# List of top-scoring protein chains for t2k-100-30-str 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 1asu 162 6.68e-12 1cxqA c.55.3.2 33626 1vsd 152 1.07e-11 1cxqA c.55.3.2 33625 1cxqA 162 1.71e-11 1cxqA c.55.3.2 33621 2itg 163 1.92e-08 1b9dA c.55.3.2 33669 1b9dA 163 5.88e-07 1b9dA c.55.3.2 33649 1hyvA 166 6.11e-07 1b9dA c.55.3.2 61424 1bl3A 160 8.23e-07 1b9dA c.55.3.2 33655 1exqA 154 9.00e-07 1b9dA c.55.3.2 33646 1itg 166 4.79e-06 1b9dA c.55.3.2 33661 1fivA 113 9.86e-03 1fmb b.50.1.1 26764 1hvc 203 1.04e-02 1hvc b.50.1.1 26614 4fiv 113 1.21e-02 1fmb b.50.1.1 26762 1difA 99 1.53e-02 1fmb b.50.1.1 26503 2fivA 116 1.56e-02 1fmb b.50.1.1 26766 1kzkA 99 1.96e-02 b.50.1.1 73371 1dazC 99 2.48e-02 1hvc b.50.1.1 26501 5hvpA 99 2.76e-02 1fmb b.50.1.1 26605 1dlc 584 2.83e-02 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1k1tA 99 3.22e-02 b.50.1.1 71995 1mfs 55 4.15e-02 1mfs g.40.1.1 45167 1bveA 99 6.91e-02 1hvc b.50.1.1 26713 1f6uA 55 7.30e-02 1a1tA g.40.1.1 45164 1a1tA 55 8.03e-02 1a1tA g.40.1.1 45165 1idaA 99 9.66e-02 1fmb b.50.1.1 26715 1aaf 55 1.06e-01 1aaf g.40.1.1 45166 1aoqA 567 1.45e-01 1qksA a.3.1.2 15934 b.70.2.1 27692 1qksA 567 1.72e-01 1qksA a.3.1.2 15951 b.70.2.1 27710 1nc8 29 2.19e-01 g.40.1.1 45170 1floA 422 5.95e-01 1floA a.60.9.1 18106 d.163.1.1 42166 1dsqA 21 8.71e-01 g.40.1.1 45173 1ciy 590 1.05e+00 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1fmb 104 1.13e+00 1fmb b.50.1.1 26777 1ds6B 180 1.19e+00 1rhoA b.1.18.8 21898 1eybA 471 1.26e+00 1ey2A b.82.1.4 28115 1a6bB 40 1.35e+00 1a6bB g.40.1.1 45172 1qmyA 167 1.67e+00 1qmyA d.3.1.2 37094 1lj5A 379 1.71e+00 e.1.1.1 73928 1a7cA 379 1.80e+00 1sek e.1.1.1 42660 1gnlA 544 2.03e+00 e.26.1.1 70287 1djxB 624 2.16e+00 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1qasA 622 2.44e+00 1djxB a.39.1.7 17340 b.7.1.1 23157 c.1.18.1 29585 1ki1B 352 2.64e+00 a.87.1.1 72497 b.55.1.1 72498 1kriA 186 2.78e+00 b.29.1.14 72897 1ey2A 471 3.10e+00 1ey2A b.82.1.4 28116 1rhoA 145 3.19e+00 1rhoA b.1.18.8 21899 1vnc 609 3.26e+00 1vns a.111.1.3 19065 1dvpA 220 3.48e+00 1dvpA a.118.9.2 19216 g.50.1.1 45358 1jj22 92 3.71e+00 1ffkZ 1rhoC 145 3.79e+00 1rhoA b.1.18.8 21901 1dc1A 323 4.03e+00 1dc1A c.52.1.11 33321 1djxA 624 4.19e+00 1djxB a.39.1.7 17342 b.7.1.1 23159 c.1.18.1 29587 1lxkA 721 4.21e+00 a.102.3.2 74331 b.24.1.1 74332 b.30.5.2 74333 2rspB 124 4.27e+00 2rspB b.50.1.1 26772 1ffkZ 92 4.31e+00 1ffkZ g.41.8.3 45317 2rspA 124 4.34e+00 2rspB b.50.1.1 26771 1vns 609 4.39e+00 1vns a.111.1.3 19061 1eguA 731 4.53e+00 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.5.2 24423 1bg1A 722 4.63e+00 1bg1A a.47.1.1 17767 b.2.5.5 22461 d.93.1.1 40527 