# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1z54A 132 3.30e-16 1njkA 156 7.30e-16 d.38.1.1 85818 1s5uA 138 7.96e-16 d.38.1.1 98573 2cyeA 133 1.84e-15 2av9A 147 2.28e-13 2aliA 158 7.23e-13 2gf6A 135 1.58e-11 1bvqA 141 8.85e-10 1bvqA d.38.1.1 38542 1lo7A 141 1.03e-09 d.38.1.1 74144 2essA 248 9.68e-09 2h4uA 145 2.72e-08 1yliA 153 8.34e-07 1wluA 136 1.02e-06 1j1yA 136 3.39e-06 d.38.1.5 90776 1vpmA 169 3.96e-06 2fs2A 151 8.72e-06 1psuA 140 2.86e-05 d.38.1.5 88285 2gvhA 288 6.31e-05 1ixlA 131 1.99e-04 d.38.1.5 90717 1zkiA 133 2.21e-04 2b3nA 159 2.36e-04 1q4uA 151 9.16e-04 d.38.1.5 95828 1t82A 155 1.24e-03 d.38.1.5 106639 1u1zA 168 9.98e-03 d.38.1.6 107602 2cwzA 141 1.01e-02 1o0iA 138 2.07e-02 d.38.1.5 86532 2b6eA 146 2.64e-02 1vh5A 148 6.99e-02 d.38.1.5 100642 1c8uA 285 9.33e-02 1c8uA d.38.1.3,d.38.1.3 38547,38548 1z6bA 154 1.11e-01 1iq6A 134 5.63e-01 d.38.1.4 76755 1yq2A 1024 5.73e-01 1b8aA 438 7.29e-01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1fib 269 9.82e-01 3fib d.171.1.1 42456 1jeoA 180 1.12e+00 c.80.1.3 66611 2f71A 298 1.25e+00 1yocA 147 1.27e+00 3fib 249 1.48e+00 3fib d.171.1.1 42455 2fibA 269 1.50e+00 3fib d.171.1.1 42457 1sh8A 154 1.63e+00 d.38.1.5 105549 1a5y 330 1.63e+00 1pty c.45.1.2 32673 1pty 321 1.98e+00 1pty c.45.1.2 32656 1txqA 93 2.17e+00 1ylxA 103 2.26e+00 1go4A 205 2.56e+00 d.135.1.1 70292 1aax 321 2.66e+00 1pty c.45.1.2 32657 1aohB 147 2.69e+00 1aohA b.2.2.2 22402 1ptvA 321 2.71e+00 1pty c.45.1.2 32665 1eeoA 321 3.30e+00 1pty c.45.1.2 32655 1pa1A 310 3.79e+00 c.45.1.2 94404 1g7fA 298 3.96e+00 1pty c.45.1.2 60330 1t3tA 1303 4.05e+00 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1n4xH 120 4.52e+00 b.1.1.1 85324 1aqjA 421 5.29e+00 2admA c.66.1.27 34242 1xc3A 302 5.95e+00 1klqA 197 7.44e+00 d.135.1.1 68689 1w9hA 427 7.79e+00 1ztuA 341 7.82e+00 1jv4A 162 8.12e+00 b.60.1.1 67343 1v2dA 381 8.13e+00 c.67.1.1 108281 1zndA 174 8.14e+00 1i05A 180 8.41e+00 1mup b.60.1.1 27130 1i06A 180 8.43e+00 1mup b.60.1.1 27131 1mup 166 8.45e+00 1mup b.60.1.1 27133 1oglA 283 8.46e+00 a.204.1.1 92922 1a8i 842 8.71e+00 1a8i c.87.1.4 35490 1gpb 842 8.74e+00 1a8i c.87.1.4 35478 1qy1A 174 8.74e+00 b.60.1.1 96568 1ig8A 486 8.81e+00 2yhx c.55.1.3,c.55.1.3 64746,64747 1g38A 393 9.00e+00 2admA c.66.1.27 60235 1h5uA 842 9.19e+00 1a8i c.87.1.4 60655 1a3yA 149 9.51e+00 1obpA b.60.1.1 27110 1lfo 128 9.83e+00 1hmt b.60.1.2 27223 1c8kA 842 1.01e+01 1a8i c.87.1.4 35491 1dzkA 157 1.04e+01 1obpA b.60.1.1 27096 1yqgA 