# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1t62A 166 1.55e-06 1fjgQ 105 7.07e-02 1fjfQ b.40.4.5 25352 1j54A 186 9.48e-02 c.55.3.5 77077 1dm9A 133 1.42e-01 1dm9A d.66.1.3 39560 1vif 62 1.53e-01 1vie b.34.4.1 24593 1vie 62 1.67e-01 1vie b.34.4.1 24592 1k3sA 113 1.87e-01 d.198.1.1 68120 1cfyA 143 2.98e-01 1cof d.109.1.2 40858 1cof 143 3.02e-01 1cof d.109.1.2 40860 1mrzA 293 4.01e-01 b.43.5.1 -4048 c.26.1.3 -6616 1h9oA 112 4.19e-01 1qadA d.93.1.1 60837 1r6xA 395 4.94e-01 b.122.1.3 -5125 c.26.1.5 -6620 1ckaA 57 4.96e-01 1ckaA b.34.2.1 24459 1qadA 111 6.31e-01 1qadA d.93.1.1 40498 1griA 217 6.67e-01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 1n27A 96 7.05e-01 b.34.9.2 -3585 1khiA 176 7.43e-01 b.34.5.2 77408 b.40.4.5 77409 1zfpE 98 7.55e-01 1griA d.93.1.1 40465 1shg 62 7.61e-01 1ckaA b.34.2.1 24493 1qcsA 211 8.79e-01 1qcsA b.52.2.3 26927 d.31.1.1 38461 1semA 58 9.04e-01 1ckaA b.34.2.1 24544 1pwt 61 1.04e+00 1tud b.34.2.1 24490 1rpyA 114 1.12e+00 d.93.1.1 -10636 1rl6A 177 1.17e+00 1rl6A d.141.1.1 41473 d.141.1.1 41474 1tuc 63 1.20e+00 1tuc b.34.2.1 24492 1pyaB 228 1.28e+00 1pyaB 1azeA 56 1.33e+00 b.34.2.1 24536 1ov3A 138 1.41e+00 b.34.2.1 87451 b.34.2.1 87452 1gmuA 143 1.56e+00 b.107.1.1 65335 d.58.38.1 65336 1g2bA 62 1.62e+00 1tud b.34.2.1 24488 1tud 62 1.91e+00 1tud b.34.2.1 24489 1gmwA 143 2.15e+00 b.107.1.1 65347 d.58.38.1 65348 1esgA 213 2.28e+00 1bam c.52.1.3 33286 1aiw 62 2.40e+00 1aiw b.72.2.1 27808 1iujA 106 2.43e+00 unknown_sccs -9953 1g8fA 511 2.49e+00 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 1e9rA 437 2.51e+00 c.37.1.11 64827 1bco 327 2.60e+00 1bco b.48.1.1 26431 c.55.3.3 33676 1jyrA 96 2.67e+00 d.93.1.1 71969 1lckA 175 2.85e+00 1lckA b.34.2.1 24552 d.93.1.1 40421 1earA 147 2.91e+00 b.107.1.1 64875 d.58.38.1 64876 1dvoA 152 3.17e+00 1dvoA a.136.1.1 19623 1b3jA 274 3.27e+00 1agdA b.1.1.2 20855 d.19.1.1 38319 821p 166 3.33e+00 1ctqA c.37.1.8 31969 3bamB 213 3.36e+00 1bam c.52.1.3 33289 1g3gA 164 3.43e+00 1g6gA b.26.1.2 23918 1qwzA 235 3.47e+00 b.100.1.1 -4543 1oz7A 131 3.66e+00 d.169.1.1 -11622 1rie 129 3.75e+00 1rie b.33.1.1 24427 1exmA 405 3.83e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1bmbA 123 3.90e+00 1griA d.93.1.1 40466 1l6oA 95 3.99e+00 b.36.1.1 84534 1o54A 277 4.12e+00 c.66.1.13 -8095 1kyqA 274 4.12e+00 c.2.1.11 73281 e.37.1.1 73282 1fh6A 282 4.38e+00 1fh6A 1eb0A 147 4.52e+00 