# List of top-scoring protein chains for t04-100-30-alpha 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 1o5uA 101 2.69e-02 b.82.1.8 -4845 1uxxX 133 6.23e-02 b.18.1.10 -3107 1gmmA 133 8.49e-02 b.18.1.10 65314 1jnyA 435 1.80e-01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1p9kA 79 3.10e-01 unknown_sccs -10238 1khiA 176 3.17e-01 b.34.5.2 77408 b.40.4.5 77409 1uheA 97 3.75e-01 1e0tA 470 3.86e-01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 2arcA 164 4.22e-01 2arcA b.82.4.1 28148 1plc 99 4.53e-01 1plc b.6.1.1 22846 1k47A 337 5.21e-01 d.14.1.5 72040 d.58.26.4 72041 1qcsA 211 5.96e-01 1qcsA b.52.2.3 26927 d.31.1.1 38461 1v8cA 168 6.10e-01 d.15.3.1 -9175 unknown_sccs -11012 1ahxA 396 6.49e-01 1ajsA c.67.1.1 34293 1ars 396 6.52e-01 1ajsA c.67.1.1 34287 1geqA 248 6.93e-01 2tysA c.1.2.4 28589 1ejxC 567 7.12e-01 b.92.1.1 83184 c.1.9.2 83185 1i8dA 213 7.32e-01 b.43.4.3 61953 b.43.4.3 61954 1g2bA 62 7.41e-01 1tud b.34.2.1 24488 1gcqC 70 7.86e-01 1gcpA b.34.2.1 60436 1aonO 97 8.31e-01 b.35.1.1 24642 1cei 94 8.53e-01 1cei a.28.2.1 16939 4ubpB 126 9.60e-01 1ubpB b.85.3.1 28345 2rslA 140 9.69e-01 2rslA c.53.1.1 33345 1rc6A 261 9.75e-01 unknown_sccs -4868 1f56A 91 9.75e-01 2cbp b.6.1.1 22896 1e4fT 419 9.88e-01 1e4fT c.55.1.1 33453 c.55.1.1 33454 2plc 274 1.04e+00 2plc c.1.18.2 29614 1ltlA 279 1.10e+00 b.40.4.11 84701 1bypA 99 1.15e+00 1plc b.6.1.1 22858 1eu1A 780 1.23e+00 1dmr b.52.2.2 26903 c.81.1.1 35311 1fjgD 209 1.27e+00 1c05A d.66.1.2 39553 1r61A 207 1.28e+00 unknown_sccs -6086 1unkA 87 1.41e+00 1cei a.28.2.1 16935 1lgpA 116 1.42e+00 b.26.1.2 73890 1aac 105 1.43e+00 1aac b.6.1.1 22838 1bxaA 105 1.48e+00 1aac b.6.1.1 22839 1r6xA 395 1.56e+00 b.122.1.3 -5125 c.26.1.5 -6620 1earA 147 1.61e+00 b.107.1.1 64875 d.58.38.1 64876 1f60A 458 1.63e+00 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 2napA 723 1.67e+00 2napA b.52.2.2 26926 c.81.1.1 35334 1d2eA 397 1.68e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1qisA 396 1.82e+00 1ajsA c.67.1.1 34284 1ckaA 57 1.97e+00 1ckaA b.34.2.1 24459 1ndh 272 1.99e+00 1ndh b.43.4.2 25662 c.25.1.1 31552 2plt 98 2.04e+00 1plc b.6.1.1 22862 1r13A 148 2.05e+00 d.169.1.1 -11646 h.1.1.1 -12895 1a49A 530 2.10e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1pmy 123 2.18e+00 1bqk b.6.1.1 22888 3ullA 132 2.23e+00 3ullA b.40.4.3 25282 4ubpC 570 2.23e+00 1ubpC b.92.1.1 28431 c.1.9.2 29053 1p1cA 199 2.24e+00 c.66.1.16 87669 1mxiA 160 2.36e+00 c.116.1.1 79646 1iv3A 152 2.41e+00 d.79.5.1 76828 1ky3A 182 2.60e+00 