# List of top-scoring protein chains for t04-100-30-str2 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 1onxA 390 2.20e-01 b.92.1.7 87176 c.1.9.13 87177 1erjA 393 2.43e-01 1erjA b.69.4.1 27660 2cpl 165 4.45e-01 2cpl b.62.1.1 27420 1onwA 390 4.96e-01 b.92.1.7 87172 c.1.9.13 87173 1s72Q 96 5.28e-01 1jj2P 95 6.26e-01 1ffkN b.34.5.1 63101 1awqA 164 6.35e-01 2cpl b.62.1.1 27461 1dypA 271 7.21e-01 1dypA b.29.1.2 24185 1awsA 164 8.81e-01 2cpl b.62.1.1 27431 1k6wA 426 1.10e+00 b.92.1.2 68236 c.1.9.5 68237 2trxA 108 1.21e+00 1thx c.47.1.1 32719 1lrzA 426 1.43e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1h2rL 534 1.48e+00 1h2rL e.18.1.1 43298 1mgqA 83 1.52e+00 b.38.1.1 79099 1ubkL 534 1.56e+00 e.18.1.1 88422 1pcfA 66 1.56e+00 1pcfA d.18.1.1 38142 1q7zA 566 1.66e+00 c.1.21.2 -5638 c.1.26.1 -5666 1o8bA 219 1.82e+00 unknown_sccs 81180 d.58.40.1 81181 1bqyA 234 1.89e+00 5ptp b.47.1.2 26332 1j6pA 418 1.96e+00 b.92.1.4 77089 c.1.9.9 77090 1deuA 277 2.14e+00 1theB d.3.1.1 37085 1p1mA 406 2.19e+00 b.92.1.4 87696 c.1.9.9 87697 1r6jA 82 2.21e+00 b.36.1.1 -3732 1ivg 388 2.25e+00 2qwc b.68.1.1 27578 1a65A 504 2.35e+00 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1r7lA 110 2.44e+00 1e19A 314 2.50e+00 1b7bA c.73.1.1 34967 1mkaA 171 2.52e+00 1mkaA d.38.1.2 38543 1theA 260 2.59e+00 1theB d.3.1.1 37056 1nteA 82 2.67e+00 b.36.1.1 86163 1ush 550 3.05e+00 1ush d.114.1.1 40923 d.159.1.2 42079 1ljoA 77 3.14e+00 b.38.1.1 73941 1m4tA 392 3.23e+00 c.95.1.1 78617 c.95.1.1 78618 1ton 235 3.29e+00 5ptp b.47.1.2 26307 1e3dB 542 3.32e+00 1h2rL e.18.1.1 59189 1qflA 389 3.47e+00 1afwA c.95.1.1 35908 c.95.1.1 35909 1h9oA 112 3.66e+00 1qadA d.93.1.1 60837 1gmyA 261 3.99e+00 d.3.1.1 76236 4uagA 437 4.20e+00 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1m3kA 392 4.42e+00 c.95.1.1 78565 c.95.1.1 78566 1hp1A 516 4.62e+00 d.114.1.1 70976 d.159.1.2 70977 1ihgA 370 4.75e+00 2cpl a.118.8.1 62380 b.62.1.1 62381 1hfuA 503 4.88e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1q3eA 207 4.89e+00 b.82.3.2 -4922 1g3qA 237 5.01e+00 1hyqA c.37.1.10 60237 1qmvA 197 5.15e+00 1qq2A c.47.1.10 33066 1pysA 350 5.27e+00 1pysA d.104.1.1 40775 1memA 215 5.39e+00 1cs8A d.3.1.1 37069 1nscA 390 5.56e+00 2qwc b.68.1.1 27591 1nnhA 294 5.83e+00 d.104.1.1 -10772 1ca1 370 6.01e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1rxxA 421 6.81e+00 unknown_sccs -10982 1v5sA 126 7.58e+00 1gbg 214 8.15e+00 1axkA b.29.1.2 24171 1p49A 562 8.19e+00 c.76.1.2 -8432 1kcxA 518 8.34e+00 b.92.1.3 -5074 c.1.9.6 -5426 1eu1A 780 8.39e+00 1dmr b.52.2.2 26903 c.81.1.1 35311 1j1nA 492 8.64e+00 c.94.1.1 83978 1rk8A 165 8.94e+00 d.58.7.1 -10018 1l1zA 274 8.96e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1e8pA 46 9.17e+00 g.55.1.1 59385 1gttA 429 9.27e+00 d.177.1.1 70529 d.177.1.1 70530 1li4A 432 9.31e+00 c.2.1.4 84616 c.23.12.3 84617 1b7yA 350 9.60e+00 1pysA d.104.1.1 40776 1fxjA 331 9.63e+00 1fwyA b.81.1.4 28062 c.68.1.5 34520 1sdwA 314 1.02e+01 b.121.1.2 -3024 b.121.1.2 -3025 1pvdA 537 