# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 3fruA 269 1.51e-01 1agdA b.1.1.2 20657 d.19.1.1 38150 1ewjA 126 2.57e-01 1ecsA d.32.1.2 59526 1ecsA 126 3.46e-01 1ecsA d.32.1.2 59407 1ln1A 214 3.53e-01 d.129.3.2 74038 1n13B 113 5.74e-01 1bupA 386 5.96e-01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1ba1 386 8.68e-01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1kay 381 9.77e-01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1mmiA 366 1.58e+00 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1ewqA 765 1.72e+00 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1obwA 175 2.59e+00 2prd b.40.5.1 25416 1n3gA 113 2.65e+00 d.204.1.1 79962 1k99A 99 2.71e+00 a.21.1.1 68341 1i40A 175 2.76e+00 b.40.5.1 66024 2rn2 155 3.15e+00 2rn2 c.55.3.1 33551 1egaA 301 3.36e+00 1egaA c.37.1.8 32150 d.52.3.1 38836 1lhpA 312 3.53e+00 c.72.1.5 77960 1f21A 155 3.56e+00 2rn2 c.55.3.1 33550 1g2rA 100 3.64e+00 1g2rA d.192.1.1 60231 1rch 155 3.66e+00 2rn2 c.55.3.1 33570 1tkaA 678 4.25e+00 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 1kfuS 184 4.26e+00 a.39.1.8 68574 1egpA 45 4.46e+00 1egpA d.40.1.1 38561 1trkA 680 4.60e+00 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1f66C 128 4.68e+00 1aoiC a.22.1.1 16442 1nw1A 429 4.76e+00 d.144.1.8 86286 1i0aA 466 4.77e+00 1auwA a.127.1.1 61479 1jl1A 155 5.09e+00 c.55.3.1 66821 1l6oA 95 5.26e+00 b.36.1.1 84534 1cpzA 68 5.30e+00 1aw0 d.58.17.1 39351 1ipwA 175 5.38e+00 2prd b.40.5.1 25427 2polA 366 5.79e+00 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1ge8A 249 5.79e+00 1plq d.131.1.2 41398 d.131.1.2 41399 1psdA 409 5.92e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 2occH 85 6.23e+00 2occH a.51.1.1 17796 1gk8I 140 6.25e+00 d.73.1.1 65242 1gpuA 680 6.28e+00 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1n7hA 381 6.30e+00 c.2.1.2 80250 1mw7A 240 6.35e+00 e.39.1.1 79557 1l4sA 112 6.36e+00 d.204.1.1 77693 1fj7A 101 6.66e+00 1fj7A d.58.7.1 39209 1rwzA 245 6.71e+00 d.131.1.2 -11106 d.131.1.2 -11107 1dgsA 667 7.18e+00 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1e3yA 104 7.47e+00 1fadA a.77.1.2 18426 1op0A 234 7.75e+00 1h6kA 757 8.13e+00 unknown_sccs 60675 unknown_sccs 60676 unknown_sccs 60677 1i3jA 116 8.36e+00 1i3jA e.30.1.1 61594 1v54H 85 8.65e+00 a.51.1.1 -979 1ohfA 644 8.95e+00 unknown_sccs -3012 1alvA 173 8.98e+00 1alvA a.39.1.8 17370 1ayaA 101 9.29e+00 1qadA d.93.1.1 40460 1suh 146 9.39e+00 1edhA b.1.6.1 22206 1kveA 63 1.09e+01 1kveA d.70.1.2 39590 1ogiA 303 1.12e+01 b.43.4.2 -4042 c.25.1.1 -6587 1b2rA 304 1.12e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1que 