263 1.04e+01 1hbp 183 1.07e+01 1aqb b.60.1.1 27079 1b5pA 385 1.08e+01 c.67.1.1 90403 1aohA 147 1.12e+01 1aohA b.2.2.2 22401 2admA 421 1.12e+01 2admA c.66.1.27 34238 1quqA 129 1.12e+01 1quqA b.40.4.3 25303 1bjwA 382 1.18e+01 1bjwA c.67.1.1 34349 1kt6A 183 1.19e+01 b.60.1.1 84466 1hn0A 1021 1.24e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 2hnp 321 1.25e+01 1pty c.45.1.2 32678 1hbq 183 1.30e+01 1aqb b.60.1.1 27078 1adqL 213 1.31e+01 8fabA b.1.1.1,b.1.1.2 20272,21272 1zwyA 185 1.32e+01 1fqtA 112 1.43e+01 1fqtA b.33.1.1 24441 1tc5A 194 1.43e+01 c.110.1.1 106752 1l0wA 580 1.56e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1ga3A 113 1.56e+01 1ga3A a.26.1.2 60411 1xnpA 202 1.58e+01 1widA 130 1.62e+01 1a14L 104 1.66e+01 8fabA b.1.1.1 20060 1fx3B 169 1.67e+01 1fx3B d.33.1.1 38525 1abbA 828 1.70e+01 1a8i c.87.1.4 35536 1wxcB 134 1.71e+01 1mqoA 227 1.76e+01 d.157.1.1 103846 1mxtA 504 1.78e+01 c.3.1.2,d.16.1.1 79671,79672 1n1pA 504 1.78e+01 c.3.1.2,d.16.1.1 91546,91547 1n4wA 504 1.78e+01 c.3.1.2,d.16.1.1 91676,91677 1wleA 501 1.80e+01 1ijhA 504 1.81e+01 c.3.1.2,d.16.1.1 66161,66162 1rbp 182 1.82e+01 1aqb b.60.1.1 27085 1oaqH 121 1.83e+01 b.1.1.1 92707 2cwaA 263 1.86e+01 1rcqA 357 1.87e+01 b.49.2.2,c.1.6.1 104882,104883 1pkp 150 1.88e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1edhA 226 1.89e+01 1edhA b.1.6.1,b.1.6.1 22198,22199 1c3oB 382 1.89e+01 1c3oB c.8.3.1,c.23.16.1 30744,31421 2b69A 343 1.90e+01 1df3A 162 1.90e+01 1mup b.60.1.1 27134 1iicA 422 1.91e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1ih7A 903 2.01e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1a0p 290 2.02e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 2fhfA 1083 2.02e+01 2bi0A 337 2.03e+01 1clqA 903 2.08e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1c30B 382 2.10e+01 c.8.3.1,c.23.16.1 30736,31413 1hkfA 122 2.12e+01 b.1.1.1 83553 1ltm 320 2.13e+01 1ltm d.2.1.6 36992 1qusA 322 2.13e+01 1ltm d.2.1.6 36991 1s98A 107 2.14e+01 b.124.1.1 105377 1tyjA 170 2.14e+01 1crzA 403 2.14e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1hr0W 71 2.20e+01 1ah9 b.40.4.5 25329 1i3uA 127 2.21e+01 1gc1H b.1.1.1 61636 1cs0B 382 2.24e+01 1c3oB c.8.3.1,c.23.16.1 30740,31417 1c0pA 363 2.25e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1spiA 358 2.29e+01 1frpA e.7.1.1 42939 1pcfA 66 2.31e+01 1pcfA d.18.1.1 38142 1jud 232 2.35e+01 1qq5A c.108.1.1 43325 1p0zA 131 2.35e+01 d.110.6.1 93882 1zrn 232 2.36e+01 1qq5A c.108.1.1 43323 1a6wH 