b.107.1.1 64890 d.58.38.1 64891 1r0pA 312 4.76e+00 d.144.1.7 -11377 1je6A 275 4.93e+00 b.1.1.2 71638 d.19.1.1 71639 1ha3A 405 5.04e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1r3eA 309 5.08e+00 b.122.1.1 -5118 unknown_sccs -10146 1ibvB 229 5.08e+00 1v38A 78 5.51e+00 a.60.1.2 -1016 1n0lA 224 5.71e+00 b.1.11.1 79744 b.7.2.1 79745 1nrvA 105 5.97e+00 d.93.1.1 86126 1hywA 68 6.03e+00 1hywA d.186.1.1 61425 1o26A 232 6.04e+00 d.207.1.1 86566 1ng5A 215 6.06e+00 b.100.1.1 -4541 1f2fA 104 6.08e+00 1fmk d.93.1.1 40455 1f3fA 155 6.38e+00 1npk d.58.6.1 39101 1npk 154 6.41e+00 1npk d.58.6.1 39099 1pueE 89 6.43e+00 1awcA a.4.5.21 16165 1bfi 112 6.43e+00 1qadA d.93.1.1 40499 1g5cA 170 6.51e+00 1g5cA c.53.2.1 60264 1quqB 121 6.53e+00 1quqB b.40.4.3 25305 1shdA 107 6.54e+00 1fmk d.93.1.1 40440 1ctqA 166 6.74e+00 1ctqA c.37.1.8 31965 1b0jA 754 7.09e+00 1amj c.8.2.1 30719 c.83.1.1 35395 1olzA 663 7.13e+00 b.1.1.4 -2678 unknown_sccs -4626 unknown_sccs -12590 1m7bA 184 7.15e+00 c.37.1.8 74572 1pt1A 143 7.28e+00 b.52.2.1 -4322 1f7zA 233 7.28e+00 5ptp b.47.1.2 59681 1quqA 129 7.39e+00 1quqA b.40.4.3 25303 1amj 754 7.46e+00 1amj c.8.2.1 30725 c.83.1.1 35401 2eifA 136 7.49e+00 1bkb b.34.5.2 24607 b.40.4.5 25339 1dpo 223 7.54e+00 5ptp b.47.1.2 25975 1jo8A 58 7.62e+00 b.34.2.1 71774 1g9mC 185 7.62e+00 1cdy b.1.1.1 19721 b.1.1.3 21660 1aw8B 91 7.81e+00 1aw8B 1ndk 155 7.88e+00 1npk d.58.6.1 39118 1vjhA 122 7.91e+00 d.129.3.1 -11037 1kq4A 232 7.91e+00 d.207.1.1 68791 1gmmA 133 8.30e+00 b.18.1.10 65314 8acn 754 8.53e+00 1amj c.8.2.1 30724 c.83.1.1 35400 1j34A 129 8.66e+00 d.169.1.1 84048 1xnaA 183 8.66e+00 1xnaA b.18.1.8 23773 1gcqA 61 8.75e+00 1ckaA b.34.2.1 60434 1ijaA 148 9.18e+00 1ijaA b.100.1.1 62484 1aohA 147 9.32e+00 1aohA b.2.2.2 22401 1kebA 108 9.43e+00 c.47.1.1 77341 1i0cA 60 9.55e+00 1aojA b.34.2.1 61485 1etc 110 9.63e+00 1awcA a.4.5.21 16162 1jwiA 131 9.75e+00 d.169.1.1 67383 1aipE 405 9.77e+00 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1bbzA 58 9.78e+00 1bbzA b.34.2.1 24477 1ark 60 1.00e+01 1bb9 b.34.2.1 24473 1dfuP 94 1.00e+01 1dfuP b.53.1.1 26936 1aboA 62 1.01e+01 1bbzA b.34.2.1 24474 1qgbA 93 1.02e+01 1qgbA g.27.1.1 44952 g.27.1.1 44953 1oivA 191 1.03e+01 c.37.1.8 -7074 3cd4 182 1.03e+01 1cdy b.1.1.1 19720 b.1.1.3 21659 1fvuB 125 1.04e+01 1ixxB d.169.1.1 42346 1o4rA 108 1.06e+01 d.93.1.1 -10624 7acn 754 1.08e+01 1amj c.8.2.1 