# List of top-scoring protein chains for t04-100-30-bys-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 1dnlA 199 7.96e-18 1ci0A b.45.1.1 25753 1g79A 218 1.22e-17 1ci0A b.45.1.1 25752 1rfeA 162 8.01e-17 2fhqA 141 7.72e-15 1nrgA 261 9.58e-15 b.45.1.1 80694 1t9mA 214 2.75e-14 2asfA 137 5.10e-14 1xxoA 147 2.11e-13 2aq6A 147 2.26e-13 1w9aA 147 3.55e-13 1ty9A 222 1.05e-12 1vl7A 157 3.09e-11 b.45.1.1 108732 2arzA 247 4.74e-11 2fg9A 178 6.09e-11 2furA 209 1.24e-08 1xhnA 184 2.87e-07 1w3oA 216 4.35e-07 1flmA 122 2.41e-06 1axj b.45.1.1 25747 1ejeA 192 8.81e-04 1ejeA b.45.1.2 25757 1ko3A 230 2.95e-01 d.157.1.1 90974 1s2wA 295 5.81e-01 c.1.12.7 98407 1tr8A 102 7.67e-01 2bgiA 272 8.27e-01 1snzA 344 9.96e-01 b.30.5.4 98930 1i24A 404 1.06e+00 c.2.1.2 83663 1i0rA 169 1.26e+00 1i0rA b.45.1.2 61489 1i0sA 169 1.55e+00 1i0rA b.45.1.2 61491 2fauA 341 1.85e+00 1pymA 295 2.04e+00 1pymA c.1.12.7 29308 1zd7A 159 2.26e+00 1vqoE 178 2.46e+00 1n9lA 109 2.59e+00 d.110.3.6 85468 1qrrA 394 2.67e+00 1qrrA c.2.1.2 29824 2gukA 120 3.13e+00 1sdjA 310 3.26e+00 d.21.1.2,d.21.1.2 98807,98808 2f6uA 234 3.51e+00 1ojrA 274 3.70e+00 c.74.1.1 93147 1obpA 159 4.30e+00 1obpA b.60.1.1 27092 1qmyA 167 4.43e+00 1qmyA d.3.1.2 37094 1qyaA 307 5.10e+00 d.21.1.2,d.21.1.2 104653,104654 1j5kA 89 5.56e+00 d.51.1.1 71565 1ta0A 197 5.58e+00 c.108.1.16 106729 1agqA 135 5.77e+00 1agqA g.17.1.2 44789 1qksA 567 7.27e+00 1qksA a.3.1.2,b.70.2.1 15951,27710 1pysA 350 7.99e+00 1pysA d.104.1.1 40775 1m40A 263 8.00e+00 e.3.1.1 74437 1btl 263 8.37e+00 1btl e.3.1.1 42691 1q74A 303 8.74e+00 c.134.1.1 96019 1h6lA 353 8.76e+00 b.68.3.1 60687 1jjtA 228 8.82e+00 1a7tA d.157.1.1 63139 1j9lA 247 9.07e+00 c.106.1.1 62762 2fh1A 344 9.61e+00 2ganA 190 1.01e+01 1do6A 124 1.06e+01 1do6A b.1.13.1 22361 1so7A 382 1.08e+01 1yoaA 159 1.09e+01 1r5lA 262 1.11e+01 a.5.3.1,c.13.1.1 97099,97100 1h7zA 194 1.18e+01 1qhvA b.21.1.1 60733 1v0wA 506 1.18e+01 d.136.1.2,d.136.1.2 108220,108221 1plc 99 1.18e+01 1plc b.6.1.1 22846 1jjeA 222 1.19e+01 1a7tA d.157.1.1 63117 1ermA 263 1.20e+01 1btl e.3.1.1 42690 2pooA 355 1.23e+01 1qlgA b.68.3.1 27626 1jj2E 177 1.26e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1ye8A 178 1.26e+01 1dqiA 124 1.33e+01 1do6A b.1.13.1 22357 1j58A 385 1.36e+01 b.82.1.2 71531 1jyoA 130 1.37e+01 d.198.1.1 67483 2fvgA 340 1.42e+01 2b4wA 315 1.43e+01 1z0mA 96 1.45e+01 1f0iA 504 1.45e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 2axoA 270 1.46e+01 1vqoS 85 1.47e+01 1njhA 119 1.49e+01 b.128.1.1 85787 1s72E 178 1.52e+01 d.141.1.1,d.141.1.1 105323,105324 1zzkA 82 1.57e+01 2culA 232 1.57e+01 1qsoA 149 1.59e+01 1qsmA d.108.1.1 40812 1r5mA 425 1.62e+01 1s1dA 331 1.74e+01 b.67.3.1 98344 1qsmA 152 1.74e+01 1qsmA d.108.1.1 40808 1o98A 511 1.74e+01 c.105.1.1,c.76.1.3 86684,86685 1lrzA 426 1.76e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1widA 130 1.84e+01 1b7yA 350 1.89e+01 1pysA d.104.1.1 