c.37.1.8 73193 1ag6 99 2.64e+00 1plc b.6.1.1 22857 1iz6A 138 2.67e+00 b.34.5.2 76976 b.40.4.5 76977 1qzzA 374 2.83e+00 a.4.5.29 -277 c.66.1.12 -8045 1vhuA 211 2.83e+00 c.50.1.2 -7934 1hjzA 192 2.88e+00 c.50.1.2 83520 1dgwY 93 2.88e+00 1caxB 1bqk 124 2.90e+00 1bqk b.6.1.1 22889 2dpmA 284 2.95e+00 2dpmA c.66.1.28 34246 1bkb 136 2.98e+00 1bkb b.34.5.2 24609 b.40.4.5 25341 1g8kA 825 3.00e+00 1g8jA b.52.2.2 26920 c.81.1.1 35328 1i7pA 274 3.05e+00 b.43.4.2 66048 c.25.1.1 66049 1db3A 372 3.06e+00 1db3A c.2.1.2 29813 1fm0D 81 3.14e+00 1fmaD d.15.3.1 37642 1tuc 63 3.18e+00 1tuc b.34.2.1 24492 1reqA 727 3.28e+00 1reqA c.1.19.1 29620 c.23.6.1 31247 1o9yA 84 3.29e+00 unknown_sccs -4105 1kzlA 208 3.37e+00 b.43.4.3 77635 b.43.4.3 77636 1bb9 115 3.38e+00 1bb9 b.34.2.1 24554 5reqA 727 3.43e+00 1reqA c.1.19.1 29632 c.23.6.1 31259 1izcA 339 3.58e+00 c.1.12.5 83838 1eemA 241 3.71e+00 1eemA a.45.1.1 17717 c.47.1.5 33011 2cbp 96 3.74e+00 2cbp b.6.1.1 22895 1k0hA 117 3.87e+00 b.106.1.2 71975 1agjA 242 4.05e+00 1agjA b.47.1.1 25827 1j58A 385 4.15e+00 b.82.1.2 71531 1g8fA 511 4.21e+00 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 1uy4A 145 4.41e+00 1vioA 243 4.59e+00 unknown_sccs -10154 d.66.1.5 -10240 1q1gA 276 4.62e+00 c.56.2.1 -7846 1qu9A 128 4.64e+00 1qu9A d.79.1.1 39755 1pfzA 380 4.65e+00 1smrA b.50.1.2 26881 1mfgA 95 4.66e+00 b.36.1.1 79043 1uxzA 131 4.72e+00 b.18.1.10 -3110 1e0gA 48 4.79e+00 1e01A d.7.1.1 37325 1i6pA 220 5.13e+00 1ddzA c.53.2.1 61848 1h0hA 977 5.23e+00 b.52.2.2 76435 c.81.1.1 76436 1semA 58 5.42e+00 1ckaA b.34.2.1 24544 1euwA 152 5.43e+00 1dupA b.85.4.1 28349 1g38A 393 5.70e+00 2admA c.66.1.27 60235 1nnxA 109 5.76e+00 unknown_sccs -3899 1rie 129 5.93e+00 1rie b.33.1.1 24427 1mg4A 113 6.12e+00 d.15.11.1 84953 1gttA 429 6.23e+00 d.177.1.1 70529 d.177.1.1 70530 1sb8A 352 6.30e+00 1ujxA 119 6.37e+00 b.26.1.2 -3325 1fqtA 112 6.49e+00 1fqtA b.33.1.1 24441 1paz 123 6.49e+00 1bqk b.6.1.1 22878 1vj0A 380 6.80e+00 b.35.1.2 -3697 c.2.1.1 -5721 1ru4A 400 6.88e+00 unknown_sccs -4778 1bg6 359 6.97e+00 1bg6 a.100.1.5 18810 c.2.1.6 30214 2eifA 136 7.19e+00 1bkb b.34.5.2 24607 b.40.4.5 25339 4uagA 437 7.43e+00 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1dm9A 133 7.46e+00 1dm9A d.66.1.3 39560 1o4tA 133 7.49e+00 b.82.1.9 86622 7pcy 98 7.67e+00 1plc b.6.1.1 22863 1e2tA 284 7.86e+00 1e2tA d.3.1.5 37121 1oruA 195 7.99e+00 unknown_sccs -4390 1i1jA 108 8.03e+00 1i1jA b.34.2.1 61531 1uzcA 71 8.08e+00 a.159.2.1 -339 1danU 121 8.10e+00 1boy b.1.2.1 21954 1qxyA 252 