1agdA d.19.1.1 38258 2fr2A 172 3.36e+01 1zarA 282 3.36e+01 1z4rA 168 3.37e+01 1zzkA 82 3.38e+01 1gmwA 143 3.40e+01 b.107.1.1,d.58.38.1 65347,65348 1gmuA 143 3.41e+01 b.107.1.1,d.58.38.1 65335,65336 1j5wA 298 3.54e+01 d.104.1.1 71589 1bolA 222 3.62e+01 1bolA d.124.1.1 41120 1a9r 282 3.64e+01 1b8oA c.56.2.1 33767 1b9hA 388 3.65e+01 1b9hA c.67.1.4 34488 2bc2A 227 3.67e+01 1a7tA d.157.1.1 42031 1i9zA 347 3.68e+01 1i9yA d.151.1.2 62102 1snzA 344 3.68e+01 b.30.5.4 98930 1a9s 289 3.73e+01 1b8oA c.56.2.1 33768 1vs0A 310 3.81e+01 1bj7 156 3.82e+01 1bj7 b.60.1.1 27113 1f7dA 136 3.83e+01 1dun b.85.4.1 28353 1zesA 125 3.95e+01 1sr4A 206 4.00e+01 b.42.2.1 105948 1eo6A 117 4.02e+01 1eo6A d.15.1.3 37609 2cveA 191 4.08e+01 1jlyA 304 4.08e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 2pcy 99 4.10e+01 1plc b.6.1.1 22849 1aisA 182 4.17e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1itvA 195 4.17e+01 b.66.1.1 76791 2f9dP 43 4.29e+01 2glfA 450 4.36e+01 1wxaA 116 4.38e+01 1plc 99 4.41e+01 1plc b.6.1.1 22846 1z0nA 96 4.43e+01 1gmlA 178 4.43e+01 c.8.5.2 70273 1yghA 164 4.43e+01 1yghA d.108.1.1 40802 1pczA 191 4.44e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1j5kA 89 4.48e+01 d.51.1.1 71565 1nr4A 71 4.51e+01 d.9.1.1 92077 1bo4A 168 4.54e+01 1bo4A d.108.1.1 40798 1wmsA 177 4.55e+01 c.37.1.8 109414 1mqoA 227 4.55e+01 d.157.1.1 103846 1auvA 311 4.56e+01 1auvA c.30.1.5,d.142.1.3 31723,41558 1g9mG 321 4.59e+01 1gc1G d.172.1.1 42492 1kwiA 101 4.59e+01 d.17.1.3 77564 1o5uA 101 4.60e+01 b.82.1.8 92518 2b4wA 315 4.60e+01 2b5oA 402 4.61e+01 1wvhA 134 4.61e+01 1qm4A 396 4.62e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1td5A 202 4.62e+01 d.110.2.2 106767 1s3zA 165 4.68e+01 d.108.1.1 105250 1ogsA 497 4.69e+01 b.71.1.2,c.1.8.3 86997,86998 1h1aA 191 4.75e+01 b.29.1.11 83450 1wj9A 211 4.77e+01 2bvpA 276 4.81e+01 1j5vA 351 4.88e+01 c.72.1.1 71585 1tcvA 287 4.89e+01 1xkpC 143 4.92e+01 1dutA 133 4.94e+01 1dun b.85.4.1 28355 2f69A 261 4.94e+01 1d3uA 181 4.95e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1hbp 183 4.97e+01 1aqb b.60.1.1 27079 1cmxA 236 4.98e+01 1uch d.3.1.6 37130 1z0mA 96 5.05e+01 1n9lA 109 5.10e+01 d.110.3.6 85468 1bo4B 168 5.11e+01 1bo4A d.108.1.1 40799 1tl2A 236 5.13e+01 1tl2A b.67.1.1 27541 1hsbA 270 5.20e+01 1agdA b.1.1.2,d.19.1.1 20736,38257 1aky 221 5.27e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1g8kB 133 5.29e+01 1g8jB b.33.1.1 24435 1mg4A 113 5.39e+01 d.15.11.1 84953 1quqB 121 5.39e+01 1quqB b.40.4.3 25305 1v8yA 170 5.41e+01 1m40A 263 5.43e+01 e.3.1.1 74437 1tt8A 164 5.43e+01 1qr4B 186 5.44e+01 1qr4B b.1.2.1,b.1.2.1 21988,21989 1vyfA 135 5.46e+01 b.60.1.2 108902 1a7cA 379 5.48e+01 1sek e.1.1.1 42660 1mt6A 280 5.51e+01 b.76.2.1,b.85.7.1 79446,79447 2bc4A 211 5.58e+01 1n6aA 259 5.60e+01 b.76.2.1,b.85.7.1 80121,80122 1syyA 346 5.64e+01 a.25.1.2 106126 1cy9A 264 5.64e+01 1ecl e.10.1.1 43236 2h1tA 188 5.70e+01 1io1A 398 5.73e+01 1io1A e.32.1.1 62611 1chrA 370 5.73e+01 1mucA c.1.11.2,d.54.1.1 29252,38896 1yymG 313 5.74e+01 1af6A 421 5.79e+01 2mprA f.4.3.2 43772 1ykjA 394 5.79e+01 1fw9A 164 5.86e+01 1fw9A d.190.1.1 60059 2g6bA 180 5.91e+01 1e2wA 251 5.94e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1t3yA 141 5.94e+01 1vr5A 547 5.95e+01 2culA 232 5.99e+01 1ztcA 221 5.99e+01 1mdoA 393 