40776 1uthA 315 1.91e+01 c.94.1.1 108032 1ei1A 391 1.93e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 2ak4E 245 1.96e+01 1ag6 99 1.96e+01 1plc b.6.1.1 22857 1wj9A 211 2.00e+01 1r4uA 301 2.13e+01 d.96.1.4,d.96.1.4 97047,97048 2aebA 322 2.20e+01 1wsrA 375 2.25e+01 7pcy 98 2.30e+01 1plc b.6.1.1 22863 1vrbA 342 2.31e+01 2abqA 306 2.33e+01 1z0nA 96 2.35e+01 1w0hA 204 2.44e+01 1jj2R 84 2.45e+01 1ffkP d.12.1.1 63103 1m2dA 110 2.46e+01 c.47.1.11 78476 1xdfA 157 2.54e+01 2fb1A 226 2.54e+01 1eqjA 511 2.55e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1s72S 85 2.56e+01 d.12.1.1 105338 2fvvA 194 2.61e+01 1u9aA 160 2.65e+01 1u9aA d.20.1.1 38333 1rz1A 161 2.66e+01 b.45.1.2 98124 1vk8A 106 2.66e+01 d.58.48.1 108636 1l0qA 391 2.70e+01 b.1.3.1,b.69.2.3 77644,77645 1vq0A 302 2.71e+01 2fs2A 151 2.75e+01 1kuuA 202 2.77e+01 d.153.2.1 73019 1aisA 182 2.77e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 2grrA 161 2.81e+01 2f4iA 197 2.81e+01 1b8aA 438 2.83e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 2b5oA 402 2.89e+01 2bnuB 241 2.89e+01 2ewrA 170 2.93e+01 1hr0W 71 2.94e+01 1ah9 b.40.4.5 25329 2axcA 264 2.97e+01 1zboA 210 2.98e+01 1vi2A 300 2.98e+01 c.2.1.7,c.58.1.5 100726,100727 1pne 140 3.00e+01 1pne d.110.1.1 40866 2atpB 115 3.12e+01 1htp 131 3.14e+01 1htp b.84.1.1 28220 1llnA 262 3.19e+01 d.165.1.1 84625 1wmmA 145 3.22e+01 1q5xA 161 3.23e+01 c.8.7.1 95947 1dgwX 79 3.27e+01 1caxB b.82.1.2 28091 2bjuA 453 3.29e+01 1zfjA 491 3.29e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1x88A 359 3.32e+01 1b6a 478 3.36e+01 1bn5 a.4.5.25,d.127.1.1 16223,41160 1zarA 282 3.38e+01 1pjjA 271 3.40e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1y7bA 542 3.42e+01 2fgtA 417 3.44e+01 1p9yA 121 3.48e+01 d.241.2.1 94402 1c8uA 285 3.59e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1repC 251 3.60e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1ujqA 305 3.61e+01 c.1.12.7 99463 1of8A 370 3.63e+01 c.1.10.4 92819 1ki9A 192 3.63e+01 c.37.1.1 84404 1fepA 724 3.65e+01 1fepA f.4.3.3 43808 1ogaE 252 3.65e+01 b.1.1.1,b.1.1.2 86992,86993 2ai4A 119 3.66e+01 1uroA 367 3.67e+01 1uroA c.1.22.1 29675 1gal 583 3.68e+01 1gpeA c.3.1.2,d.16.1.1 30386,37950 1w6sA 599 3.71e+01 2b61A 377 3.74e+01 1s9aA 257 3.80e+01 b.3.6.1 105379 1ir3A 306 3.83e+01 1fmk d.144.1.7 41702 1qtnA 164 3.85e+01 1pauA c.17.1.1 30999 1nv8A 284 3.94e+01 c.66.1.30 86224 1kcqA 104 3.94e+01 d.109.1.1 68449 1psuA 140 3.96e+01 d.38.1.5 88285 2cxvA 219 3.96e+01 1hfoA 113 3.99e+01 d.80.1.3 61006 1t5yA 190 4.14e+01 b.122.1.1,d.17.6.3 106495,106496 1zesA 125 4.15e+01 1okiA 210 4.23e+01 b.11.1.1,b.11.1.1 93255,93256 1nmeA 146 4.37e+01 c.17.1.1 85874 1x72A 334 4.40e+01 d.126.1.6 109495 1fnuA 221 4.43e+01 3seb b.40.2.2,d.15.6.1 25212,37801 1k8kD 300 4.49e+01 d.198.2.1,d.198.2.1 68309,68310 1rocA 155 4.54e+01 b.1.22.1 97673 1bkb 136 4.54e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1v6tA 