# List of top-scoring protein chains for t2k-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 2gkeA 274 4.97e-07 1gqzA 274 8.37e-07 d.21.1.1,d.21.1.1 83311,83312 1bwzA 274 1.37e-06 1bwzA d.21.1.1,d.21.1.1 38337,38338 1w61A 414 1.96e-06 1tm0A 350 8.97e-04 d.21.1.3 107147 1u1wA 298 2.12e-02 1xubA 298 3.13e-02 1sdjA 310 5.85e-02 d.21.1.2,d.21.1.2 98807,98808 2g6yA 217 1.01e-01 1t6kA 278 1.50e-01 2azpA 318 1.80e-01 1usyA 275 2.07e-01 1ym5A 300 3.80e-01 1o97D 320 3.81e-01 c.26.2.3,c.31.1.2 81233,81234 1qyaA 307 5.63e-01 d.21.1.2,d.21.1.2 104653,104654 1l1nA 183 6.52e-01 b.47.1.4 73476 1z94A 147 1.13e+00 1u9yA 284 1.66e+00 1e3aB 560 2.62e+00 1ajqB 1zcjA 463 2.69e+00 1hzdA 272 3.02e+00 c.14.1.3 65969 1pnkB 557 4.89e+00 1ajqB 1ajqB 557 4.95e+00 1ajqB 1gk9B 557 4.97e+00 1oe4A 247 4.97e+00 c.18.1.3 86895 1gm7B 557 4.99e+00 1gkfB 557 5.00e+00 1s7jA 262 5.74e+00 d.21.1.2 98647 1gm9B 557 5.78e+00 1wc3A 219 5.80e+00 1i1iP 681 6.16e+00 1i1iP d.92.1.5 40297 1qupA 222 6.83e+00 1qupA b.1.8.1,d.58.17.1 22301,39352 1lj5A 379 6.96e+00 e.1.1.1 73928 1z5hA 780 7.10e+00 1ut9A 609 7.44e+00 a.102.1.2,b.1.18.2 99912,99913 1gt8D 1025 7.70e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70433,70434,70435,70436,70437 1lybB 241 7.89e+00 1smrA 1gthB 1025 8.02e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70488,70489,70490,70491,70492 1v61A 132 8.31e+00 b.55.1.1 108389 1d0iA 156 8.36e+00 2dhqA c.23.13.1 31383 1yg9A 330 8.58e+00 1gthA 1025 8.87e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70483,70484,70485,70486,70487 1gt8B 1025 9.58e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70423,70424,70425,70426,70427 2myr 501 1.02e+01 1h7xA 1025 1.04e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15687,28632,30328,30613,39011 1q47A 495 1.16e+01 b.69.12.1 104532 1ycoA 279 1.17e+01 1gtzA 156 1.18e+01 c.23.13.1 70539 1erjA 393 1.20e+01 1erjA b.69.4.1 27660 1wucA 250 1.20e+01 1omrA 201 1.21e+01 a.39.1.5 93349 1vdkA 466 1.21e+01 a.127.1.1 100561 1rec 201 1.25e+01 1rec a.39.1.5 17326 1e6qM 501 1.26e+01 1e70M c.1.8.4 28920 1h7xD 1025 1.30e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15690,28635,30331,30616,39014 2acfA 182 1.34e+01 1gthC 1025 1.35e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70493,70494,70495,70496,70497 1ciy 590 1.38e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1bupA 386 1.39e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1hpm 386 1.39e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1ba1 386 1.43e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1viwB 198 1.43e+01 1led b.29.1.1 24170 1mrzA 293 1.48e+01 b.43.5.1,c.26.1.3 91452,91453 1bkb 136 1.58e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1xtqA 177 1.60e+01 1e4mM 501 1.61e+01 1e70M c.1.8.4 59226 1rzuA 485 1.62e+01 c.87.1.8 105140 1gthD 1025 1.64e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70498,70499,70500,70501,70502 1ut1A 148 1.65e+01 b.2.3.6 108014 1gteD 1025 1.66e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70455,70456,70457,70458,70459 1u6zA 513 1.67e+01 1e70M 501 1.68e+01 1e70M c.1.8.4 28926 1kay 381 