# List of top-scoring protein chains for t2k-100-30-alpha 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 1ngvA 534 8.40e-03 c.111.1.2 85698 1qs8A 329 2.46e-02 1smrA b.50.1.2 26887 1gbg 214 8.57e-02 1axkA b.29.1.2 24171 1mq7A 154 8.58e-02 b.85.4.1 79404 1cpn 208 1.18e-01 1axkA b.29.1.2 24175 1sixA 174 1.31e-01 b.85.4.1 -5030 2ayh 214 1.50e-01 1axkA b.29.1.2 24172 1ee6A 197 2.92e-01 1ee6A b.80.1.1 28024 1bywA 110 2.97e-01 1bywA d.110.3.6 40912 1miqA 375 3.29e-01 b.50.1.2 79151 1vzoA 355 3.36e-01 1czfA 362 3.59e-01 1czfA b.80.1.3 28031 1lf2A 331 3.74e-01 b.50.1.2 77914 1axkA 394 5.06e-01 1axkA b.29.1.2 24181 b.29.1.11 24315 1lmeA 176 5.06e-01 d.167.1.1 84629 1ospO 257 7.53e-01 1ospO b.76.1.1 27971 1hv9A 456 8.70e-01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1k5cA 335 1.01e+00 b.80.1.3 72076 1b12A 248 1.05e+00 1b12A b.87.1.2 28388 1kcxA 518 1.09e+00 b.92.1.3 -5074 c.1.9.6 -5426 1smeA 329 1.11e+00 1smrA b.50.1.2 26885 1aj6 219 1.18e+00 1aj6 d.122.1.2 41106 1gw5M 435 1.20e+00 b.2.7.1 70631 d.110.4.2 70632 1n9pA 207 1.53e+00 b.1.18.16 80343 1ei5A 520 1.56e+00 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1n67A 359 1.56e+00 b.2.3.4 85354 b.2.3.4 85355 1hm9A 468 1.61e+00 b.81.1.4 65866 c.68.1.5 65867 1d3bA 75 1.65e+00 1d3bA b.38.1.1 24798 1kn9A 249 1.65e+00 b.87.1.2 68699 1imvA 398 1.67e+00 e.1.1.1 62591 1hg8A 349 1.69e+00 b.80.1.3 65830 1j2gA 319 1.87e+00 1ep0A 185 1.91e+00 1dzrA b.82.1.1 28080 1nhcA 336 1.94e+00 b.80.1.3 -4768 1ln1A 214 2.06e+00 d.129.3.2 74038 1dun 134 2.07e+00 1dun b.85.4.1 28371 1h6kX 97 2.36e+00 d.58.7.1 60684 1oroA 213 2.38e+00 1opr c.61.1.1 34093 1h2vZ 156 2.58e+00 d.58.7.1 76595 1bhe 376 2.60e+00 1bhe b.80.1.3 28030 1vbd4 69 2.88e+00 1pvc4 1f7dA 136 2.89e+00 1dun b.85.4.1 28353 1r2zA 274 2.90e+00 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1jjuA 489 2.96e+00 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 1s5aA 150 3.35e+00 unknown_sccs -9300 1tahA 318 3.66e+00 1cvl c.69.1.18 34775 2pec 353 3.92e+00 1air b.80.1.1 28019 1oghA 204 3.93e+00 b.85.4.1 86994 1l1zA 274 4.02e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1air 353 4.15e+00 1air b.80.1.1 28018 1dqtA 117 4.19e+00 1ah1 b.1.1.1 20653 1o88A 353 4.22e+00 b.80.1.1 81178 1tahB 318 4.31e+00 1cvl c.69.1.18 34774 1ac5 483 4.34e+00 1ac5 c.69.1.5 34653 1gh7A 419 4.38e+00 b.1.2.1 65194 b.1.2.1 65195 b.1.2.1 65196 b.1.2.1 65197 1i3uA 127 4.43e+00 1gc1H b.1.1.1 61636 1hjp 203 4.53e+00 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1ia8A 289 4.65e+00 1ia8A d.144.1.7 62112 1cuk 203 4.89e+00 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1vcaA 202 5.12e+00 1vcaA b.1.1.3 21649 b.1.1.4 21685 1gm6A 175 5.18e+00 b.60.1.1 70272 1pz4A 116 5.48e+00 d.106.1.1 -10780 1lh0A 213 5.65e+00 c.61.1.1 73896 1dd5A 185 5.81e+00 