30717 c.83.1.1 35393 1db3A 372 1.09e+01 1db3A c.2.1.2 29813 1o5uA 101 1.10e+01 b.82.1.8 -4845 1rsy 152 1.10e+01 1rsy b.7.1.2 23192 1bbzE 58 1.14e+01 1bbzA b.34.2.1 24479 1cr5A 189 1.15e+01 1cr5A b.52.2.3 26931 d.31.1.1 38465 1ocrD 147 1.18e+01 1ocrD f.23.1.1 43541 1qhsA 178 1.19e+01 1qhsA c.37.1.3 31938 1uv0A 149 1.21e+01 d.169.1.1 -11610 1bam 213 1.21e+01 1bam c.52.1.3 33285 5p21 166 1.23e+01 1ctqA c.37.1.8 31966 1iz5A 249 1.23e+01 d.131.1.2 83834 d.131.1.2 83835 1ayyA 151 1.24e+01 1apyA d.153.1.5 42016 2occD 147 1.24e+01 1ocrD f.23.1.1 43521 1n3yA 198 1.27e+01 c.62.1.1 79976 1irqA 71 1.28e+01 unknown_sccs 66297 1aihA 170 1.28e+01 1aihA d.163.1.1 42149 1o22A 170 1.29e+01 d.238.1.1 86557 1uj0A 62 1.30e+01 b.34.2.1 -3570 1i58A 189 1.34e+01 1b3qA d.122.1.3 61773 1khcA 147 1.34e+01 b.34.9.2 68608 1iz6A 138 1.37e+01 b.34.5.2 76976 b.40.4.5 76977 1h6kA 757 1.37e+01 unknown_sccs 60675 unknown_sccs 60676 unknown_sccs 60677 1k0rA 366 1.38e+01 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1c96A 753 1.40e+01 1amj c.8.2.1 30727 c.83.1.1 35403 1g6gA 127 1.42e+01 1g6gA b.26.1.2 23916 1k3eA 156 1.44e+01 d.198.1.1 68103 1pqhA 143 1.44e+01 b.52.2.1 -4318 1v54D 147 1.46e+01 f.23.1.1 -12100 1cdy 178 1.47e+01 1cdy b.1.1.1 19719 b.1.1.3 21658 1uxxX 133 1.48e+01 b.18.1.10 -3107 1utiA 58 1.51e+01 b.34.2.1 -3552 3bamA 213 1.55e+01 1bam c.52.1.3 33288 1ju5A 109 1.56e+01 d.93.1.1 77173 1g4wR 383 1.61e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1efcA 393 1.61e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1hj9A 226 1.62e+01 b.47.1.2 65845 1eaxA 241 1.62e+01 b.47.1.2 64889 1fmtB 314 1.63e+01 1fmtA b.46.1.1 25759 c.65.1.1 34175 1b6fA 159 1.66e+01 1bv1 d.129.3.1 41316 1g5gB 481 1.70e+01 f.12.1.1 65157 h.3.2.1 65158 5ptp 223 1.71e+01 5ptp b.47.1.2 25831 1b3qA 379 1.72e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1cawB 184 1.72e+01 1caxB b.82.1.2 28113 1k7kA 221 1.75e+01 c.51.4.1 72104 6acn 754 1.78e+01 1amj c.8.2.1 30721 c.83.1.1 35397 1qppA 218 1.78e+01 1qpxA b.1.11.1 22320 b.7.2.1 23202 1ootA 60 1.80e+01 b.34.2.1 -3576 1ixlA 131 1.80e+01 d.38.1.5 -9705 1bh5A 183 1.81e+01 1qipA d.32.1.1 38476 1qhxA 178 1.81e+01 1qhsA c.37.1.3 31936 1aohB 147 1.83e+01 1aohA b.2.2.2 22402 1urrA 102 1.85e+01 1lcjA 109 1.85e+01 1qadA d.93.1.1 40414 1rz2A 254 1.87e+01 1azsB 212 1.87e+01 1azsA d.58.29.1 39423 1bynA 128 1.88e+01 1rsy b.7.1.2 23193 1m4zA 