120 2.38e+01 1mfa b.1.1.1 20253 2db9A 149 2.42e+01 1forL 210 2.47e+01 8fabA b.1.1.1,b.1.1.2 19988,21044 1zupA 315 2.49e+01 2bm3A 166 2.51e+01 1c5cH 215 2.53e+01 1igtB b.1.1.1,b.1.1.2 20475,21439 1pn2A 280 2.54e+01 d.38.1.4,d.38.1.4 94930,94931 2b59A 187 2.57e+01 3pvaA 335 2.58e+01 3pvaA d.153.1.3 41854 1iq3A 110 2.59e+01 1iq3A a.39.1.6 62640 1gzcA 239 2.61e+01 b.29.1.1 70803 1vprA 374 2.65e+01 1ap2B 123 2.69e+01 1mfa b.1.1.1 20183 1nszA 347 2.78e+01 b.30.5.4 80724 1l7jB 347 2.79e+01 b.30.5.4 73661 1l7jA 347 2.79e+01 b.30.5.4 73660 1e1xA 299 2.80e+01 1hcl d.144.1.7 59157 1ax0 239 2.92e+01 1led b.29.1.1 24042 3kar 346 2.92e+01 1bg2 c.37.1.9 32198 1lkkA 105 2.93e+01 1lckA d.93.1.1 40412 1p6pA 125 2.97e+01 b.60.1.2 87839 1jl2A 156 3.01e+01 c.55.3.1 66822 2f4lA 297 3.01e+01 1m3sA 186 3.04e+01 c.80.1.3 78573 1u2hA 99 3.05e+01 1wxxA 382 3.07e+01 1b7yA 350 3.11e+01 1pysA d.104.1.1 40776 1t5rA 284 3.17e+01 f.6.1.1 106465 1zowA 313 3.21e+01 1ab0 131 3.23e+01 1hmt b.60.1.2 27190 1zc6A 305 3.26e+01 1iw2A 182 3.28e+01 b.60.1.1 71468 1i12A 160 3.32e+01 1i21A d.108.1.1 61515 1k4nA 192 3.34e+01 d.32.1.5 72059 2fxqA 264 3.42e+01 1lf7A 182 3.46e+01 b.60.1.1 73878 1wznA 252 3.47e+01 1a9xB 379 3.48e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1s5jA 847 3.49e+01 1c5kA 439 3.56e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 1n67A 359 3.65e+01 b.2.3.4,b.2.3.4 85354,85355 1d5bB 221 3.73e+01 8fabA b.1.1.1,b.1.1.2 20205,21221 1inp 400 3.74e+01 1inp e.7.1.1 42972 1o4yA 288 3.75e+01 b.29.1.2 92473 1bu8A 452 3.76e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 1otvA 259 3.96e+01 a.132.1.4 93526 1kv9A 668 3.96e+01 a.3.1.6,b.70.1.1 73056,73057 1anu 138 4.02e+01 1aohA b.2.2.2 22403 1gz8A 299 4.03e+01 d.144.1.7 83405 1bbzE 58 4.06e+01 1bbzA b.34.2.1 24479 1mkaA 171 4.16e+01 1mkaA d.38.1.2 38543 1w2fA 276 4.23e+01 d.143.1.3 109125 1b8sA 504 4.26e+01 1b8sA c.3.1.2,d.16.1.1 30335,37866 1j1iA 296 4.26e+01 c.69.1.10 83977 1b4vA 504 4.26e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 2booA 247 4.27e+01 1em9A 154 4.27e+01 1d1dA a.73.1.1 18333 1ne8A 117 4.29e+01 b.34.6.2 80424 1lid 131 4.29e+01 1hmt b.60.1.2 27184 2ae5B 528 4.34e+01 2aq6A 147 4.37e+01 1r94A 118 4.43e+01 b.124.1.1 97251 1m93C 41 4.44e+01 1aqb 183 4.49e+01 1aqb b.60.1.1 27084 1w68A 390 4.50e+01 a.25.1.2 109216 1oe9A 795 4.57e+01 b.34.3.1,c.37.1.9 92792,92793 1yx1A 264 4.58e+01 1w2iA 91 4.59e+01 d.58.10.1 109127 1b63A 333 4.65e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1w66A 