1dd5A d.67.3.1 39564 1pbyA 489 5.99e+00 a.3.1.7 -178 a.3.1.7 -179 b.1.18.14 -2762 b.1.18.14 -2763 b.61.4.1 -4528 1iqrA 420 6.08e+00 a.99.1.1 66275 c.28.1.1 66276 1bxxA 285 6.59e+00 1bw8A b.2.7.1 22483 1smvA 260 6.60e+00 1smvA b.121.4.7 23288 1kv9A 668 6.62e+00 a.3.1.6 73056 b.70.1.1 73057 1h6kZ 98 6.62e+00 d.58.7.1 60686 1l0sA 90 6.62e+00 b.81.2.1 73408 1bv1 159 7.35e+00 1bv1 d.129.3.1 41313 1e79G 272 7.44e+00 1e79G c.49.2.1 33158 1bw8A 321 7.74e+00 1bw8A b.2.7.1 22482 1e5gA 120 7.77e+00 1e5gA g.18.1.1 44843 g.18.1.1 44844 1fw9A 164 7.91e+00 1fw9A d.190.1.1 60059 1qw9A 502 8.03e+00 b.71.1.2 -4677 c.1.8.3 -5348 1v9mA 323 8.09e+00 unknown_sccs -12292 1qmrA 159 8.41e+00 1bv1 d.129.3.1 41314 1c8pA 102 8.72e+00 1c8pA b.1.2.1 22040 1opr 213 9.20e+00 1opr c.61.1.1 34091 2bc2B 227 9.31e+00 1a7tA d.157.1.1 42032 1jv2B 692 9.47e+00 b.1.15.1 67338 c.62.1.1 67339 d.200.1.1 67340 g.3.11.6 67341 g.3.11.6 67342 1qa7B 217 9.50e+00 1havA b.47.1.4 26426 1mqoA 227 9.52e+00 1c4xA 285 9.60e+00 1c4xA c.69.1.10 34684 2bc2A 227 9.65e+00 1a7tA d.157.1.1 42031 1s0yA 76 1.00e+01 d.80.1.1 -10434 1uhvA 500 1.00e+01 b.71.1.2 -4683 c.1.8.3 -5354 1ic7H 114 1.00e+01 1f3rB b.1.1.1 62258 1nofA 383 1.03e+01 b.71.1.2 -4668 c.1.8.3 -5339 1qhoA 686 1.08e+01 1cxlA b.1.18.2 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1fq0A 213 1.12e+01 1fwrA c.1.10.1 29161 1tia 279 1.15e+01 3tgl c.69.1.17 34737 1szwA 379 1.15e+01 unknown_sccs -10164 1cc1L 498 1.15e+01 1h2rL e.18.1.1 43301 1g97A 459 1.15e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1vhzA 198 1.20e+01 d.113.1.1 -10897 1f8eA 388 1.20e+01 2qwc b.68.1.1 59694 1si7A 369 1.21e+01 unknown_sccs -10163 1iyu 79 1.22e+01 1iyu b.84.1.1 28227 1euaA 213 1.22e+01 1fwrA c.1.10.1 29155 1rmg 422 1.22e+01 1rmg b.80.1.3 28029 1bv8A 138 1.23e+01 1ayoA b.2.4.1 22430 1lqwA 183 1.24e+01 d.167.1.1 74210 1pfzA 380 1.26e+01 1smrA b.50.1.2 26881 1e19A 314 1.27e+01 1b7bA c.73.1.1 34967 1v88A 130 1.27e+01 1sf8A 126 1.29e+01 1gcqA 61 1.30e+01 1ckaA b.34.2.1 60434 1p9qC 256 1.34e+01 1gwmA 153 1.36e+01 b.18.1.19 83348 3nn9 388 1.37e+01 2qwc b.68.1.1 27566 1nziA 159 1.39e+01 b.23.1.1 86449 g.3.11.1 86450 1v6fA 151 1.39e+01 1qcxA 359 1.40e+01 1qcxA b.80.1.2 28028 1pvc4 68 1.44e+01 1pvc4 1hfoA 113 1.44e+01 d.80.1.3 61006 3cbh 365 1.45e+01 1bvwA c.6.1.1 30665 1njhA 119 1.46e+01 b.128.1.1 85787 1fbr 93 1.46e+01 1fbr g.27.1.1 44948 g.27.1.1 44949 1n0xH 230 1.47e+01 b.1.1.1 -2201 b.1.1.2 -2473 1ptmA 329 1.48e+01 unknown_sccs -8456 1fwrA 213 1.49e+01 1fwrA c.1.10.1 29164 1ivg 388 1.53e+01 2qwc b.68.1.1 27578 1i31A 314 1.53e+01 1bw8A b.2.7.1 22481 5er2E 330 1.55e+01 2er7E b.50.1.2 26783 1qw2A 102 1.55e+01 unknown_sccs -9601 1gfc 59 1.56e+01 1griA b.34.2.1 24537 1i5pA 633 1.57e+01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1r5zA 