303 1.13e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1go2A 304 1.15e+01 b.43.4.2 76243 c.25.1.1 76244 1jl2A 156 1.15e+01 c.55.3.1 66822 1kfiA 572 1.15e+01 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1qh0A 295 1.19e+01 b.43.4.2 68891 c.25.1.1 68892 1ois 223 1.22e+01 1a36A e.15.1.1 43267 1ej6D 418 1.22e+01 i.7.1.1 45970 1ufoA 238 1.30e+01 unknown_sccs -8303 1b3jA 274 1.34e+01 1agdA b.1.1.2 20855 d.19.1.1 38319 1kmdA 117 1.36e+01 d.189.1.1 72744 1lo6A 223 1.38e+01 b.47.1.2 74143 1ffkU 91 1.38e+01 1ffkU d.29.1.1 38458 1hmpA 217 1.39e+01 1qk3A c.61.1.1 34075 1rsoA 60 1.40e+01 unknown_sccs -1184 1bno 87 1.42e+01 1bpyA a.60.6.1 18079 1stfI 98 1.42e+01 1stfI d.17.1.2 38006 1g10A 102 1.42e+01 1g10A d.137.1.1 60191 1iw7C 1119 1.44e+01 e.29.1.1 71474 1j3mA 129 1.45e+01 1ckv 141 1.47e+01 1ckv d.137.1.1 41452 1auz 116 1.48e+01 1auz c.13.2.1 30883 1aj6 219 1.52e+01 1aj6 d.122.1.2 41106 1jhfA 202 1.52e+01 a.4.5.2 63057 b.87.1.1 63058 1v64A 108 1.57e+01 1uv7A 110 1.57e+01 unknown_sccs -10256 1en7A 157 1.62e+01 1en7A a.140.4.1 64733 d.4.1.5 64734 1of4A 179 1.65e+01 b.18.1.18 86932 1jvr 137 1.71e+01 1jvr a.61.1.2 18132 1iz5A 249 1.71e+01 d.131.1.2 83834 d.131.1.2 83835 1rewC 135 1.71e+01 g.7.1.3 -12531 1aogA 485 1.71e+01 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1kvdA 63 1.76e+01 1kveA d.70.1.2 39592 1hy0A 466 1.82e+01 1auwA a.127.1.1 61392 1n2fA 142 1.87e+01 d.227.1.1 79853 1scjB 71 1.88e+01 1scjB d.58.3.2 39069 1b33N 67 1.93e+01 1b33N d.30.1.1 38459 1au1A 166 1.98e+01 1ifa a.26.1.3 16889 1be3D 241 1.99e+01 1be3D a.3.1.3 15955 f.23.11.1 43666 1ufyA 122 2.05e+01 d.79.1.2 88489 1cg2A 393 2.05e+01 1cg2A c.56.5.4 33844 d.58.19.1 39360 1oh4A 179 2.09e+01 b.18.1.18 -3123 1g6gA 127 2.10e+01 1g6gA b.26.1.2 23916 1lxjA 104 2.11e+01 d.58.48.1 84736 3rnt 104 2.13e+01 9rnt d.1.1.4 36069 1mk0A 97 2.15e+01 d.226.1.1 79216 1prxA 224 2.16e+01 1prxA c.47.1.10 33076 1ezvD 245 2.20e+01 1be3D a.3.1.3 59546 f.23.11.1 59547 1hymA 45 2.21e+01 1hymA d.40.1.1 38581 1i0vA 104 2.23e+01 9rnt d.1.1.4 36054 1gtxA 472 2.30e+01 1gtxA 1aoiC 116 2.30e+01 1aoiC a.22.1.1 16440 1l5pA 93 2.31e+01 d.15.4.1 73598 153l 185 2.32e+01 153l d.2.1.5 36984 1j5pA 253 2.33e+01 c.2.1.3 83092 d.81.1.3 71577 1ftpA 133 2.34e+01 1hmt b.60.1.2 27199 1j30A 144 2.35e+01 a.25.1.1 -650 1mogA 67 2.35e+01 d.230.2.1 85034 1ohvA 472 2.38e+01 c.67.1.4 -8181 1prxB 224 2.39e+01 1prxA c.47.1.10 33077 1dbdA 100 2.43e+01 2bopA d.58.8.1 39218 1ksoA 101 2.47e+01 a.39.1.2 72926 1edhA 226 2.49e+01 1edhA b.1.6.1 22198 b.1.6.1 22199 1aoiG 116 2.49e+01 1aoiC a.22.1.1 16441 1g65K 211 