1.02e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1s83A 223 1.03e+01 b.47.1.2 -4178 1ri6A 343 1.04e+01 unknown_sccs -4621 1p3dA 475 1.04e+01 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1bmv2 374 1.04e+01 1bmv2 1pbjA 125 1.05e+01 d.37.1.1 -9608 d.37.1.1 -9609 1pzxA 289 1.07e+01 c.119.1.1 -8623 1nm1G 125 1.09e+01 d.109.1.1 80653 1uj6A 227 1.09e+01 1trkA 680 1.09e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1i7oA 429 1.11e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1m2rA 327 1.12e+01 d.144.1.7 84760 1r9lA 309 1.14e+01 c.94.1.1 -8700 1g4wR 383 1.14e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1phm 310 1.15e+01 1phm b.121.1.2 59015 b.121.1.2 59016 1umgA 362 1.15e+01 2tpsA 227 1.18e+01 2tpsA c.1.3.1 28591 1ckmA 330 1.19e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1v58A 241 1.20e+01 1mp9A 198 1.20e+01 a.74.1.2 -1127 a.74.1.2 -1128 1a0jA 223 1.20e+01 5ptp b.47.1.2 26002 1a6o 332 1.24e+01 1a6o 1th8A 145 1.24e+01 1fr2B 134 1.26e+01 d.4.1.1 83257 1gpuA 680 1.28e+01 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1f7zA 233 1.30e+01 5ptp b.47.1.2 59681 1h7mA 102 1.32e+01 d.79.3.1 83485 1d7yA 408 1.39e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1h4wA 224 1.45e+01 b.47.1.2 65622 1fb6A 105 1.46e+01 1thx c.47.1.1 32739 1hd2A 161 1.46e+01 c.47.1.10 60962 1kay 381 1.49e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1d4xG 126 1.50e+01 1d0nA d.109.1.1 59109 1qyrA 252 1.53e+01 1dl5A 317 1.54e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1pxgA 382 1.54e+01 c.1.20.1 -5616 1fvgA 199 1.55e+01 1fvaA d.58.28.1 39408 1emvB 134 1.58e+01 1bxiB d.4.1.1 37135 1auvA 311 1.59e+01 1auvA c.30.1.5 31723 d.142.1.3 41558 1lcl 142 1.61e+01 1lcl b.29.1.3 24216 1op0A 234 1.62e+01 1e4fT 419 1.65e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1hj8A 222 1.65e+01 b.47.1.2 65844 1vgyA 393 1.67e+01 c.56.5.4 -7882 d.58.19.1 -10106 1dv1A 449 1.67e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1bio 228 1.69e+01 5ptp b.47.1.2 26314 1fc6A 388 1.71e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1rhfA 182 1.74e+01 b.1.1.1 -2335 b.1.1.4 -2684 1nw2A 105 1.74e+01 c.47.1.1 -7380 1sy6A 204 1.76e+01 1pgl2 370 1.77e+01 1geqA 248 1.78e+01 2tysA c.1.2.4 28589 1bupA 386 1.82e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1a9xB 379 1.82e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 2tbs 222 1.87e+01 5ptp b.47.1.2 26009 1gvzA 237 1.89e+01 b.47.1.2 76360 1j1yA 136 1.89e+01 d.38.1.5 -9671 1mctA 223 1.93e+01 5ptp b.47.1.2 25961 1bia 321 1.98e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1hdkA 141 1.98e+01 b.29.1.3 65807 2cro 71 2.04e+01 1r69 a.35.1.2 17038 1sr9A 644 2.07e+01 1ekfA 365 2.10e+01 1ekfA e.17.1.1 59445 1sjwA 144 2.13e+01 unknown_sccs -9296 1lw1A 177 2.14e+01 a.152.1.1 74290 1gw0A 559 2.15e+01 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 1pu5A 164 2.15e+01 1qniA 581 2.16e+01 1qniA b.6.1.4 23042 b.69.3.1 27642 1sefA 274 2.18e+01 1f97A 212 2.21e+01 1f97A b.1.1.1 19763 b.1.1.4 