323 1.58e+01 unknown_sccs -12289 1jd0A 263 1.60e+01 2cba b.74.1.1 62888 1ddzA 496 1.61e+01 1ddzA c.53.2.1 33372 c.53.2.1 33373 1pt1A 143 1.63e+01 b.52.2.1 -4322 2madH 373 1.64e+01 2bbkH b.69.2.1 27639 1idk 359 1.64e+01 1qcxA b.80.1.2 28025 1mv8A 436 1.65e+01 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1pkhA 204 1.66e+01 b.85.4.1 -5053 1i0vA 104 1.66e+01 9rnt d.1.1.4 36054 1ivd 388 1.72e+01 2qwc b.68.1.1 27568 1q9uA 130 1.72e+01 unknown_sccs -11025 1sdwA 314 1.74e+01 b.121.1.2 -3024 b.121.1.2 -3025 1lxdA 100 1.75e+01 1lfdA d.15.1.5 37624 1qh0A 295 1.75e+01 b.43.4.2 68891 c.25.1.1 68892 5nn9 388 1.76e+01 2qwc b.68.1.1 27563 9rnt 104 1.78e+01 9rnt d.1.1.4 36055 2dynA 122 1.78e+01 1dynA b.55.1.1 26957 1btkB 169 1.79e+01 1btkA b.55.1.1 26960 1umdA 367 1.79e+01 c.36.1.11 -6969 1n9lA 109 1.80e+01 d.110.3.6 85468 1e42A 258 1.80e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 3rnt 104 1.82e+01 9rnt d.1.1.4 36069 1snzA 344 1.88e+01 b.30.5.4 -3496 1bo1A 416 1.88e+01 1bo1A d.143.1.2 41591 2eifA 136 1.89e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1phm 310 1.91e+01 1phm b.121.1.2 59015 b.121.1.2 59016 1rhi3 236 1.91e+01 1aym3 1an9A 340 1.95e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1b56 135 1.98e+01 1hmt b.60.1.2 27183 1souA 194 1.99e+01 1c25 161 2.00e+01 1c25 c.46.1.1 32698 1p4kA 295 2.01e+01 d.153.1.5 87772 1a16 440 2.02e+01 1az9 c.55.2.1 33548 d.127.1.1 41165 2qwc 388 2.04e+01 2qwc b.68.1.1 27547 1nox 205 2.06e+01 1nox d.90.1.1 40242 1luzA 88 2.12e+01 b.40.4.5 74271 1ogoX 574 2.13e+01 unknown_sccs -3237 unknown_sccs -4783 1b2rA 304 2.14e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1vi7A 217 2.16e+01 unknown_sccs -9115 unknown_sccs -10052 1i1iP 681 2.18e+01 1i1iP d.92.1.5 40297 1qjoA 80 2.23e+01 1iyu b.84.1.1 28229 2er7E 330 2.23e+01 2er7E b.50.1.2 26779 1oewA 329 2.28e+01 b.50.1.2 86924 1ush 550 2.31e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1qhdA 398 2.35e+01 1qhdA a.115.1.2 63324 b.19.1.1 63325 1orvA 728 2.36e+01 b.70.3.1 87354 c.69.1.24 87355 1dkrA 317 2.37e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1epnE 330 2.38e+01 2er7E b.50.1.2 26780 1g99A 408 2.38e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1hkxA 147 2.38e+01 d.17.4.7 83567 1s1dA 331 2.39e+01 unknown_sccs -4566 1lmhA 184 2.40e+01 d.167.1.1 74036 1hmr 132 2.45e+01 1hmt b.60.1.2 27170 1n8fA 350 2.49e+01 c.1.10.4 85397 1j71A 334 2.49e+01 1eagA b.50.1.2 62669 1ry6A 360 2.49e+01 c.37.1.9 -7111 9gafA 295 2.49e+01 1apyA d.153.1.5 42008 1avgI 142 2.50e+01 1avgI b.60.1.3 27229 1je5A 206 2.54e+01 1je5A b.40.4.7 62909 1c9oA 66 2.54e+01 1mjc b.40.4.5 25325 1griA 217 2.55e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 1qbiA 454 2.55e+01 1c9uA b.68.2.1 27619 1hp1A 516 2.57e+01 d.114.1.1 70976 