1jmxA 494 4.73e+00 a.3.1.7 66901 a.3.1.7 66902 b.1.18.14 66903 b.1.18.14 66904 b.61.4.1 66905 1kwkA 645 4.97e+00 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1mvpA 124 5.01e+00 2rspB b.50.1.1 26775 1aomA 567 5.46e+00 1qksA b.70.2.1 27694 1kwgA 645 5.98e+00 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1iqqA 200 6.04e+00 d.124.1.1 66274 1mml 265 6.83e+00 1mml e.8.1.2 43015 1cqxA 403 6.84e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1js8A 394 7.08e+00 a.86.1.1 67219 b.112.1.1 67220 1aocA 175 7.39e+00 1aocA g.17.1.5 44817 1zin 217 7.44e+00 1zin c.37.1.1 31915 g.41.2.1 45178 1qoyA 318 7.62e+00 1qoyA h.4.4.1 45788 1ajw 145 8.07e+00 1rhoA b.1.18.8 21905 1hm2A 700 8.36e+00 1cb8A a.102.3.2 61083 b.24.1.1 61084 b.30.5.2 61085 1h1hA 134 8.38e+00 d.5.1.1 76468 1e2uA 553 8.50e+00 1e1dA e.26.1.1 43362 1gntA 553 8.55e+00 e.26.1.1 70290 1kqrA 179 9.41e+00 b.29.1.14 72886 1ayx 492 9.95e+00 1ayx a.102.1.1 18825 1smpI 101 9.97e+00 1smpI b.61.2.1 27417 1e1dA 553 1.04e+01 1e1dA e.26.1.1 43363 1jmoA 480 1.08e+01 e.1.1.1 77138 1ca1 370 1.09e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1fsoA 139 1.09e+01 1rhoA b.1.18.8 60007 1qmtA 134 1.15e+01 7rsa d.5.1.1 37290 1qatB 622 1.19e+01 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 1scfA 273 1.24e+01 1exzA a.26.1.2 16873 1miuA 738 1.24e+01 a.170.1.1 79153 a.171.1.1 79154 b.40.4.3 79155 b.40.4.3 79156 b.40.4.3 79157 1mhyD 521 1.38e+01 1mhyD a.25.1.2 16780 1i1iP 681 1.45e+01 1i1iP d.92.1.5 40297 1mat 264 1.47e+01 1c24A d.127.1.1 41152 3psg 370 1.67e+01 1smrA b.50.1.2 26841 1ieaA 192 1.69e+01 1iakA b.1.1.2 21631 d.19.1.1 38205 1jjuA 489 1.74e+01 a.3.1.7 66774 a.3.1.7 66775 b.1.18.14 66776 b.1.18.14 66777 b.61.4.1 66778 1ekgA 127 1.76e+01 1dlxA d.82.2.1 40021 1k28A 584 1.81e+01 b.40.8.1 68049 b.108.1.2 68050 d.2.1.3 68051 1csn 298 1.83e+01 1csn d.144.1.1 41664 1j7xA 302 1.86e+01 c.14.1.2 66425 1ksfX 758 1.88e+01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1ehkA 562 1.93e+01 1ehkA f.24.1.1 43624 2matA 264 1.95e+01 1c24A d.127.1.1 41146 1isaA 192 1.96e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1iscA 192 1.97e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1qqhA 144 2.05e+01 1dtoA b.91.1.1 28404 2cb5A 453 2.05e+01 3gcb d.3.1.1 37035 1e3oC 160 2.06e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1exzA 141 2.07e+01 1exzA a.26.1.2 16877 1qsaA 618 2.11e+01 1qsaA a.118.5.1 19182 d.2.1.6 36988 1miqA 375 2.16e+01 b.50.1.2 79151 1cb8A 678 2.16e+01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 3pghA 587 2.20e+01 1cqeA a.93.1.2 18726 g.3.11.1 44269 2ak3A 226 2.21e+01 1zin c.37.1.1 31892 g.41.2.1 45193 1m2oA 768 