6.01e+01 c.67.1.4 79013 1btl 263 6.04e+01 1btl e.3.1.1 42691 2fgtA 417 6.06e+01 1lfpA 249 6.15e+01 e.39.1.1 73885 1t2lA 141 6.18e+01 1h3iA 293 6.23e+01 b.76.2.1,b.85.7.1 76635,76636 1oxkB 134 6.28e+01 c.23.1.1 93691 1ae2 87 6.28e+01 1gvp b.40.4.7 25382 1tiyA 164 6.30e+01 c.97.1.2 107012 1ivg 388 6.39e+01 2qwc b.68.1.1 27578 1jb0F 164 6.39e+01 1jb0F f.23.16.1 62825 1vjqA 79 6.44e+01 k.43.1.1 100830 1csp 67 6.51e+01 1mjc b.40.4.5 25321 1rzjG 321 6.52e+01 d.172.1.1 98200 1dgwA 178 6.52e+01 1dgwA b.82.1.2 28090 1by3A 714 6.54e+01 1by5A f.4.3.3 43801 1umwA 237 6.57e+01 d.223.1.2,d.223.1.2 99631,99632 1avbA 226 6.58e+01 1led b.29.1.1 24158 1e9pA 151 6.59e+01 1mfmA b.1.8.1 22215 1sbxA 106 6.67e+01 a.6.1.4 105414 1by5A 714 6.70e+01 1by5A f.4.3.3 43800 2fivA 116 6.72e+01 1fmb b.50.1.1 26766 1xewX 182 6.72e+01 1pguA 615 6.74e+01 b.69.4.1,b.69.4.1 88069,88070 3fivA 116 6.78e+01 1fmb b.50.1.1 26768 1gvp 87 6.85e+01 1gvp b.40.4.7 25369 1i2mA 216 6.92e+01 1byuA c.37.1.8 61568 1omhA 293 6.95e+01 d.89.1.5 93348 1i1b 153 6.97e+01 2i1b b.42.1.2 25537 1tdhA 364 7.10e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1k5jA 124 7.12e+01 b.121.3.1 68201 1uch 230 7.12e+01 1uch d.3.1.6 37129 1r6wA 322 7.13e+01 c.1.11.2,d.54.1.1 97165,97166 1f5wA 126 7.15e+01 1f5wA b.1.1.1 19705 2fblA 153 7.17e+01 1fzyA 149 7.23e+01 d.20.1.1 65072 1uxxX 133 7.26e+01 b.18.1.10 100169 1kt6A 183 7.29e+01 b.60.1.1 84466 1jkeA 145 7.30e+01 c.110.1.1 66791 1a1mA 278 7.30e+01 1agdA b.1.1.2,d.19.1.1 20753,38266 1bvp1 349 7.30e+01 1bvp1 2cvbA 188 7.38e+01 1xmaA 145 7.41e+01 2apoA 357 7.42e+01 1theB 260 7.44e+01 1theB d.3.1.1 37057 1ctt 294 7.44e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 3mefA 69 7.44e+01 1mjc b.40.4.5 25320 1gifA 115 7.44e+01 1dptA d.80.1.3 39837 1ujxA 119 7.46e+01 b.26.1.2 99473 1uaiA 224 7.46e+01 b.29.1.18 107761 1wkqA 164 7.51e+01 c.97.1.2 109393 1jlxA 304 7.58e+01 1jlyA b.42.3.1,b.42.3.1 25583,25584 1ordA 730 7.67e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1fqgA 263 7.68e+01 1btl e.3.1.1 42699 2awaA 390 7.69e+01 2bitX 165 7.69e+01 1xreA 217 7.78e+01 1vqb 87 7.78e+01 1gvp b.40.4.7 25370 1egaA 301 7.79e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 1eajA 126 7.88e+01 1f5wA b.1.1.1 59401 1llfA 534 7.92e+01 c.69.1.17 78094 1zd7A 159 7.93e+01 1d4xA 375 7.94e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1ufkA 254 7.95e+01 c.66.1.39 99340 1kv7A 488 7.97e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 2av7A 275 8.04e+01 1wmhA 89 8.07e+01 2av1A 275 8.11e+01 1dgrC 178 8.19e+01 1dgwA b.82.1.2 28100 1yz1A 174 8.21e+01 1wn5A 130 8.22e+01 2bjqA 345 8.24e+01 1sur 215 8.30e+01 1sur c.26.2.2 31620 31bi 153 8.31e+01 2i1b b.42.1.2 25541 1jdiA 231 8.36e+01 c.74.1.1 66551 2gdnA 267 8.37e+01 1ile 821 8.46e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1ermA 263 8.52e+01 1btl e.3.1.1 42690 1dd5A 185 8.58e+01 1dd5A d.67.3.1 39564 1l2hA 153 8.59e+01 b.42.1.2 77655 1llwA 1520 8.62e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 2afbA 351 8.63e+01 1u7bA 261 8.70e+01 1fnmA 691 8.75e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 1p6pA 125 8.77e+01 b.60.1.2 87839 1b0uA 262 8.84e+01 1b0uA c.37.1.12 32370 1euvB 86 8.93e+01 1a5r d.15.1.1 37598 1x0pA 143 8.93e+01 1xd3A 230 8.95e+01 2rgf 97 8.99e+01 1lfdA d.15.1.5 37627