d.159.1.2 70977 1tiu 98 2.58e+01 1tit b.1.1.4 21715 1i7nA 309 2.59e+01 c.30.1.5 83681 d.142.1.3 83682 1eq2A 310 2.63e+01 1eq2A c.2.1.2 29814 1n1mA 728 2.64e+01 b.70.3.1 79815 c.69.1.24 79816 1thfD 253 2.64e+01 1thfD c.1.2.1 28535 1k4mA 213 2.67e+01 c.26.1.3 77258 1thm 279 2.80e+01 1gci c.41.1.1 32544 1jb2A 127 2.81e+01 d.17.4.2 71624 1nwbA 124 2.86e+01 b.124.1.1 86296 1h80A 464 2.86e+01 b.80.1.8 65714 1hmt 132 2.87e+01 1hmt b.60.1.2 27169 1g0xA 197 2.87e+01 1nkr b.1.1.4 21805 b.1.1.4 21806 1ko3A 230 2.89e+01 d.157.1.1 -11454 1zeiA 53 2.92e+01 1zeiA g.1.1.1 43963 1pcl 355 2.94e+01 1pcl b.80.1.1 28021 1qynA 153 2.95e+01 d.33.1.1 -9585 1aa8A 347 2.96e+01 1an9A 1fm4A 159 2.97e+01 1bv1 d.129.3.1 76186 1r17A 343 3.00e+01 b.2.3.4 -2870 b.2.3.4 -2871 1i78A 297 3.01e+01 f.4.4.1 66046 1mrzA 293 3.01e+01 b.43.5.1 -4048 c.26.1.3 -6616 1gvuA 329 3.02e+01 b.50.1.2 70619 1oz9A 150 3.05e+01 unknown_sccs -10588 1dkgD 383 3.08e+01 1ba1 c.55.1.1 33427 c.55.1.1 33428 1eagA 342 3.11e+01 1eagA b.50.1.2 26826 1cvl 319 3.11e+01 1cvl c.69.1.18 34786 1ge8A 249 3.15e+01 1plq d.131.1.2 41398 d.131.1.2 41399 1hms 132 3.16e+01 1hmt b.60.1.2 27168 1mwrA 646 3.18e+01 d.17.4.5 79586 d.175.1.1 79587 e.3.1.1 79588 1kk1A 410 3.19e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1grj 158 3.21e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1dlhB 188 3.21e+01 1iakB b.1.1.2 21598 d.19.1.1 38172 1vh7A 265 3.21e+01 c.1.2.1 -5159 1gx1A 160 3.26e+01 d.79.5.1 70675 1pbjA 125 3.26e+01 d.37.1.1 -9608 d.37.1.1 -9609 1hxmA 229 3.27e+01 1hxmA b.1.1.1 61367 b.1.1.2 61368 1is2A 661 3.31e+01 a.29.3.2 71382 a.29.3.2 71383 e.6.1.2 71384 1ounA 127 3.33e+01 1ounA d.17.4.2 38090 1bxoA 323 3.39e+01 2er7E b.50.1.2 26805 1lm6A 215 3.42e+01 d.167.1.1 84628 1tdj 514 3.44e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1ar0A 127 3.45e+01 1ounA d.17.4.2 38092 1jpeA 151 3.47e+01 b.1.17.1 77146 1f07A 321 3.49e+01 1ezwA c.1.16.3 59560 1cruA 454 3.55e+01 1c9uA b.68.2.1 27617 1h0bA 256 3.56e+01 b.29.1.11 83422 1qe5A 266 3.62e+01 1b8oA c.56.2.1 33784 1hs6A 611 3.67e+01 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1iz6A 138 3.68e+01 b.34.5.2 76976 b.40.4.5 76977 1que 303 3.69e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1s7jA 262 3.76e+01 d.21.1.2 -9424 1jofA 365 3.78e+01 b.69.10.1 71775 1xnaA 183 3.79e+01 1xnaA b.18.1.8 23773 1k6wA 426 3.83e+01 b.92.1.2 68236 c.1.9.5 68237 1go2A 304 3.84e+01 b.43.4.2 76243 c.25.1.1 76244 1ve9A 347 3.84e+01 c.4.1.2 -6056 d.16.1.3 -9214 1c9uA 454 3.86e+01 1c9uA b.68.2.1 27623 1ogiA 303 3.87e+01 b.43.4.2 -4042 c.25.1.1 -6587 1bbpA 173 3.90e+01 1bbpA b.60.1.1 27147 1eal 127 3.90e+01 1hmt b.60.1.2 27227 2nlrA 234 3.94e+01 2nlrA b.29.1.11 24344 1udvA 89 3.96e+01 d.68.6.1 -10280 1vavA 222 3.97e+01 1tfpA 130 3.98e+01 1etb1 b.3.4.1 22623