# List of top-scoring protein chains for t2k-w0.5 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 1ydd 259 9.89e-01 2cba b.74.1.1 27911 1yda 259 9.90e-01 2cba b.74.1.1 27908 1hea 260 9.91e-01 2cba b.74.1.1 27891 1heb 260 9.92e-01 2cba b.74.1.1 27892 1hed 260 1.01e+00 2cba b.74.1.1 27898 1hec 260 1.01e+00 2cba b.74.1.1 27884 1cim 257 1.05e+00 2cba b.74.1.1 27948 1mua 256 1.15e+00 2cba b.74.1.1 27831 1ydb 259 1.16e+00 2cba b.74.1.1 27870 1cva 259 1.16e+00 2cba b.74.1.1 27925 1lg5A 260 1.18e+00 1gmeA 151 1.21e+00 b.15.1.1 65305 12ca 260 1.24e+00 2cba b.74.1.1 27942 1uge 258 1.24e+00 2cba b.74.1.1 27865 1uga 258 1.24e+00 2cba b.74.1.1 27862 1ugd 258 1.24e+00 2cba b.74.1.1 27872 1ugc 258 1.25e+00 2cba b.74.1.1 27871 1cak 260 1.25e+00 2cba b.74.1.1 27863 1cvd 255 1.25e+00 2cba b.74.1.1 27918 1ugf 258 1.25e+00 2cba b.74.1.1 27885 1cai 260 1.25e+00 2cba b.74.1.1 27830 1caj 260 1.25e+00 2cba b.74.1.1 27841 1cvh 255 1.25e+00 2cba b.74.1.1 27936 1cvc 259 1.25e+00 2cba b.74.1.1 27927 1fqrA 260 1.25e+00 2cba b.74.1.1 27916 2h4n 259 1.25e+00 2cba b.74.1.1 27867 1cnk 259 1.25e+00 2cba b.74.1.1 27899 1g0eA 260 1.25e+00 2cba b.74.1.1 27825 1ugb 258 1.25e+00 2cba b.74.1.1 27876 1cni 259 1.25e+00 2cba b.74.1.1 27839 1g52A 259 1.25e+00 2cba b.74.1.1 27832 1cng 259 1.25e+00 2cba b.74.1.1 27869 1cnj 259 1.25e+00 2cba b.74.1.1 27850 1can 260 1.25e+00 2cba b.74.1.1 27846 2cba 260 1.25e+00 2cba b.74.1.1 27821 1eouA 260 1.25e+00 b.74.1.1 64904 1zsb 259 1.25e+00 2cba b.74.1.1 27868 1cnh 259 1.25e+00 2cba b.74.1.1 27880 1cvf 259 1.26e+00 2cba b.74.1.1 27917 1h9q 259 1.26e+00 2cba b.74.1.1 27923 1cnc 259 1.26e+00 2cba b.74.1.1 27919 1cve 259 1.26e+00 2cba b.74.1.1 27915 1hva 260 1.26e+00 2cba b.74.1.1 27934 1h9n 259 1.26e+00 2cba b.74.1.1 27840 1fqlA 260 1.26e+00 2cba b.74.1.1 27893 1fr7A 260 1.27e+00 2cba b.74.1.1 27828 1cct 259 1.27e+00 2cba b.74.1.1 27910 5ca2 260 1.28e+00 2cba b.74.1.1 27895 1dcb 260 1.32e+00 2cba b.74.1.1 27909 1ccu 259 1.32e+00 2cba b.74.1.1 27929 1bic 260 1.34e+00 2cba b.74.1.1 27854 1cam 260 1.37e+00 2cba b.74.1.1 27826 1ccs 259 1.39e+00 2cba b.74.1.1 27935 2rhe 114 1.48e+00 8fabA b.1.1.1 20523 1qeyA 