232 4.65e+01 1bbzA 58 4.67e+01 1bbzA b.34.2.1 24477 1wubA 178 4.74e+01 1mvuB 121 4.77e+01 b.1.1.1 91475 1o0pA 104 4.77e+01 d.58.7.1 86535 1aboA 62 4.79e+01 1bbzA b.34.2.1 24474 2kinA 238 4.80e+01 1bg2 c.37.1.9 32190 1aihA 170 4.88e+01 1aihA d.163.1.1 42149 1mmuA 347 4.91e+01 b.30.5.4 79303 3crxA 343 4.94e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1uocA 289 4.97e+01 c.55.3.9 99686 1ouoA 210 4.97e+01 d.4.1.6 93554 2pvaA 345 4.99e+01 3pvaA d.153.1.3 41850 1mg2B 131 5.03e+01 g.21.1.1 79060 1gk1B 522 5.05e+01 1h0oA 390 5.08e+01 a.25.1.2 70845 1bihA 395 5.14e+01 1bihA b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21752,21753,21754,21755 2ahrA 259 5.18e+01 1zbfA 142 5.20e+01 1xsm 390 5.21e+01 1xsm a.25.1.2 16804 1vcaA 202 5.23e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1jvpP 298 5.24e+01 d.144.1.7 67371 1fm2B 520 5.31e+01 1fm2B 2eifA 136 5.32e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1i21A 159 5.42e+01 1i21A d.108.1.1 61549 1a6vH 120 5.50e+01 1mfa b.1.1.1 20257 1jj2S 119 5.51e+01 1ffkQ b.34.5.1 63104 1s72T 120 5.52e+01 b.34.5.1 105339 2gh1A 301 5.53e+01 1xtnA 120 5.57e+01 2fuvA 549 5.58e+01 2fsjA 346 5.60e+01 1b5sA 242 5.63e+01 1eaf c.43.1.1 32626 1f5mA 180 5.65e+01 1f5mB d.110.2.1 40895 2fpeA 62 5.74e+01 1adl 131 5.76e+01 1hmt b.60.1.2 27186 1v7rA 186 5.87e+01 c.51.4.1 100482 2as0A 396 5.87e+01 1f5mB 180 5.89e+01 1f5mB d.110.2.1 40896 1xqaA 113 5.93e+01 1jroB 777 5.94e+01 d.41.1.1,d.133.1.1 67141,67142 1vqoT 120 5.99e+01 12e8H 221 5.99e+01 1igtB b.1.1.1,b.1.1.2 20269,21269 1ospL 214 5.99e+01 32c2A b.1.1.1,b.1.1.2 20116,21146 1lcjA 109 6.00e+01 1qadA d.93.1.1 40414 2a0iA 330 6.03e+01 1yrrA 382 6.03e+01 2gxfA 142 6.05e+01 2amdA 311 6.09e+01 1koqA 253 6.23e+01 2cba b.74.1.1 27964 1nmtA 392 6.32e+01 1nmtA d.108.1.2,d.108.1.2 40823,40824 1erjA 393 6.33e+01 1erjA b.69.4.1 27660 1pysA 350 6.33e+01 1pysA d.104.1.1 40775 1qftA 175 6.37e+01 1qftA b.60.1.1 27151 1zo2A 129 6.43e+01 2d1eA 248 6.44e+01 1dcuA 357 6.49e+01 1frpA e.7.1.1 42943 1ymmE 249 6.50e+01 1b0wA 108 6.59e+01 8fabA b.1.1.1 20532 1gppA 237 6.64e+01 b.86.1.2 76262 1nstA 325 6.66e+01 1nstA c.37.1.5 31951 1e1oA 504 6.71e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1se8A 301 6.73e+01 b.40.4.3 105448 1c0aA 585 6.78e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1b76A 442 7.00e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 1zmyA 142 7.01e+01 1mu5A 471 7.02e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1lylA 