# List of top-scoring protein chains for t04-100-30-str2-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 1vjkA 98 1.13e-04 d.15.3.1 108631 1xlqA 106 2.22e-03 1oqqA 106 2.31e-03 d.15.4.1 93422 1ryjA 70 7.80e-03 d.15.3.2 98104 1frrA 95 1.75e-02 1awd d.15.4.1 37674 1qorA 327 3.14e-02 1qorA b.35.1.2,c.2.1.1 24766,29782 2bb6A 414 3.68e-02 1e9mA 106 4.04e-02 1ayfA d.15.4.1 59397 1uwmA 106 4.30e-02 1zud2 66 7.70e-02 1frd 98 1.18e-01 1awd d.15.4.1 37648 1fm0D 81 1.66e-01 1fmaD d.15.3.1 37642 2bwfA 77 1.85e-01 1yb5A 351 2.38e-01 1awd 94 2.50e-01 1awd d.15.4.1 37673 1rwsA 77 2.58e-01 d.15.3.2 97991 2bpsA 81 2.74e-01 2cu3A 64 3.57e-01 1czpA 98 5.99e-01 1awd d.15.4.1 37645 1lfdA 87 6.04e-01 1lfdA d.15.1.5 37622 1c1yB 77 6.33e-01 1c1yB d.15.1.5 37618 1dg6A 191 6.92e-01 1d4vB b.22.1.1 23883 1k07A 263 7.33e-01 d.157.1.1 77218 2aj2A 208 8.07e-01 1nbfD 76 8.15e-01 d.15.1.1 80390 1a70 97 9.41e-01 1awd d.15.4.1 37678 1i7hA 111 9.67e-01 d.15.4.1 71122 1ubi 76 1.05e+00 1ubi d.15.1.1 37584 1l5pA 93 1.07e+00 d.15.4.1 73598 1yj1A 76 1.13e+00 1rfkA 98 1.15e+00 1b9rA 105 1.31e+00 1ayfA d.15.4.1 37683 1vybA 238 1.37e+00 d.151.1.1 108897 1doi 128 1.38e+00 1awd d.15.4.1 37676 1offA 97 1.41e+00 d.15.4.1 86947 1ogwA 76 1.44e+00 d.15.1.1 87001 1wjnA 97 1.44e+00 1wgrA 100 1.51e+00 2g1lA 104 1.56e+00 1ryaA 160 1.79e+00 d.113.1.5 105122 1jenA 267 1.81e+00 1jenA 1yqbA 100 1.81e+00 2pia 321 1.86e+00 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1euvB 86 2.09e+00 1a5r d.15.1.1 37598 1qlaB 239 2.30e+00 1qlaB a.1.2.1,d.15.4.2 15679,37707 2ohxA 374 2.30e+00 2ohxA b.35.1.2,c.2.1.1 24669,29685 2al3A 90 2.32e+00 1jl0A 334 2.66e+00 1jenA d.156.1.1 63155 1ayfA 105 2.66e+00 1ayfA d.15.4.1 37684 1dmhA 311 2.72e+00 1dmhA b.3.6.1 22633 2bt6A 108 2.76e+00 1wm3A 72 3.29e+00 1ra6A 461 3.53e+00 e.8.1.4 104879 2a4hA 126 4.14e+00 1u3wA 374 4.15e+00 1n2eA 300 5.37e+00 c.26.1.4 85268 2c5lC 117 5.41e+00 1rm6C 161 5.58e+00 1eb7A 323 5.98e+00 1eb7A a.3.1.5,a.3.1.5 59404,59405 1l7yA 94 6.37e+00 d.15.1.6 73676 1lm8B 118 6.44e+00 d.15.1.1 74033 1r3eA 309 6.50e+00 b.122.1.1,d.265.1.2 96907,96908 1se9A 126 6.63e+00 d.15.1.1 98821 1n8kA 374 7.02e+00 b.35.1.2,c.2.1.1 80298,80299 1hetA 374 7.03e+00 2ohxA b.35.1.2,c.2.1.1 60975,60976 1e6eB 128 7.24e+00 1ayfA d.15.4.1 59300 2cfeA 162 7.48e+00 1uh6A 100 7.49e+00 d.15.1.1 99394 1xgsA 295 7.57e+00 1bn5 a.4.5.25,d.127.1.1 16216,41153 1pl8A 356 7.62e+00 b.35.1.2,c.2.1.1 94878,94879 1wwtA 88 7.85e+00 2f96A 224 8.37e+00 1zpuA 534 8.64e+00 1v86A 95 8.77e+00 d.15.1.1 108421 1p4oA 322 8.79e+00 d.144.1.7 87775 1vcbA 118 8.82e+00 1vcbA d.15.1.1 37603 1g6oA 330 8.86e+00 1g6oA c.37.1.11 32430 1ib8A 164 9.06e+00 b.38.2.1,d.52.4.1 71168,71169 1rcqA 357 9.06e+00 b.49.2.2,c.1.6.1 104882,104883 1b4rA 80 9.30e+00 1b4rA b.1.3.1 22072 1t3qA 168 9.33e+00 a.56.1.1,d.15.4.2 106367,106368 1p0fA 373 9.34e+00 b.35.1.2,c.2.1.1 87642,87643 1n62A 166 1.04e+01 a.56.1.1,d.15.4.2 80090,80091 1o54A 277 1.05e+01 