31 2.44e+00 1qeyA h.2.1.1 45666 1tdj 514 3.24e+00 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1k3bB 164 4.85e+00 1a0cA 438 4.90e+00 1a0cA c.1.15.3 29529 1e0cA 271 5.25e+00 1e0cA c.46.1.2 32717 c.46.1.2 32718 1h4kX 271 5.25e+00 1b35C 282 5.26e+00 1b35C b.10.1.3 23335 6ca2 260 5.50e+00 2cba b.74.1.1 27950 1emvB 134 6.00e+00 1bxiB d.4.1.1 37135 1fdd 106 6.09e+00 1a6l d.58.1.2 38960 1bxiB 134 6.14e+00 1bxiB d.4.1.1 37136 1d3wA 106 6.22e+00 1a6l d.58.1.2 38957 1tyv 542 6.40e+00 1tyv b.80.1.6 28038 1frx 106 6.49e+00 1a6l d.58.1.2 38981 1ftcA 106 6.52e+00 1a6l d.58.1.2 38974 1em7A 56 6.82e+00 1d1uA 255 6.88e+00 1mml e.8.1.2 43018 1i6jA 256 6.93e+00 e.8.1.2 61845 1qajA 259 7.06e+00 1mml e.8.1.2 43016 1fd2 106 7.24e+00 1a6l d.58.1.2 38962 1fri 106 7.25e+00 1a6l d.58.1.2 38964 1mml 265 7.26e+00 1mml e.8.1.2 43015 1g3oA 106 7.46e+00 1a6l d.58.1.2 38959 1b0vA 106 7.63e+00 1a6l d.58.1.2 38982 1frm 106 7.69e+00 1a6l d.58.1.2 38973 1f5cA 106 7.70e+00 1a6l d.58.1.2 38958 1gaoA 106 7.71e+00 1a6l d.58.1.2 38977 1frl 106 7.80e+00 1a6l d.58.1.2 38976 1f5bA 106 7.97e+00 1a6l d.58.1.2 38956 1frh 106 8.01e+00 1a6l d.58.1.2 38972 7fd1A 106 8.01e+00 1a6l d.58.1.2 38953 1g6bA 106 8.01e+00 1a6l d.58.1.2 38963 2fb4L 216 8.31e+00 8fabA b.1.1.1 19846 b.1.1.2 20950 9ca2 260 8.36e+00 2cba b.74.1.1 27952 1ff2A 106 8.42e+00 1a6l d.58.1.2 38968 1frj 106 8.45e+00 1a6l d.58.1.2 38969 2fd2 106 8.46e+00 1a6l d.58.1.2 38961 1frk 106 8.56e+00 1a6l d.58.1.2 38967 1a6l 106 9.46e+00 1a6l d.58.1.2 38966 1ak7 174 1.03e+01 1cof d.109.1.2 40864 3sicI 107 1.10e+01 3ssi d.84.1.1 40028 1i9qA 259 1.32e+01 2cba b.74.1.1 62098 1clwA 554 1.38e+01 1tyv b.80.1.6 28043 1qa1A 554 1.39e+01 1tyv b.80.1.6 28047 1qq1A 559 1.39e+01 1tyv b.80.1.6 28041 1tsp 559 1.39e+01 1tyv b.80.1.6 28044 1qa2A 554 1.39e+01 1tyv b.80.1.6 28048 1qrbA 559 1.39e+01 1tyv b.80.1.6 28042 1qa3A 554 1.40e+01 1tyv b.80.1.6 28046 1tyu 543 1.40e+01 1tyv b.80.1.6 28037 1d2kA 392 1.44e+01 1d2kA c.1.8.5 29008 d.26.3.1 38442 8ca2 260 1.49e+01 2cba b.74.1.1 27941 1fjjA 159 1.50e+01 1fjjA b.17.1.2 59852 1qr9A 68 1.56e+01 1qbzA h.3.2.1 45721 1qhkA 47 1.64e+01 1qhkA d.100.1.2 40694 1k33A 68 