1.75e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1h7xB 1025 1.90e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15688,28633,30329,30614,39012 1h7xC 1025 1.90e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15689,28634,30330,30615,39013 1josA 128 1.98e+01 d.52.7.1 84191 1mqoA 227 1.98e+01 d.157.1.1 103846 1atr 386 2.00e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1ats 386 2.01e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1ryaA 160 2.02e+01 d.113.1.5 105122 1qrkA 731 2.04e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 2bgiA 272 2.14e+01 1eft 405 2.14e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 2af4C 333 2.23e+01 1h7wA 1025 2.26e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1x6zA 123 2.31e+01 1hg3A 225 2.32e+01 1hg3A c.1.1.1 61025 1lm4A 194 2.34e+01 d.167.1.1 84626 1gt8A 1025 2.35e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70418,70419,70420,70421,70422 1mqvA 125 2.36e+01 a.24.3.2 79415 2fclA 169 2.49e+01 2sli 679 2.49e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1o17A 345 2.52e+01 a.46.2.1,c.27.1.1 80765,80766 2aaiB 262 2.53e+01 1abrB b.42.2.1,b.42.2.1 25561,25562 1nnsA 326 2.53e+01 c.88.1.1 85910 4sli 679 2.54e+01 2sli b.29.1.9,b.68.1.1 24275,27612 2ewrA 170 2.55e+01 1gjuA 637 2.56e+01 b.71.1.1,c.1.8.1 60580,60581 1umzA 278 2.58e+01 b.29.1.2 99639 1jscA 630 2.63e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1ds6B 180 2.64e+01 1rhoA b.1.18.8 21898 1f76A 336 2.68e+01 c.1.4.1 76160 1ycdA 243 2.69e+01 1xfjA 261 2.70e+01 d.194.1.2 109585 2a19A 175 2.78e+01 1gteA 1025 2.80e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1h7wD 1025 2.82e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15686,28631,30327,30612,39010 1lmhA 184 2.87e+01 d.167.1.1 74036 1sk4A 163 2.91e+01 d.118.1.1 105664 1wgoA 123 2.95e+01 1tafB 70 3.00e+01 1tafB a.22.1.3 16482 1jofA 365 3.00e+01 b.69.10.1 71775 1d2sA 170 3.09e+01 1d2sA b.29.1.4 24221 1a02N 301 3.12e+01 1a02N b.1.18.1,b.2.5.3 21923,22440 1gyvA 120 3.19e+01 b.1.10.2 70790 2pcfB 250 3.21e+01 1hcz i.4.1.1 45911 1iw7C 1119 3.21e+01 e.29.1.1 71474 1led 243 3.26e+01 1led b.29.1.1 24039 1klfB 279 3.27e+01 b.2.3.2,b.2.3.2 72684,72685 1wekA 217 3.30e+01 1o0pA 104 3.33e+01 d.58.7.1 86535 1dhkB 223 3.34e+01 1led b.29.1.1 24157 1h7wB 1025 3.36e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15684,28629,30325,30610,39008 2hrvA 142 3.41e+01 2hrvA b.47.1.4 26429 1eriA 276 3.44e+01 1ckqA c.52.1.1 33231 1gjwA 637 3.45e+01 b.71.1.1,c.1.8.1 60582,60583 1ioaA 240 3.54e+01 1led b.29.1.1 24168 1p4uA 153 3.58e+01 b.1.10.2 87780 1ckqA 276 3.64e+01 1ckqA c.52.1.1 33229 1uisA 231 3.65e+01 d.22.1.1 99431 1hx0A 496 3.65e+01 b.71.1.1,c.1.8.1 61346,61347 1x6vA 630 3.66e+01 1iq6A 134 3.66e+01 d.38.1.4 76755 1kn9A 249 3.70e+01 b.87.1.2 68699 1lqwA 183 3.70e+01 d.167.1.1 74210 1vrmA 325 3.71e+01 1js8A 394 3.77e+01 a.86.1.1,b.112.1.1 67219,67220 1cl8A 276 3.78e+01 1ckqA c.52.1.1 33230 1kiuB 279 3.78e+01 b.2.3.2,b.2.3.2 72525,72526 1diwA 441 3.79e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1gt8C 1025 3.79e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70428,70429,70430,70431,70432 