c.66.1.13 92482 1z2mA 155 1.12e+01 1xc3A 302 1.12e+01 1siqA 392 1.14e+01 a.29.3.1,e.6.1.1 105585,105586 1d2eA 397 1.15e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1krhA 338 1.21e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 2dafA 118 1.22e+01 2ex2A 458 1.25e+01 1kevA 351 1.27e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1t0qC 86 1.27e+01 d.15.12.1 106222 2c1vA 338 1.33e+01 1gskA 513 1.33e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 2azwA 148 1.33e+01 2fnjB 118 1.41e+01 2b5wA 357 1.44e+01 1jqbA 351 1.45e+01 b.35.1.2,c.2.1.1 77151,77152 1pgs 314 1.47e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 2gk3A 256 1.47e+01 1v2yA 105 1.51e+01 d.15.1.1 100275 1m93B 245 1.53e+01 2bh1A 250 1.57e+01 1pvmA 184 1.60e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1r5lA 262 1.61e+01 a.5.3.1,c.13.1.1 97099,97100 1z06A 189 1.63e+01 1ynmA 247 1.65e+01 1f1uA 323 1.66e+01 d.32.1.3,d.32.1.3 83200,83201 1s0uA 408 1.68e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1yqzA 438 1.69e+01 1f1xA 322 1.69e+01 d.32.1.3,d.32.1.3 83208,83209 1x1mA 107 1.74e+01 1woqA 267 1.78e+01 c.55.1.10,c.55.1.10 109462,109463 1meoA 209 1.78e+01 c.65.1.1 79035 2fm8A 135 1.80e+01 1agjA 242 1.80e+01 1agjA b.47.1.1 25827 1xe1A 116 1.80e+01 b.43.3.1 109571 1avbA 226 1.80e+01 1led b.29.1.1 24158 1iueA 98 1.85e+01 d.15.4.1 90697 1rdr 461 1.87e+01 1rdr e.8.1.4 43116 1ooyA 481 1.92e+01 c.124.1.3,c.124.1.2 93388,93389 1q8rA 120 1.92e+01 d.79.6.1 96225 1pcxA 810 1.92e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 1so9A 164 1.95e+01 b.146.1.1 105842 2aefA 234 1.96e+01 1p99A 295 2.08e+01 c.94.1.1 94384 1fsz 372 2.14e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1whxA 111 2.20e+01 1k8kC 372 2.31e+01 b.69.4.1 68308 1wzlA 585 2.33e+01 1oqyA 368 2.35e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1wojA 214 2.36e+01 2sak 121 2.37e+01 2sak d.15.5.1 37711 2a5kA 307 2.40e+01 1q2wA 308 2.48e+01 b.47.1.4 88355 2amdA 311 2.51e+01 2fcr 173 2.51e+01 1rcf c.23.5.1 31151 1wmhB 86 2.64e+01 1pvc3 238 2.65e+01 1aym3 1hlrA 907 2.73e+01 1vlbA 907 2.73e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1tjxA 159 2.76e+01 1sv6A 269 2.79e+01 d.177.1.1 106043 1drw 273 2.79e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1omzA 293 2.82e+01 c.68.1.15 87093 1vc3B 97 2.84e+01 1x8bA 289 2.85e+01 2fcfA 103 2.85e+01 1qysA 106 2.91e+01 k.41.1.1 96603 4tsvA 150 2.94e+01 2tnfA b.22.1.1 23860 1h9sA 140 3.01e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1vmiA 355 3.05e+01 1dljA 402 3.08e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1cbf 285 3.09e+01 1cbf c.90.1.1 35587 1wruA 379 3.21e+01 2bkrB 77 3.22e+01 2bwnA 401 3.23e+01 1rkuA 206 3.29e+01 c.108.1.11 97627 1zq7A 207 3.32e+01 1bt0A 76 3.44e+01 1ubi d.15.1.1 37607 1wriA 93 3.44e+01 1t9fA 187 3.47e+01 b.42.6.1 106710 1bxeA 113 3.48e+01 1bxeA d.55.1.1 38898 1wvqA 167 3.51e+01 1knmA 130 3.54e+01 b.42.2.1 72781 1epfA 191 