8.41e+00 d.127.1.1 -10993 1k66A 149 8.60e+00 c.23.1.1 -6406 1q7hA 153 8.62e+00 b.122.1.1 -5124 unknown_sccs -9313 1dgwA 178 8.65e+00 1dgwA b.82.1.2 28090 1cl1A 395 8.69e+00 1cl2A c.67.1.3 34395 2hft 218 8.86e+00 1boy b.1.2.1 21951 b.1.2.1 21952 1oq1A 223 9.01e+00 unknown_sccs -3455 1ne6A 283 9.03e+00 b.82.3.2 -4918 b.82.3.2 -4919 1ny4A 82 9.27e+00 b.40.4.5 -3944 1mv3A 213 9.29e+00 b.34.2.1 -3555 1a9xB 379 9.34e+00 1c3oB c.8.3.1 30732 c.23.16.1 31409 1i7oA 429 9.40e+00 1i7oA d.177.1.1 61893 d.177.1.1 61894 1lzjA 292 9.43e+00 c.68.1.9 74352 5ukdA 194 9.61e+00 1zin c.37.1.1 31851 1qauA 112 1.02e+01 1qauA b.36.1.1 24779 1qf9A 194 1.05e+01 1zin c.37.1.1 31848 1jb3A 131 1.06e+01 1jc7A b.40.3.2 62833 1mr7A 209 1.06e+01 b.81.1.3 -4798 1ir3A 306 1.07e+01 1fmk d.144.1.7 41702 1czfA 362 1.07e+01 1czfA b.80.1.3 28031 1bxvA 91 1.09e+01 1aac b.6.1.1 22875 1cb0A 283 1.11e+01 1cb0A c.56.2.1 33790 1dfuP 94 1.12e+01 1dfuP b.53.1.1 26936 1pht 85 1.13e+01 1ckaA b.34.2.1 24483 1t9fA 187 1.14e+01 1ixkA 315 1.16e+01 unknown_sccs -8099 1eg3A 261 1.17e+01 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1zin 217 1.20e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1i1nA 226 1.21e+01 c.66.1.7 71102 1t46A 313 1.22e+01 1o7iA 119 1.25e+01 b.40.4.3 86642 1jv2B 692 1.27e+01 b.1.15.1 67338 c.62.1.1 67339 d.200.1.1 67340 g.3.11.6 67341 g.3.11.6 67342 1mw7A 240 1.31e+01 e.39.1.1 79557 1bdo 80 1.32e+01 1bdo b.84.1.1 28214 1htrP 43 1.32e+01 1htrP b.50.1.2 26852 1iuz 98 1.33e+01 1plc b.6.1.1 22861 1vjhA 122 1.33e+01 d.129.3.1 -11037 1hyoA 421 1.33e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1udxA 416 1.34e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 2tnfA 156 1.34e+01 2tnfA b.22.1.1 23880 1uj0A 62 1.37e+01 b.34.2.1 -3570 1oniA 137 1.37e+01 d.79.1.1 87144 1okcA 297 1.37e+01 unknown_sccs -12339 1gl4B 98 1.38e+01 b.1.1.4 65288 1je0A 236 1.38e+01 c.56.2.1 66581 1a8vA 121 1.39e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1jcfA 344 1.40e+01 c.55.1.1 62878 c.55.1.1 62879 1gkpA 458 1.40e+01 b.92.1.3 70231 c.1.9.6 70232 1vhwA 253 1.43e+01 c.56.2.1 -7765 1el5A 389 1.47e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1vcaA 202 1.47e+01 1vcaA b.1.1.3 21649 b.1.1.4 21685 1mjc 69 1.48e+01 1mjc b.40.4.5 25319 1nw2A 105 1.49e+01 c.47.1.1 -7380 1gmuA 143 1.50e+01 b.107.1.1 65335 d.58.38.1 65336 1gzwA 134 1.51e+01 b.29.1.3 -3412 1ov3A 138 1.53e+01 b.34.2.1 87451 b.34.2.1 87452 1ek6A 348 1.53e+01 1xel c.2.1.2 29800 1jpc 109 1.58e+01 1b2pA b.78.1.1 27986 1ixlA 131 1.59e+01 