2.49e+01 d.153.1.4 41907 1hq1A 105 2.50e+01 1dulA a.36.1.1 17120 1bfa 134 2.59e+01 1bea a.52.1.2 17827 1aisA 182 2.59e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1edzA 320 2.61e+01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1ee9A 320 2.68e+01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1q7lA 198 2.71e+01 c.56.5.4 -7886 1auwA 468 2.74e+01 1auwA a.127.1.1 19416 1shsA 147 2.75e+01 1shsA b.15.1.1 23675 1qu9A 128 2.75e+01 1qu9A d.79.1.1 39755 1qu9C 128 2.75e+01 1qu9A d.79.1.1 39757 1fecA 490 2.78e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1kb9D 246 2.80e+01 a.3.1.3 77317 f.23.11.1 77318 1vjqA 79 2.81e+01 unknown_sccs -13478 1lddA 74 2.81e+01 a.4.5.34 73841 1ct5A 256 2.82e+01 1ct5A c.1.6.2 28663 1kyoD 248 2.86e+01 a.3.1.3 73254 f.23.11.1 73255 1rboC 123 2.86e+01 1rboC d.73.1.1 39634 1d7qA 143 2.97e+01 1d7qA b.40.4.5 25331 2hdhA 293 3.08e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 2reb 352 3.10e+01 2reb c.37.1.11 32282 d.48.1.1 38767 1hf2A 210 3.11e+01 1hf2A b.80.3.1 60992 c.102.1.1 60993 1ki1B 352 3.15e+01 a.87.1.1 72497 b.55.1.1 72498 1o9iA 266 3.20e+01 unknown_sccs -698 1jj2W 91 3.20e+01 1ffkU d.29.1.1 63108 1ocsA 162 3.25e+01 d.189.1.1 -9929 1osdA 72 3.25e+01 1s72X 92 3.26e+01 8rucI 123 3.26e+01 1rboC d.73.1.1 39629 1jkvA 266 3.27e+01 unknown_sccs 71719 1bea 127 3.28e+01 1bea a.52.1.2 17826 1ceeB 59 3.28e+01 1ceeB 1dq3A 454 3.33e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1vkbA 161 3.34e+01 1p32A 209 3.34e+01 1p32A d.25.1.1 38379 1b54 257 3.35e+01 1ct5A c.1.6.2 28664 1quqB 121 3.36e+01 1quqB b.40.4.3 25305 1mp9A 198 3.38e+01 a.74.1.2 -1127 a.74.1.2 -1128 9rnt 104 3.39e+01 9rnt d.1.1.4 36055 1db3A 372 3.49e+01 1db3A c.2.1.2 29813 1jy2O 56 3.54e+01 h.1.8.1 67441 1jy3O 56 3.54e+01 h.1.8.1 67447 1pytA 94 3.55e+01 1pytA d.58.3.1 39064 1a32 88 3.58e+01 1a32 a.16.1.2 16384 1skoA 143 3.60e+01 1o4sA 389 3.68e+01 c.67.1.1 86620 1p5hA 428 3.70e+01 c.123.1.1 87802 1gy6A 127 3.70e+01 d.17.4.2 70736 1ggzA 148 3.73e+01 a.39.1.5 70176 1k4iA 233 3.73e+01 d.115.1.2 72056 1ejdA 419 3.75e+01 1uae d.68.2.2 39576 1ntn 72 3.75e+01 3ebx g.7.1.1 44414 1ifp 44 3.76e+01 1ifp h.1.4.1 45570 1f08A 148 3.81e+01 1f08A d.89.1.2 59564 1xvaA 292 3.83e+01 1xvaA c.66.1.5 34183 1e7lA 157 3.87e+01 1en7A a.140.4.1 64728 d.4.1.5 64729 1imuA 107 3.88e+01 d.204.1.1 66218 1ck7A 631 3.88e+01 1ck7A a.20.1.2 58969 b.66.1.1 27538 d.92.1.11 58970 g.14.1.2 44674 g.14.1.2 44675 g.14.1.2 44676 1kx5A 135 3.90e+01 a.22.1.1 77593 2bopA 85 3.96e+01 2bopA d.58.8.1 39217 1r6rA 100 3.98e+01 unknown_sccs -1071 1rypL 212 3.99e+01 d.153.1.4 41880