3.55e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1q1oA 98 3.59e+01 d.15.2.2 95596 2et1A 201 3.59e+01 1v5mA 136 3.60e+01 b.55.1.1 108379 1k8wA 327 3.62e+01 b.122.1.1,d.265.1.2 83094,90388 1vj0A 380 3.62e+01 b.35.1.2,c.2.1.1 100786,100787 1f0cA 305 3.66e+01 1c8oA e.1.1.1 42676 1gg4A 452 3.71e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1f4qA 165 3.76e+01 1alvA a.39.1.8 17360 1h2bA 359 3.80e+01 b.35.1.2,c.2.1.1 90543,90544 2cwpA 112 3.82e+01 1uuqA 440 3.90e+01 c.1.8.3 100015 1ef1A 294 3.90e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 2btzA 394 3.94e+01 1zx8A 136 3.96e+01 2fqmA 75 3.97e+01 2fug1 438 4.00e+01 1udkA 51 4.02e+01 g.3.14.1 99211 1y1nA 291 4.02e+01 1qfxA 460 4.03e+01 1qfxA c.60.1.2 33994 1mq7A 154 4.09e+01 b.85.4.1 79404 1k94A 165 4.15e+01 a.39.1.8 68333 1bbhA 131 4.15e+01 1bbhA a.24.3.2 16546 1tmxA 293 4.17e+01 2blnA 305 4.19e+01 1snzA 344 4.20e+01 b.30.5.4 98930 1fi2A 201 4.29e+01 1fi2A b.82.1.2 59845 2a84A 300 4.30e+01 1e0gA 48 4.30e+01 1e01A d.7.1.1 37325 2f4pA 147 4.31e+01 1h0hA 977 4.32e+01 b.52.2.2,c.81.1.1 76435,76436 1vqoT 120 4.33e+01 1nls 237 4.41e+01 1nls b.29.1.1 23928 1k47A 337 4.44e+01 d.14.1.5,d.58.26.4 72040,72041 1vbiA 344 4.46e+01 1o5oA 221 4.47e+01 c.61.1.1 92509 1x8qA 184 4.47e+01 1jj2S 119 4.52e+01 1ffkQ b.34.5.1 63104 1s72T 120 4.53e+01 b.34.5.1 105339 2fazA 78 4.53e+01 1c24A 263 4.59e+01 1c24A d.127.1.1 41148 2cyjA 118 4.59e+01 2azeB 106 4.60e+01 2giyA 191 4.65e+01 1vqb 87 4.67e+01 1gvp b.40.4.7 25370 3prn 289 4.67e+01 3prn f.4.3.1 43761 1gvp 87 4.67e+01 1gvp b.40.4.7 25369 1j4nA 271 4.70e+01 f.19.1.1 71510 1o0xA 262 4.71e+01 d.127.1.1 80755 1uowA 159 4.72e+01 b.7.1.2 107975 1t6aA 126 4.73e+01 d.129.8.1 106555 1f8vA 355 4.73e+01 2bbvA b.121.4.4 23329 1ygs 234 4.74e+01 1ygs b.26.1.1 23907 2bzoB 79 4.77e+01 1iow 306 4.77e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1cf2O 337 4.78e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 1oruA 195 4.83e+01 b.58.1.2 93464 2gptA 523 4.86e+01 2bw0A 329 4.89e+01 1e3jA 352 4.93e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1s9jA 341 4.93e+01 1gcqC 70 4.98e+01 1gcpA b.34.2.1 60436 1u94A 356 5.08e+01 c.37.1.11,d.48.1.1 107743,107744 1mugA 168 5.15e+01 1mugA c.18.1.2 31030 1ov3A 138 5.16e+01 b.34.2.1,b.34.2.1 87451,87452 2bbvA 363 5.22e+01 2bbvA b.121.4.4 23323 1iqcA 308 5.23e+01 a.3.1.5,a.3.1.5 66266,66267 2gupA 292 5.23e+01 1kk1A 410 5.25e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1sfe 180 5.27e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1zu0A 529 5.30e+01 1b9mA 265 5.32e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1wlpB 138 5.35e+01 1uwwA 191 5.36e+01 b.18.1.23 108079 1umuA 116 5.36e+01 1umuA b.87.1.1 28382 1k0eA 453 5.39e+01 d.161.1.1 67938 2bw3A 534 5.41e+01 1zvtA 256 5.45e+01 2rspA 124 5.56e+01 2rspB b.50.1.1 26771 1u09A 476 5.64e+01 e.8.1.4 107545 1gzcA 239 5.69e+01 b.29.1.1 70803 1fiqB 350 5.74e+01 1fiqB d.87.2.1,d.145.1.3 40229,41760 1wloA 136 5.75e+01 