238 1.88e+01 b.34.12.1 78630 1bsvA 321 1.90e+01 1bsvA c.2.1.2 29809 1kqqA 139 1.91e+01 a.4.3.1 72885 1qpxA 218 1.91e+01 1qpxA b.1.11.1 22318 b.7.2.1 23200 1shbA 104 1.96e+01 1fmk d.93.1.1 40425 1lkkA 105 2.00e+01 1lckA d.93.1.1 40412 1mdc 133 2.03e+01 1hmt b.60.1.2 27198 1bowA 159 2.07e+01 1bowA d.60.1.1 39528 1kao 167 2.07e+01 1ctqA c.37.1.8 32014 1jt8A 102 2.10e+01 b.40.4.5 63279 1whi 122 2.15e+01 1whi b.39.1.1 24810 1ab8A 220 2.22e+01 1azsA d.58.29.1 39414 1e79H 146 2.22e+01 1e79H a.2.10.1 15721 b.93.1.1 28438 1giqA 413 2.22e+01 d.166.1.1 76224 d.166.1.1 76225 1shaA 104 2.23e+01 1fmk d.93.1.1 40424 1at0 145 2.23e+01 1at0 b.86.1.1 28374 1d2eA 397 2.27e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1k32A 1045 2.30e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 2gcc 70 2.32e+01 2gcc d.10.1.2 37484 1ge8A 249 2.33e+01 1plq d.131.1.2 41398 d.131.1.2 41399 1t2aA 375 2.33e+01 c.2.1.2 -5764 1knqA 175 2.37e+01 c.37.1.17 72786 1gfsA 321 2.37e+01 c.2.1.2 29811 1shfA 59 2.37e+01 1bbzA b.34.2.1 24462 1kyfA 247 2.38e+01 b.1.10.1 73220 d.105.1.1 73221 1fu1A 203 2.38e+01 1fu1B b.59.1.1 27076 h.1.11.1 45630 1ebmA 317 2.40e+01 1ebmA a.96.1.3 18751 d.129.1.2 41300 1lwyA 324 2.41e+01 a.96.1.3 78285 d.129.1.2 78286 1gg4A 452 2.42e+01 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 1bv1 159 2.44e+01 1bv1 d.129.3.1 41313 1ayaA 101 2.46e+01 1qadA d.93.1.1 40460 1qavA 90 2.49e+01 1qauA b.36.1.1 24777 1fmtA 314 2.49e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1mhnA 59 2.50e+01 b.34.9.1 84964 1jmtA 104 2.54e+01 d.58.7.3 63180 1i7kA 179 2.56e+01 1u9aA d.20.1.1 61889 1of5B 184 2.58e+01 d.17.4.2 86934 1az3A 244 2.60e+01 1rvaA c.52.1.2 33276 1qzzA 374 2.60e+01 a.4.5.29 -277 c.66.1.12 -8045 1ey4A 149 2.60e+01 1snc b.40.1.1 24815 7catA 506 2.67e+01 1cf9A e.5.1.1 42781 1d5yA 292 2.68e+01 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1omzA 293 2.68e+01 c.68.1.15 87093 1nb9A 147 2.69e+01 b.43.5.1 85515 1mctA 223 2.73e+01 5ptp b.47.1.2 25961 1gfc 59 2.85e+01 1griA b.34.2.1 24537 1caxB 184 2.85e+01 1caxB b.82.1.2 28105 1ohgA 282 2.87e+01 d.183.1.1 -11727 1r13A 148 2.88e+01 d.169.1.1 -11646 h.1.1.1 -12895 1ko6A 187 2.89e+01 b.119.1.1 77471 6prcH 258 2.94e+01 6prcH b.41.1.1 25457 f.23.10.1 43436 1kmdA 117 3.00e+01 d.189.1.1 72744 1aim 215 3.01e+01 1cs8A d.3.1.1 37044 1c20A 128 3.01e+01 1c20A a.4.3.1 16079 1mjnA 179 3.03e+01 c.62.1.1 