21764 1ejxC 567 2.21e+01 b.92.1.1 83184 c.1.9.2 83185 1r26A 125 2.22e+01 c.47.1.1 -7389 1jcfA 344 2.22e+01 c.55.1.1 62878 c.55.1.1 62879 1un3A 123 2.22e+01 d.5.1.1 -8933 1g13A 162 2.23e+01 1g13A b.95.1.1 60194 1hv9A 456 2.24e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1ktaA 365 2.26e+01 e.17.1.1 77533 1f60B 94 2.32e+01 1b64 d.58.12.1 39307 1rg9A 383 2.34e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1g24A 211 2.38e+01 1g24A d.166.1.1 42270 1o4tA 133 2.39e+01 b.82.1.9 86622 1mup 166 2.39e+01 1mup b.60.1.1 27133 1wkqA 164 2.40e+01 1uqxA 113 2.43e+01 b.115.1.1 -3230 1g1cA 99 2.50e+01 b.1.1.4 65078 1d4fA 431 2.56e+01 1b3rA c.2.1.4 30110 c.23.12.3 31370 1cx4A 305 2.57e+01 b.82.3.2 59099 b.82.3.2 59100 1g9oA 91 2.60e+01 1pdr b.36.1.1 60400 1tf4A 605 2.60e+01 1tf4A a.102.1.2 18827 b.2.2.2 22393 2sli 679 2.62e+01 2sli b.29.1.9 24274 b.68.1.1 27611 1i6aA 219 2.64e+01 c.94.1.1 61827 2ayh 214 2.69e+01 1axkA b.29.1.2 24172 1gpiA 431 2.73e+01 b.29.1.10 65450 4ptp 223 2.73e+01 2fcbA 173 2.74e+01 2fcbA b.1.1.4 21781 b.1.1.4 21782 1r2zA 274 2.77e+01 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1jv4A 162 2.80e+01 b.60.1.1 67343 1kzfA 230 2.83e+01 d.108.1.3 73354 1euwA 152 2.86e+01 1dupA b.85.4.1 28349 1s14A 194 2.87e+01 d.122.1.2 -10973 1o50A 157 2.87e+01 d.37.1.1 -9604 d.37.1.1 -9605 1orc 71 2.93e+01 1orc a.35.1.2 17054 1o5uA 101 2.94e+01 b.82.1.8 -4845 1p5fA 189 2.97e+01 c.23.16.2 -6508 1ltsA 185 3.01e+01 1lt3A d.166.1.1 42229 1fvrA 327 3.02e+01 d.144.1.7 60047 1i4fB 100 3.04e+01 1agdB b.1.1.2 61689 1nd4A 264 3.04e+01 d.144.1.6 -11381 1i05A 180 3.04e+01 1mup b.60.1.1 27130 1huxA 270 3.13e+01 1huxA c.55.1.5 61278 1nh1A 330 3.17e+01 unknown_sccs -11798 1om1A 332 3.23e+01 d.144.1.7 -11318 1hskA 326 3.24e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1pv9A 348 3.24e+01 c.55.2.1 -7610 d.127.1.1 -11000 1v04A 355 3.25e+01 unknown_sccs -4592 1h8uA 117 3.25e+01 1h8uA d.169.1.1 60793 1lkkA 105 3.26e+01 1lckA d.93.1.1 40412 1k92A 455 3.27e+01 c.26.2.1 68325 d.210.1.1 68326 1f9vA 347 3.31e+01 1bg2 c.37.1.9 59745 1c8zA 265 3.33e+01 1c8zA d.23.1.1 38375 1a78A 134 3.33e+01 1c1lA b.29.1.3 24212 1ubi 76 3.35e+01 1ubi d.15.1.1 37584 1l7mA 211 3.38e+01 c.108.1.4 73664 1dekA 241 3.38e+01 1dekA c.37.1.1 31842 1i19A 561 3.47e+01 1i19A d.58.32.3 61522 d.145.1.1 61523 1fct 32 3.53e+01 1fct j.36.1.1 46283 1aiu 105 3.56e+01 1erv c.47.1.1 32746 1psdA 409 3.61e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1aua 296 3.62e+01 1aua a.5.3.1 16290 c.13.1.1 30882 1ogwA 76 3.62e+01 d.15.1.1 87001 1fehA 574 3.65e+01 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1s5aA 150 3.65e+01 unknown_sccs -9300 1suuA 312 3.77e+01 unknown_sccs -4610 1bgp 309 3.77e+01 1bgp a.93.1.1 18690 1lt3A 240 3.80e+01 1lt3A d.166.1.1 42230 1bvoA 175 3.91e+01 1a3qA b.2.5.3 22457 1oa8A 133 3.92e+01 unknown_sccs -5142 1l8aA 886 3.95e+01 c.36.1.6 73678 c.36.1.10 73677 c.48.1.1 73679 1mb4A 370 3.96e+01 c.2.1.3 78908 d.81.1.1 78909 1nvmA 345 3.99e+01 a.5.7.1 86249 c.1.10.5 86250