255 4.56e+01 2biiA 424 4.56e+01 1cqqA 180 4.57e+01 1cqqA b.47.1.4 26422 2etjA 250 4.57e+01 1eyqA 222 4.68e+01 1eypA d.36.1.1 38534 2bbsA 290 4.69e+01 2fexA 188 4.71e+01 1iejA 332 4.72e+01 1nnt c.94.1.2 62328 1zx8A 136 4.72e+01 1aszB 490 4.75e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 2bwrA 401 4.75e+01 1amp 291 4.79e+01 1amp c.56.5.4 33837 1vi4A 174 4.80e+01 c.8.7.1 100731 2cw5A 255 4.80e+01 1xsoA 150 4.82e+01 1mfmA b.1.8.1 22273 1jfuA 186 4.91e+01 c.47.1.10 62940 1sqwA 188 4.93e+01 1e6wA 260 5.00e+01 1e6wA c.2.1.2 59326 1j71A 334 5.08e+01 1eagA b.50.1.2 62669 1bupA 386 5.09e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 2choA 716 5.13e+01 1qxrA 189 5.15e+01 b.82.1.7 96552 1ub4A 110 5.18e+01 b.34.6.2 88399 2bt6A 108 5.20e+01 2chnA 716 5.23e+01 1xmaA 145 5.26e+01 2fcjA 119 5.30e+01 1o22A 170 5.39e+01 d.238.1.1 86557 1lbvA 252 5.40e+01 e.7.1.1 73813 1uox 296 5.42e+01 1uox 1goiA 499 5.45e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 2f15A 96 5.46e+01 1rlmA 271 5.47e+01 1tdzA 272 5.48e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 2phlA 397 5.56e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1je5A 206 5.57e+01 1je5A b.40.4.7 62909 1zwxA 301 5.61e+01 2b06A 155 5.61e+01 1kwgA 645 5.64e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1eu3A 210 5.67e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1dykA 394 5.67e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1p4oA 322 5.70e+01 d.144.1.7 87775 1i8dA 213 5.72e+01 b.43.4.3,b.43.4.3 61953,61954 1jhfA 202 5.75e+01 a.4.5.2,b.87.1.1 63057,63058 2gimA 106 5.82e+01 1pbyA 489 5.83e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1ew0A 130 5.83e+01 1drmA d.110.3.2 40905 1bolA 222 5.84e+01 1bolA d.124.1.1 41120 2c5uA 375 5.85e+01 1smoA 119 5.86e+01 b.1.1.1 105764 1erjA 393 5.87e+01 1erjA b.69.4.1 27660 1i2kA 269 5.90e+01 e.17.1.1 90661 1dmhA 311 5.91e+01 1dmhA b.3.6.1 22633 1rtqA 299 5.92e+01 c.56.5.4 97819 1ssfA 156 5.93e+01 b.34.9.1,b.34.9.1 105982,105983 1xyiA 66 5.97e+01 1ivg 388 5.98e+01 2qwc b.68.1.1 27578 1xipA 388 6.04e+01 1vmaA 306 6.08e+01 a.24.13.1,c.37.1.10 108887,108888 1z83A 196 6.08e+01 1tlk 154 6.08e+01 1tlk b.1.1.4 21707 1t6eX 381 6.12e+01 b.50.1.2 106564 1p57B 255 6.14e+01 b.47.1.2 94126 1jdpA 441 6.17e+01 c.93.1.1 62906 1lfdA 87 6.20e+01 1lfdA d.15.1.5 37622 1zm8A 259 6.23e+01 1ogoX 574 6.25e+01 b.133.1.1,b.80.1.10 92925,92926 1q40B 219 6.27e+01 d.17.4.2 95771 2dexX 671 6.29e+01 1zgzA 122 6.30e+01 1iw7C 1119 6.33e+01 e.29.1.1 71474 2gibA 103 6.38e+01 1dgwA 178 6.43e+01 1dgwA b.82.1.2 28090 2bitX 165 6.44e+01 1s28A 132 6.46e+01 d.198.1.1 105223 2cveA 191 6.50e+01 1b00A 127 6.52e+01 3chy c.23.1.1 31122 2bkrB 77 6.54e+01 1gefA 123 6.62e+01 1gefA c.52.1.18 60465 1ztpA 251 6.63e+01 1lokA 291 6.68e+01 c.56.5.4 78122 1vc1A 110 6.76e+01 c.13.2.1 108493 2f4mA 295 6.81e+01 1g8fA 511 6.82e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1wrrA 