1.66e+01 h.3.2.1 68092 3ifbA 131 1.66e+01 1hmt b.60.1.2 27182 1hrhA 136 1.72e+01 1rthA c.55.3.1 33577 1k34A 68 1.74e+01 h.3.2.1 68093 1eweA 363 1.82e+01 1fbaA c.1.10.1 29136 1bjmA 216 1.82e+01 8fabA b.1.1.1 20524 b.1.1.2 21460 1qcrD 75 1.82e+01 1qcrD a.3.1.3 15956 f.2.1.8 43674 1rdhA 146 1.87e+01 1rthA c.55.3.1 33588 1szt 68 1.90e+01 1aikN h.3.2.1 45725 1df4A 68 1.90e+01 1aikN h.3.2.1 45719 1dlbA 68 1.92e+01 1qbzA h.3.2.1 45722 1ffkI 194 1.99e+01 1ffkI d.12.1.2 37494 7ca2 260 2.02e+01 2cba b.74.1.1 27949 1flgA 582 2.04e+01 4aahA b.70.1.1 27682 1aqkL 216 2.05e+01 8fabA b.1.1.1 20192 b.1.1.2 21208 1a0dA 440 2.14e+01 1a0cA c.1.15.3 29533 1ewxA 146 2.27e+01 1ewxA c.47.1.10 33062 1qk8A 146 2.27e+01 1ewxA c.47.1.10 33061 1ezkA 153 2.29e+01 1ewxA c.47.1.10 33063 1bwuQ 109 2.39e+01 1b2pA b.78.1.1 27996 1b0tA 106 2.45e+01 1a6l d.58.1.2 38965 1qsoA 149 2.49e+01 1qsmA d.108.1.1 40812 1kj1D 109 2.51e+01 b.78.1.1 68639 1qsmA 152 2.55e+01 1qsmA d.108.1.1 40808 1fd6A 57 2.57e+01 d.15.7.1 59769 2sicI 107 2.66e+01 3ssi d.84.1.1 40031 1kj1A 109 2.69e+01 b.78.1.1 68638 1k0vA 73 2.69e+01 d.58.17.1 67986 1ly1A 181 2.76e+01 3ssi 113 2.84e+01 3ssi d.84.1.1 40032 1dnyA 91 2.88e+01 1dnyA a.28.1.2 16934 1bwuP 106 2.93e+01 1b2pA b.78.1.1 27995 1pfo 500 2.96e+01 1pfo f.9.1.1 43826 1bwuD 109 3.03e+01 1b2pA b.78.1.1 27994 1fiqC 763 3.06e+01 1fiqC d.41.1.1 38588 d.133.1.1 41418 1nplA 109 3.13e+01 1b2pA b.78.1.1 27997 1kl9A 182 3.17e+01 1qr8A 68 3.23e+01 1qbzA h.3.2.1 45724 2at2A 300 3.34e+01 3csuA c.78.1.1 35196 c.78.1.1 35197 1fexA 59 3.36e+01 a.4.1.3 59803 1h77A 605 3.43e+01 2liv 344 3.44e+01 2liv c.93.1.1 35708 1bwuA 106 3.46e+01 1b2pA b.78.1.1 27993 1gff2 177 3.49e+01 2bpa2 1gb4 57 3.59e+01 2igd d.15.7.1 37833 1bg3A 919 3.67e+01 1qhaA c.55.1.3 33491 c.55.1.3 33492 c.55.1.3 33493 c.55.1.3 33494 1bucA 383 3.81e+01 3mdeA a.29.3.1 16590 e.6.1.1 42851 1eliA 389 3.85e+01 1b3mA c.3.1.2 30375 d.16.1.3 37943 6aldA 363 3.88e+01 1fbaA c.1.10.1 29144 1i27A 73 3.88e+01 1i27A a.4.5.30 61555 1ewdA 363 3.89e+01 1fbaA c.1.10.1 29132 1ex5A 363 3.94e+01 1fbaA c.1.10.1 29140 1ewgA 363 3.95e+01 1fbaA c.1.10.1 29128 1j4eA 363 3.96e+01 c.1.10.1 66375