79210 1ow1A 195 3.03e+01 unknown_sccs -4422 2shpA 525 3.04e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1cknA 330 3.05e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1or0B 528 3.05e+01 1ixxA 129 3.05e+01 1ixxB d.169.1.1 42335 1btu 240 3.06e+01 5ptp b.47.1.2 26241 1cdi 179 3.08e+01 1cdy b.1.1.1 19727 b.1.1.3 21666 1gvkB 240 3.09e+01 b.47.1.2 70610 1n6eA 1071 3.11e+01 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1fniA 223 3.12e+01 5ptp b.47.1.2 25962 1f5mB 180 3.15e+01 1f5mB d.110.2.1 40896 1jegA 83 3.18e+01 b.34.2.1 66610 1oebA 62 3.21e+01 b.34.2.1 86909 1nu0A 138 3.23e+01 unknown_sccs -7658 1hyp 80 3.27e+01 1hyp a.52.1.1 17806 1aw8E 91 3.29e+01 1aw8B 2dhqA 146 3.29e+01 2dhqA c.23.13.1 31382 1qkfA 92 3.31e+01 1qkfA d.28.1.1 38456 1a81A 254 3.33e+01 1a81A d.93.1.1 40507 d.93.1.1 40508 2pna 104 3.35e+01 1qadA d.93.1.1 40501 1i18A 97 3.41e+01 b.43.4.3 61520 1od3A 168 3.41e+01 b.18.1.10 86825 1dxrH 258 3.43e+01 6prcH b.41.1.1 25456 f.23.10.1 43433 1s8fA 177 3.44e+01 1gcpA 70 3.44e+01 1gcpA b.34.2.1 60430 2pldA 105 3.44e+01 1qadA d.93.1.1 40521 1iyeA 309 3.46e+01 e.17.1.1 83786 1rypH 205 3.46e+01 d.153.1.4 41876 1ng2A 193 3.47e+01 b.34.2.1 85660 b.34.2.1 85661 2u1a 88 3.47e+01 2u1a d.58.7.1 39164 1vg8A 207 3.52e+01 3ullA 132 3.57e+01 3ullA b.40.4.3 25282 1ig8A 486 3.58e+01 2yhx c.55.1.3 64746 c.55.1.3 64747 1l4sA 112 3.61e+01 d.204.1.1 77693 1qnjA 240 3.65e+01 5ptp b.47.1.2 26238 1e0tA 470 3.67e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1fu1B 203 3.67e+01 1fu1B b.59.1.1 27077 h.1.11.1 45631 1kmqA 184 3.72e+01 c.37.1.8 84412 1uy4A 145 3.72e+01 1qtsA 247 3.74e+01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1qc5A 192 3.74e+01 1aoxA c.62.1.1 34147 1du3A 130 3.75e+01 1d4vA g.24.1.1 44927 g.24.1.1 44928 g.24.1.1 44929 1bwzA 274 3.79e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1e79A 510 3.81e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1hnnA 282 3.82e+01 c.66.1.15 65895 1n08A 163 3.82e+01 b.43.5.1 79730 1uisA 231 3.83e+01 d.22.1.1 -9450 1ge9A 184 3.86e+01 1dd5A d.67.3.1 60463 1mdwA 328 3.87e+01 d.3.1.3 84934 1eza 259 3.88e+01 1zymA a.60.10.1 18113 c.8.1.2 30708 1pjpA 226 3.90e+01 5ptp b.47.1.2 26301 1qwlA 505 3.90e+01 e.5.1.1 -11823 1ksr 100 3.91e+01 1qfhA b.1.18.10 21897 1lfaA 187 3.92e+01 1ido c.62.1.1 34122 1csp 67 3.96e+01 1mjc b.40.4.5 25321 1d6bA 42 3.99e+01 1b8wA g.9.1.1 44594