301 6.83e+01 1tmy 120 6.84e+01 1dbwA c.23.1.1 31083 1b25A 619 6.90e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1h1wA 289 6.90e+01 d.144.1.7 83460 1f37A 110 6.93e+01 1f37A c.47.1.11 33088 1vdnA 162 6.98e+01 1kveB 77 7.00e+01 1kveB 1rlmB 271 7.02e+01 1frpA 335 7.06e+01 1frpA e.7.1.1 42875 2plt 98 7.07e+01 1plc b.6.1.1 22862 2fneA 117 7.11e+01 1e3dA 266 7.12e+01 2frvA e.19.1.1 59188 1kgcE 242 7.13e+01 b.1.1.1,b.1.1.2 77386,77387 2bgzA 299 7.14e+01 1u0sY 118 7.14e+01 c.23.1.1 107566 1yn9A 169 7.14e+01 1z92B 219 7.18e+01 1cbjA 151 7.18e+01 1mfmA b.1.8.1 22213 1k3eA 156 7.19e+01 d.198.1.1 68103 1wlgA 299 7.23e+01 1ymiA 334 7.23e+01 1am2 199 7.24e+01 1am2 b.86.1.2 28381 1gg1A 350 7.27e+01 1qr7A c.1.10.4 29187 1avbA 226 7.27e+01 1led b.29.1.1 24158 1o7tA 309 7.27e+01 c.94.1.1 86645 2ci1A 275 7.30e+01 1mo7A 213 7.31e+01 d.220.1.1 85028 1gr0A 367 7.42e+01 c.2.1.3,d.81.1.3 70379,70380 1nnjA 271 7.42e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1vpjA 192 7.44e+01 2b1yA 104 7.45e+01 1al3 324 7.53e+01 1al3 c.94.1.1 35835 1rcqA 357 7.56e+01 b.49.2.2,c.1.6.1 104882,104883 2cmuA 342 7.66e+01 2glfA 450 7.66e+01 1e6pA 499 7.66e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1crzA 403 7.66e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1ox0A 430 7.66e+01 c.95.1.1,c.95.1.1 87495,87496 1a2zA 220 7.67e+01 1a2zA c.56.4.1 33794 2a5hA 416 7.70e+01 1z8gA 372 7.74e+01 1htwA 158 7.75e+01 c.37.1.18 71083 1q7fA 286 7.76e+01 b.68.9.1 96036 2bwqA 129 7.85e+01 1b2pA 119 7.85e+01 1b2pA b.78.1.1 27998 1hcnB 145 7.87e+01 1hcnB g.17.1.4 44810 1wk8A 194 7.91e+01 2pia 321 7.91e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1qauA 112 7.93e+01 1qauA b.36.1.1 24779 2basA 431 7.94e+01 3seb 238 7.94e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1xc1A 309 7.97e+01 c.94.1.1 109543 1n8fA 350 7.98e+01 c.1.10.4 85397 1cjxA 357 8.04e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1wv2A 265 8.06e+01 2gm6A 208 8.11e+01 1xhfA 123 8.12e+01 1rz3A 201 8.14e+01 c.37.1.6 98132 1plq 258 8.19e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1rp0A 284 8.22e+01 1vp4A 425 8.24e+01 1e9pA 151 8.25e+01 1mfmA b.1.8.1 22215 1ryaA 160 8.30e+01 d.113.1.5 105122 1udzA 182 8.35e+01 b.51.1.1 99239 1gheA 177 8.40e+01 d.108.1.1 76222 1xv2A 237 8.44e+01 2fe7A 166 8.45e+01 2axjA 242 8.47e+01 1vzyA 291 8.50e+01 1q5qA 259 8.51e+01 d.153.1.4 95904 1l8bA 190 8.53e+01 d.86.1.1 73683 1hpcA 131 8.53e+01 1htp b.84.1.1 28221 1w66A 232 8.54e+01 1oapA 109 8.58e+01 d.79.7.1 92706 2oatA 439 8.61e+01 2dkb c.67.1.4 34452 1vs0A 310 8.61e+01 1wnyA 186 8.62e+01 2arpA 116 8.63e+01 1wy7A 207 8.66e+01 1q9jA 422 8.74e+01 c.43.1.2,c.43.1.2 104590,104591 1g5cA 170 8.74e+01 1g5cA c.53.2.1 60264 2axhA 242 8.74e+01 2anpA 291 8.77e+01 1ylxA 103 8.82e+01 2akrA 285 8.82e+01 1ou8A 111 8.89e+01 b.136.1.1 93543 1x82A 190 8.92e+01 1qreA 247 8.96e+01 1qreA b.81.1.5 28066