2.23e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1uteA 313 2.24e+01 1uteA d.159.1.1 42078 1o0xA 262 2.25e+01 d.127.1.1 80755 1c24A 263 2.27e+01 1c24A d.127.1.1 41148 1hg2A 289 2.40e+01 1hg5A a.118.10.1 61024 1mhyG 169 2.42e+01 1mtyG a.23.3.1 16518 1qsmA 152 2.44e+01 1qsmA d.108.1.1 40808 9gafA 295 2.59e+01 1apyA d.153.1.5 42008 1ldjA 760 2.61e+01 a.4.5.34 73847 a.118.17.1 73848 e.40.1.1 73849 1k3iA 656 2.63e+01 b.1.18.2 68113 b.18.1.1 68114 b.69.1.1 68115 1io1A 398 2.64e+01 1io1A e.32.1.1 62611 1kblA 873 2.68e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1qlpA 394 2.68e+01 1ovaA e.1.1.1 42628 1ez0A 510 2.70e+01 1eyyA c.82.1.1 35385 1dytA 133 2.73e+01 7rsa d.5.1.1 37288 1jnyA 435 2.76e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1gvmA 136 2.87e+01 b.109.1.1 70612 1deuA 277 2.90e+01 1theB d.3.1.1 37085 1hz4A 373 2.97e+01 a.118.8.2 65960 1l5zA 155 3.01e+01 c.23.1.1 77722 1etpA 190 3.02e+01 1etpA a.3.1.4 15962 a.3.1.4 15963 1fha 183 3.02e+01 2fha a.25.1.1 16675 1hf8A 289 3.05e+01 1hg5A a.118.10.1 19219 1ppo 216 3.13e+01 1cs8A d.3.1.1 37020 1hg5A 289 3.13e+01 1hg5A a.118.10.1 19221 1go3E 187 3.14e+01 b.40.4.5 65406 1dtoA 221 3.14e+01 1dtoA b.91.1.1 28405 1ef1A 294 3.14e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1e2tA 284 3.17e+01 1e2tA d.3.1.5 37121 4matA 278 3.19e+01 1c24A d.127.1.1 41150 1lxtA 561 3.22e+01 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 2fha 183 3.26e+01 2fha a.25.1.1 16674 1hzgA 295 3.31e+01 1hzgA d.194.1.1 61436 1b78A 193 3.32e+01 1b78A c.51.4.1 33221 1qhdA 398 3.32e+01 1qhdA a.115.1.2 63324 b.19.1.1 63325 1pyp 285 3.32e+01 1wgjA b.40.5.1 25409 1ifa 158 3.35e+01 1ifa a.26.1.3 16892 1eyyA 510 3.38e+01 1eyyA c.82.1.1 35389 1rlr 761 3.41e+01 1rlr a.98.1.1 18753 c.7.1.2 30679 1hqcA 324 3.42e+01 1hqcA a.4.5.11 16127 c.37.1.20 32424 2bc2A 227 3.48e+01 1a7tA d.157.1.1 42031 1qkkA 155 3.48e+01 1dbwA c.23.1.1 31104 1pot 325 3.52e+01 1pot c.94.1.1 35807 1sly 618 3.54e+01 1qsaA a.118.5.1 19184 d.2.1.6 36990 5nseA 444 3.55e+01 d.174.1.1 74644 1k8wA 327 3.56e+01 d.58.35.2 68317 d.58.35.2 68318 1f2eA 201 3.57e+01 1a0fA a.45.1.1 17745 c.47.1.5 33039 1i5pA 633 3.58e+01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1hq0A 295 3.60e+01 1hzgA d.194.1.1 61122 3gcb 470 3.64e+01 3gcb d.3.1.1 37032 1d1vA 444 3.67e+01 1nseA d.174.1.1 59101 1g4uS 383 3.72e+01 1g4uS a.24.11.1 16643 c.45.1.2 32691 1aew 174 3.83e+01 2fha a.25.1.1 16676 1iapA 211 3.84e+01 a.91.1.1 62119 1nseA 444 3.85e+01 1nseA d.174.1.1 42534 1l3kA 196 3.89e+01 d.58.7.1 73539 d.58.7.1 73540 1gcb 454 3.93e+01 3gcb d.3.1.1 37034 2mjpA 193 3.94e+01 1b78A c.51.4.1 33223 1gcyA 527 3.94e+01 1jdc b.71.1.1 27788 c.1.8.1 28775