1kr5A 226 3.82e+01 c.66.1.7 68847 1hl8A 449 3.85e+01 b.71.1.3,c.1.8.11 90646,90647 1h6rA 236 3.90e+01 d.22.1.1 65683 1ac5 483 3.91e+01 1ac5 c.69.1.5 34653 1yqzA 438 3.94e+01 1wosA 364 3.96e+01 b.44.2.1,d.250.1.1 109468,109469 1t0pB 86 3.97e+01 1g86A 142 3.97e+01 b.29.1.3 70161 1lcl 142 3.97e+01 1lcl b.29.1.3 24216 1xssA 225 4.00e+01 2dddA 225 4.02e+01 2fomB 185 4.03e+01 1egxA 115 4.04e+01 1evhA b.55.1.4 27000 1n26A 325 4.08e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1hr6B 443 4.09e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1tx4B 178 4.12e+01 1ctqA c.37.1.8 32045 1ejxC 567 4.16e+01 b.92.1.1,c.1.9.2 83184,83185 2b4rO 345 4.17e+01 1mh1 186 4.20e+01 1eesA c.37.1.8 32002 1fsoA 139 4.23e+01 1rhoA b.1.18.8 60007 1gr3A 160 4.26e+01 b.22.1.1 65476 1n9pA 207 4.29e+01 b.1.18.16 80343 1dzoA 123 4.30e+01 1dzoA d.24.1.1 38378 1c1bB 440 4.32e+01 1rthA e.8.1.2 43077 1a8d 452 4.38e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1hl9A 449 4.48e+01 b.71.1.3,c.1.8.11 90650,90651 1a5mC 566 4.48e+01 1ubpC b.92.1.1,c.1.9.2 28423,29045 1a5lC 566 4.54e+01 1ubpC b.92.1.1,c.1.9.2 28426,29048 2cxkA 95 4.56e+01 1a5kC 566 4.56e+01 1ubpC b.92.1.1,c.1.9.2 28425,29047 1i1nA 226 4.65e+01 c.66.1.7 71102 1ejrC 567 4.65e+01 1ubpC b.92.1.1,c.1.9.2 28420,29042 1kypA 237 4.68e+01 d.22.1.1 73280 1avbA 226 4.70e+01 1led b.29.1.1 24158 1spiA 358 4.78e+01 1frpA e.7.1.1 42939 1xqbA 247 4.79e+01 1fwcC 567 4.86e+01 1ubpC b.92.1.1,c.1.9.2 28410,29032 1mxmA 254 4.91e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 2a35A 215 4.94e+01 1m2oB 190 4.95e+01 c.37.1.8 78485 1eysH 259 4.96e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 1kshB 152 4.97e+01 b.1.18.8 72915 1tg7A 971 5.02e+01 1upsA 420 5.07e+01 2emo 237 5.07e+01 1ema d.22.1.1 38366 1xhlA 297 5.07e+01 c.2.1.2 109591 2a6hC 1119 5.08e+01 1hdkA 141 5.08e+01 b.29.1.3 65807 1esc 306 5.12e+01 1esc c.23.10.1 31334 1hcz 252 5.12e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 1oxdA 227 5.15e+01 d.22.1.1 93687 1v54F 98 5.19e+01 g.41.5.3 100327 1xe7A 203 5.20e+01 1iu1A 146 5.26e+01 b.1.10.2 71428 1sg4A 260 5.27e+01 1ci3M 249 5.30e+01 1hcz b.2.6.1,b.84.2.2 22480,28266 1igtB 444 5.36e+01 1igtB b.1.1.1,b.1.1.2,b.1.1.2,b.1.1.2 19765,20867,20868,20869 1ca1 370 5.38e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1v7wA 807 5.42e+01 a.102.1.4,b.30.5.3 108411,108412 1b0tA 106 5.44e+01 1a6l d.58.1.2 38965 1qunB 279 5.57e+01 b.2.3.2,b.2.3.2 22411,22412 2fuqA 747 5.57e+01 1h4aX 173 5.61e+01 b.11.1.1,b.11.1.1 83479,83480 1k3tA 359 5.73e+01 c.2.1.3,d.81.1.1 72022,72023 1zc3B 113 5.78e+01 1qpsA 261 5.84e+01 1ckqA c.52.1.1 33234 1dykA 394 5.90e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1ej8A 140 5.93e+01 1qupA b.1.8.1 22300 2cxcA 144 5.94e+01 1evuA 731 5.96e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1a6l 106 6.05e+01 1a6l d.58.1.2 38966 1ajw 145 6.06e+01 1rhoA b.1.18.8 21905 2b3yA 888 6.10e+01 1z0nA 96 6.14e+01 2etvA 346 6.19e+01 2bjqA 345 6.27e+01 2awkA 228 6.28e+01 1fonA 240 6.30e+01 5ptp b.47.1.2 26231 1iqsA 88 6.32e+01 d.214.1.1 71278 1ok7A 366 6.32e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1hka 