d.38.1.5 -9705 1cx4A 305 1.59e+01 b.82.3.2 59099 b.82.3.2 59100 1lkoA 191 1.60e+01 a.25.1.1 78063 g.41.5.1 78064 1ahsA 126 1.60e+01 1ahsA b.19.1.1 23794 1pbwA 216 1.64e+01 1pbwA a.116.1.1 19103 1o7dE 126 1.68e+01 1od5A 492 1.70e+01 b.82.1.2 86832 b.82.1.2 86833 1s6cA 183 1.72e+01 a.39.1.5 -858 1rlkA 117 1.74e+01 unknown_sccs -7526 1np7A 489 1.75e+01 a.99.1.1 80677 c.28.1.1 80678 1sltA 134 1.78e+01 1c1lA b.29.1.3 24186 1vjnA 220 1.79e+01 unknown_sccs -11458 1hf2A 210 1.81e+01 1hf2A b.80.3.1 60992 c.102.1.1 60993 1sixA 174 1.86e+01 b.85.4.1 -5030 1uok 558 1.86e+01 1uok b.71.1.1 27801 c.1.8.1 28788 1nngA 153 1.87e+01 d.38.1.1 -9636 1tyv 542 1.88e+01 1tyv b.80.1.6 28038 1te5A 257 1.90e+01 1f3z 161 1.90e+01 1gpr b.84.3.1 28273 1rxyA 253 1.91e+01 c.56.2.1 -7834 1ryt 190 1.97e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 1ccwA 137 2.00e+01 1be1 c.23.6.1 31238 1jer 138 2.00e+01 2cbp b.6.1.1 23022 1aie 31 2.01e+01 1aie a.53.1.1 17829 1epwA 1290 2.03e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1sefA 274 2.03e+01 1whi 122 2.04e+01 1whi b.39.1.1 24810 1odkA 235 2.05e+01 c.56.2.1 86863 1b71A 191 2.08e+01 1ryt a.25.1.1 16647 g.41.5.1 45246 1s1hC 192 2.11e+01 1kte 105 2.18e+01 1kte c.47.1.1 32771 1gppA 237 2.19e+01 b.86.1.2 76262 1gcqA 61 2.20e+01 1ckaA b.34.2.1 60434 1l6oA 95 2.21e+01 b.36.1.1 84534 1tluA 130 2.23e+01 1nhcA 336 2.26e+01 b.80.1.3 -4768 1dyr 206 2.28e+01 1aoeA c.71.1.1 34916 1hnnA 282 2.28e+01 c.66.1.15 65895 1lcyA 325 2.28e+01 b.36.1.4 73834 b.47.1.1 73835 1pmi 440 2.29e+01 1pmi b.82.1.3 28114 1j24A 143 2.31e+01 c.52.1.20 84008 1j30A 144 2.34e+01 a.25.1.1 -650 1hc7A 477 2.36e+01 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1ofcX 304 2.37e+01 a.4.1.3 -195 unknown_sccs -199 unknown_sccs -978 1ha3A 405 2.38e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1igwA 434 2.41e+01 c.1.12.7 62370 1oflA 481 2.42e+01 1m93A 55 2.44e+01 e.1.1.1 -11751 1fjgQ 105 2.45e+01 1fjfQ b.40.4.5 25352 1v6sA 390 2.48e+01 c.86.1.1 -8567 1dkqA 410 2.49e+01 1dklA c.60.1.2 33998 1exmA 405 2.50e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1pjxA 314 2.53e+01 1jqbA 351 2.53e+01 b.35.1.2 77151 c.2.1.1 77152 4tsvA 150 2.53e+01 2tnfA b.22.1.1 23860 1o6aA 96 2.54e+01 unknown_sccs -4101 1hdfA 102 2.55e+01 1ag4 b.11.1.1 23627 1jilA 420 2.58e+01 c.26.1.1 66745 1oxdA 227 2.60e+01 d.22.1.1 -9438 1e1aA 314 2.60e+01 1e1aA b.68.6.1 59155 1mdc 133 2.64e+01 1hmt b.60.1.2 27198 1o54A 277 2.66e+01 c.66.1.13 -8095 1s2kA 206 2.74e+01 unknown_sccs -3494 1c3gA 170 2.77e+01 