1mtpA 323 5.77e+01 e.1.1.1 85107 1yopA 83 5.77e+01 1xnzA 264 5.77e+01 1zy4A 303 5.79e+01 1jj2H 167 5.80e+01 1ffkF d.41.4.1 63093 1zldA 120 5.83e+01 1yf5L 254 5.86e+01 1atiA 505 5.91e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 2b3hA 329 6.10e+01 1tpm 50 6.15e+01 1tpg g.27.1.1 44957 1ku0A 388 6.16e+01 c.69.1.18 72994 2reb 352 6.19e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1ng2A 193 6.27e+01 b.34.2.1,b.34.2.1 85660,85661 1w3iA 293 6.30e+01 c.1.10.1 109152 1qm4A 396 6.32e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1y9aA 360 6.35e+01 1uhgA 385 6.35e+01 e.1.1.1 88491 1shsA 147 6.36e+01 1shsA b.15.1.1 23675 1lurA 339 6.38e+01 b.30.5.4 84717 1z6bA 154 6.38e+01 1imbA 277 6.39e+01 1imbA e.7.1.1 42957 1whvA 100 6.40e+01 1xi1A 575 6.47e+01 1s55A 156 6.48e+01 1gsmA 210 6.50e+01 b.1.1.4,b.1.1.4 65535,65536 1p5tA 127 6.56e+01 b.55.1.2 94148 1gttA 429 6.57e+01 d.177.1.1,d.177.1.1 70529,70530 1ovaA 386 6.66e+01 1ovaA e.1.1.1 42619 2as0A 396 6.68e+01 1pv9A 348 6.70e+01 c.55.2.1,d.127.1.1 95157,95158 2apoA 357 6.73e+01 2hhmA 276 6.73e+01 1imbA e.7.1.1 42955 3seb 238 6.74e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1he7A 126 6.75e+01 1wwcA b.1.1.4 60970 2fkcA 247 6.75e+01 1gpr 162 6.82e+01 1gpr b.84.3.1 28267 1rx0A 393 6.84e+01 a.29.3.1,e.6.1.1 98007,98008 1b8gA 429 6.88e+01 1b8gA c.67.1.4 34499 1tg7A 971 6.94e+01 1befA 181 6.96e+01 1befA b.47.1.3 26419 1e79H 146 6.97e+01 1e79H a.2.10.1,b.93.1.1 15721,28438 1gyvA 120 6.99e+01 b.1.10.2 70790 2a7bA 120 6.99e+01 2ggcA 263 7.01e+01 1ubeA 349 7.02e+01 c.37.1.11,d.48.1.1 88412,88413 1c4zA 358 7.13e+01 1c4zA d.148.1.1 41766 2bh8A 101 7.20e+01 1i7oA 429 7.21e+01 1i7oA d.177.1.1,d.177.1.1 61893,61894 1iyjB 817 7.21e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 76948,76949,76950,76951,76952 1by2 119 7.21e+01 1by2 d.170.1.1 42452 1sg1X 161 7.22e+01 g.24.1.1,g.24.1.1,g.24.1.1,g.24.1.1 105515,105516,105517,105518 1ug1A 92 7.32e+01 b.34.2.1 99360 1qniA 581 7.42e+01 1qniA b.6.1.4,b.69.3.1 23042,27642 1z3qA 200 7.44e+01 1wkaA 147 7.44e+01 2d7nA 93 7.46e+01 1xhcA 367 7.47e+01 2tgi 112 7.47e+01 2tgi g.17.1.2 44777 1jb3A 131 7.58e+01 1jc7A b.40.3.2 62833 1mgpA 313 7.63e+01 c.119.1.1 79098 1grj 158 7.76e+01 1grj a.2.1.1,d.26.1.2 15691,38433 2fp7B 172 7.86e+01 1yf9A 171 7.89e+01 1k2eA 156 8.10e+01 d.113.1.1 72010 1dxy 333 8.23e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1jsdA 319 8.31e+01 b.19.1.2 63258 1vdeA 454 8.33e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1sphA 88 8.34e+01 1ptf d.94.1.1 40544 1z9zA 60 8.41e+01 1yoxA 250 8.42e+01 1c96A 753 8.45e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1w5fA 353 8.54e+01 1v5tA 90 8.59e+01 d.15.1.1 108385 2gaxA 135 8.74e+01 2a6zA 222 8.76e+01 1ofuA 320 8.78e+01 c.32.1.1,d.79.2.1 86972,86973 1jer 138 8.78e+01 2cbp b.6.1.1 23022 1fc4A 401 8.79e+01 1bs0A c.67.1.4 59760 1rypI 222 8.85e+01 d.153.1.4 41877 1pkp 150 8.99e+01 1pkp d.14.1.1,d.50.1.2 37551,38787