158 6.33e+01 1hka d.58.30.1 39433 1mo9A 523 6.34e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1kid 203 6.35e+01 1derA c.8.5.1 30771 1lf6A 684 6.38e+01 a.102.1.5,b.30.5.5 77918,77919 1fieA 731 6.39e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21879,22167,22168,37109 1f0cA 305 6.55e+01 1c8oA e.1.1.1 42676 1d0hA 469 6.55e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 1exmA 405 6.70e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1j48A 110 6.72e+01 b.1.7.1 84112 1m93B 245 6.74e+01 2bmoB 194 6.74e+01 3ait 74 6.77e+01 1hoe b.5.1.1 22835 1rm6A 769 6.77e+01 2c78A 405 6.77e+01 1hyvA 166 6.78e+01 1b9dA c.55.3.2 61424 1rypE 242 6.80e+01 1rypE d.153.1.4 41936 1szoA 257 6.81e+01 c.14.1.3 106164 1iqoA 88 6.84e+01 d.214.1.1 71277 1tag 324 6.86e+01 1cipA a.66.1.1,c.37.1.8 18197,32080 1mkeA 152 6.86e+01 b.55.1.4 79231 1fkoB 440 6.87e+01 1rthA e.8.1.2 43095 1q25A 432 6.94e+01 b.64.1.1,b.64.1.1,b.64.1.1 104493,104494,104495 1kr7A 110 6.95e+01 a.1.1.4 72890 1smd 496 6.97e+01 1smd b.71.1.1,c.1.8.1 27768,28755 1cjsA 219 6.98e+01 1cjsA e.24.1.1 43354 1zmoA 244 6.99e+01 1pyoA 167 7.04e+01 c.17.1.1 95370 1z0mA 96 7.07e+01 1e2wA 251 7.09e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1nmtA 392 7.17e+01 1nmtA d.108.1.2,d.108.1.2 40823,40824 1wab 232 7.17e+01 1wab c.23.10.3 31341 2ch4A 320 7.17e+01 1ri5A 298 7.19e+01 c.66.1.34 97502 1w77A 228 7.20e+01 1fl9A 161 7.24e+01 c.37.1.18 70137 1mmiA 366 7.29e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 2polA 366 7.35e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 2a7bA 120 7.38e+01 1ksgB 152 7.56e+01 b.1.18.8 72913 1jg8A 347 7.57e+01 1jg8A c.67.1.1 62946 1m6sA 347 7.57e+01 c.67.1.1 78701 1bl3A 160 7.63e+01 1b9dA c.55.3.2 33655 3mefA 69 7.66e+01 1mjc b.40.4.5 25320 1pgs 314 7.69e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 1b9dA 163 7.76e+01 1b9dA c.55.3.2 33649 1u7nA 336 7.82e+01 c.77.1.4 107726 1qi9A 556 7.83e+01 1qhbA a.111.1.2 19053 2f62A 161 7.87e+01 1gmwA 143 8.03e+01 b.107.1.1,d.58.38.1 65347,65348 1ov3A 138 8.08e+01 b.34.2.1,b.34.2.1 87451,87452 1sotA 320 8.14e+01 b.36.1.4,b.47.1.1 105852,105853 1b12A 248 8.22e+01 1b12A b.87.1.2 28388 1a7vA 125 8.30e+01 1cpq a.24.3.2 16562 1h2rL 534 8.30e+01 1h2rL e.18.1.1 43298 1ubkL 534 8.32e+01 e.18.1.1 88422 1o0xA 262 8.34e+01 d.127.1.1 80755 1bqsA 209 8.34e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1wuiL 534 8.36e+01 1d3bA 75 8.45e+01 1d3bA b.38.1.1 24798 1ema 236 8.46e+01 1ema d.22.1.1 38339 1fuxA 166 8.57e+01 1fjjA b.17.1.2 60034 1ixlA 131 8.59e+01 d.38.1.5 90717 1p3dA 475 8.60e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1gmuA 143 8.67e+01 b.107.1.1,d.58.38.1 65335,65336 1y43B 173 8.67e+01 1suwA 249 8.67e+01 e.52.1.1 106027 1guzA 310 8.73e+01 c.2.1.5,d.162.1.1 65586,65587 1wtaA 275 8.77e+01 1g0dA 695 8.78e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 1rhoA 145 8.81e+01 1rhoA b.1.18.8 21899 1b59A 370 8.82e+01 1bn5 a.4.5.25,d.127.1.1 16225,41162 1qidA 537 8.83e+01 2bce c.69.1.1 34593 2b61A 377 8.84e+01 2a0kA 161 8.84e+01 2f2tA 161 8.84e+01 1zq1A 438 8.97e+01 1es9A 232 9.00e+01 1wab c.23.10.3 31340