1c3gA b.4.1.1 22831 b.4.1.1 22832 1gvnB 287 2.77e+01 c.37.1.21 76354 1ema 236 2.80e+01 1ema d.22.1.1 38339 1fbr 93 2.81e+01 1fbr g.27.1.1 44948 g.27.1.1 44949 1lcl 142 2.84e+01 1lcl b.29.1.3 24216 1gtmA 419 2.85e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1opjA 293 2.85e+01 d.144.1.7 87230 1fukA 165 2.86e+01 1fukA c.37.1.19 32409 1hdkA 141 2.93e+01 b.29.1.3 65807 1c9oA 66 2.94e+01 1mjc b.40.4.5 25325 1ejxB 101 2.94e+01 b.85.3.1 83183 1rl6A 177 2.96e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1fi2A 201 2.96e+01 1fi2A b.82.1.2 59845 1f6fB 210 2.97e+01 1axiB b.1.2.1 22033 b.1.2.1 22034 4enl 436 3.01e+01 4enl c.1.11.1 29202 d.54.1.1 38846 1dekA 241 3.02e+01 1dekA c.37.1.1 31842 1umuA 116 3.05e+01 1umuA b.87.1.1 28382 1ng2A 193 3.07e+01 b.34.2.1 85660 b.34.2.1 85661 1oneA 436 3.11e+01 4enl c.1.11.1 29200 d.54.1.1 38844 1qwrA 319 3.11e+01 b.82.1.3 -4880 1nrzA 164 3.12e+01 c.38.1.1 86131 1kqfA 1015 3.13e+01 b.52.2.2 72871 c.81.1.1 72872 1kdj 102 3.13e+01 1plc b.6.1.1 22864 1go3E 187 3.14e+01 b.40.4.5 83054 d.230.1.1 83055 1led 243 3.18e+01 1led b.29.1.1 24039 1dbgA 506 3.18e+01 1dbgA b.80.1.4 28033 1kamA 194 3.19e+01 c.26.1.3 72254 1b00A 127 3.20e+01 3chy c.23.1.1 31122 1elqA 390 3.20e+01 1elqA c.67.1.3 34436 1kk1A 410 3.21e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1gc0A 398 3.25e+01 c.67.1.3 70168 1b12A 248 3.31e+01 1b12A b.87.1.2 28388 1feuA 206 3.33e+01 1feuA b.53.1.1 59801 1qavA 90 3.36e+01 1qauA b.36.1.1 24777 1g8iA 190 3.36e+01 1rec a.39.1.5 60363 1o0yA 260 3.41e+01 c.1.10.1 80756 1plzA 189 3.42e+01 b.82.1.7 88160 1dboA 506 3.43e+01 1dbgA b.80.1.4 28034 1q7lB 88 3.43e+01 1r26A 125 3.49e+01 c.47.1.1 -7389 1vjqA 79 3.51e+01 unknown_sccs -13478 1fm0E 150 3.54e+01 1fmaE d.41.5.1 38629 1kevA 351 3.55e+01 1pedA b.35.1.2 24749 c.2.1.1 29765 1miwA 404 3.59e+01 a.173.1.1 79162 d.218.1.4 79163 1regX 122 3.59e+01 1regX d.58.27.1 39406 1utiA 58 3.61e+01 b.34.2.1 -3552 1pqhA 143 3.64e+01 b.52.2.1 -4318 1juhA 350 3.65e+01 b.82.1.5 71884 1v3vA 333 3.66e+01 1r6jA 82 3.67e+01 b.36.1.1 -3732 1kypA 237 3.68e+01 d.22.1.1 73280 1t82A 155 3.70e+01 1l7yA 94 3.74e+01 d.15.1.6 73676 1q7eA 428 3.75e+01 c.123.1.1 -8768 1o08A 221 3.77e+01 c.108.1.6 86525 1rl2A 137 3.87e+01 1rl2A b.34.5.3 24610 b.40.4.5 25342 1m1nA 491 3.90e+01 c.92.2.3 78417 1v5lA 103 3.91e+01 1e9rA 437 3.92e+01 c.37.1.11 64827 1dzkA 157 3.93e+01 1obpA b.60.1.1 27096 1uwwA 191 3.95e+01 1a8p 258 3.99e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 1erv 105 4.00e+01 1erv c.47.1.1 32743