504 7.11e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1nb5I 98 7.15e+01 d.17.1.2 80381 1tf4A 605 7.16e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1kcmA 270 7.23e+01 d.129.3.4 72300 1ncwH 222 7.28e+01 b.1.1.1,b.1.1.2 85555,85556 2bbkH 355 7.33e+01 2bbkH b.69.2.1 27634 2i1b 153 7.36e+01 2i1b b.42.1.2 25538 1x3sA 195 7.41e+01 1i1b 153 7.42e+01 2i1b b.42.1.2 25537 1g7sA 594 7.43e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 2ezvA 269 7.49e+01 1yts 278 7.52e+01 1ytw c.45.1.2 32690 1k32A 1045 7.52e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1o9yA 84 7.52e+01 b.139.1.1 92692 1vj0A 380 7.55e+01 b.35.1.2,c.2.1.1 100786,100787 1j05B 121 7.58e+01 b.1.1.1 90736 1xteA 154 7.59e+01 1upiA 225 7.60e+01 b.82.1.1 99757 1uisA 231 7.60e+01 d.22.1.1 99431 1eal 127 7.63e+01 1hmt b.60.1.2 27227 1fnlA 175 7.64e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 2bx2L 517 7.64e+01 1upsA 420 7.69e+01 2bsfA 176 7.71e+01 4cms 323 7.72e+01 1smrA b.50.1.2 26866 1j6uA 469 7.78e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 2cqeA 98 7.88e+01 1ljoA 77 7.94e+01 b.38.1.1 73941 2bc4B 211 7.95e+01 1noa 113 7.98e+01 2mcm b.1.7.1 22208 1n0xH 230 7.98e+01 b.1.1.1,b.1.1.2 91528,91529 1qqjA 419 8.01e+01 1qcnA b.34.8.1,d.177.1.1 59034,59035 2awiA 317 8.02e+01 3cms 323 8.07e+01 1smrA b.50.1.2 26865 1c1lA 136 8.09e+01 1c1lA b.29.1.3 24219 1nfiA 301 8.24e+01 1a3qA b.1.18.1,b.2.5.3 21942,22455 1iy8A 267 8.28e+01 c.2.1.2 83774 1s1dA 331 8.28e+01 b.67.3.1 98344 4pep 326 8.32e+01 1smrA b.50.1.2 26843 2a38A 194 8.41e+01 1bazA 53 8.45e+01 1bazA a.43.1.1 17421 2gujA 155 8.45e+01 1fl1A 230 8.52e+01 1at3A b.57.1.1 27023 1is3A 135 8.55e+01 b.29.1.3 76773 1ulrA 88 8.58e+01 1smxA 96 8.59e+01 b.40.4.5 105772 1nfiC 301 8.60e+01 b.1.18.1,b.2.5.3 21943,22456 1jf0A 195 8.62e+01 1ej3A a.39.1.5 62926 1mylA 53 8.66e+01 1bazA a.43.1.1 17427 1hyoA 421 8.67e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1w6nA 134 8.69e+01 1fvzA 271 8.71e+01 1fvzA 1f21A 155 8.72e+01 2rn2 c.55.3.1 33550 1zy1B 197 8.74e+01 1qcoA 423 8.74e+01 1qcnA b.34.8.1,d.177.1.1 59021,59022 1nqbA 256 8.75e+01 1mfa b.1.1.1,b.1.1.1 20042,20043 1b66A 140 8.81e+01 1b66A d.96.1.2 40657 1r2mA 71 8.81e+01 b.138.1.1 96871 2b97A 71 8.81e+01 3pchM 238 8.83e+01 3pchM b.3.6.1 22748 1ldnA 316 8.85e+01 1hyhA c.2.1.5,d.162.1.1 30166,42133 1gotB 340 8.86e+01 1tbgA b.69.4.1 27648 1us8A 147 8.89e+01 c.37.1.12 99859 1hmr 132 8.90e+01 1hmt b.60.1.2 27170 2b0vA 153 8.98e+01