# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1uag 437 3.69e-33 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 4uagA 437 3.84e-33 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1gg4A 452 3.93e-33 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 3uagA 437 4.99e-33 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 1e8cA 498 7.55e-33 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1jbwA 428 3.05e-22 c.59.1.2 62860 c.72.2.2 62861 1fgs 428 3.42e-21 1fgs c.59.1.2 33959 c.72.2.2 34962 1yer 228 1.91e-03 1yer d.122.1.1 41101 1byqA 228 2.84e-03 1yer d.122.1.1 41100 1j8mF 297 3.74e-03 1ng1 a.24.13.1 62742 c.37.1.10 62743 1fts 295 5.43e-03 1ng1 a.24.13.1 16968 c.37.1.10 32279 1g3qA 237 2.24e-02 1hyqA c.37.1.10 60237 1esmA 316 2.32e-02 1esmA c.37.1.6 31953 1ah6 220 2.99e-02 1yer d.122.1.1 41094 1eg7A 557 4.37e-02 1eg7A c.37.1.10 32241 2reb 352 5.94e-02 2reb c.37.1.11 32282 d.48.1.1 38767 1htwA 158 6.41e-02 1lxtA 561 6.93e-02 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1hyqA 263 7.97e-02 1hyqA c.37.1.10 61412 3pmgA 561 1.08e-01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1aipE 405 1.89e-01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1e3mA 800 1.99e-01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1kk1A 410 2.15e-01 1ha3A 405 2.56e-01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1bhjA 292 2.85e-01 1xvaA c.66.1.5 34189 1exmA 405 2.93e-01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1dj0A 264 2.98e-01 1dj0A d.58.35.1 39497 d.58.35.1 39498 2ng1 293 3.18e-01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1a7j 290 3.53e-01 1a7j c.37.1.6 31952 1d2eA 397 3.77e-01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1dar 691 3.85e-01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1jg1A 235 3.96e-01 c.66.1.7 66661 1jpnA 296 4.41e-01 a.24.13.1 67039 c.37.1.10 67040 1xvaA 292 4.42e-01 1xvaA c.66.1.5 34183 1fvkA 189 4.56e-01 1fvkA a.44.1.1 17490 c.47.1.4 32784 1g5rA 196 4.57e-01 1g5rA c.37.1.11 32367 1g5tA 196 4.57e-01 1g5rA c.37.1.11 32366 1dsbA 189 4.72e-01 1fvkA a.44.1.1 17497 c.47.1.4 32791 1a8l 226 6.32e-01 1a8l c.47.1.2 32777 c.47.1.2 32778 1efcA 393 7.25e-01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1bix 287 7.53e-01 1bix d.151.1.1 41781 1eluA 390 8.27e-01 1elqA c.67.1.3 34434 1hd7A 318 8.56e-01 1bix d.151.1.1 41780 1elqA 390 9.65e-01 1elqA c.67.1.3 34436 1ng1 294 9.82e-01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1jbkA 195 9.94e-01 1clxA 347 1.05e+00 1taxA c.1.8.3 28899 1xo1A 291 1.10e+00 1exnA a.60.7.1 18086 c.53.1.2 33356 1gjwA 637 1.17e+00 b.71.1.1 60582 c.1.8.1 60583 1gthD 1025 1.17e+00 1eluB 390 1.19e+00 1elqA c.67.1.3 34435 1efm 393 1.22e+00 1efcA c.37.1.8 64732 1exnA 290 1.30e+00 1exnA a.60.7.1 18088 c.53.1.2 33358 1pbn 289 1.30e+00 1b8oA c.56.2.1 33771 1gjuA 637 1.33e+00 b.71.1.1 60580 c.1.8.1 60581 1f60A 458 1.38e+00 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1nksA 194 1.44e+00 1nksA c.37.1.1 31886 1exnB 290 1.50e+00 1exnA a.60.7.1 18089 c.53.1.2 33359 1gc5A 467 1.51e+00 1gc5A c.72.1.3 60429 1gt8A 1025 1.52e+00 1gr0A 367 1.55e+00 1qj2C 285 1.64e+00 1qj2C d.87.2.1 40221 d.145.1.3 41752 1h61A 364 1.78e+00 1oyc c.1.4.1 60657 1gt8B 1025 1.82e+00 4tmkA 213 1.85e+00 5tmpA c.37.1.1 31930 1b8oA 284 1.88e+00 1b8oA c.56.2.1 33762 3pnp 289 1.90e+00 1b8oA c.56.2.1 33763 1e4fT 419 1.90e+00 1e4fT c.55.1.1 33453 c.55.1.1 33454 1bia 321 1.91e+00 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1arzC 273 1.95e+00 1drw c.2.1.3 30061 d.81.1.3 39976 5tmpA 213 1.96e+00 5tmpA c.37.1.1 31931 1gthB 1025 2.28e+00 1yasA 257 2.36e+00 1qj4A c.69.1.20 34801 1aj0 282 2.37e+00 1aj2 c.1.21.1 29667 1iqpA 327 2.37e+00 a.80.1.1 62649 c.37.1.13 62650 1aj2 282 2.41e+00 1aj2 c.1.21.1 29665 1efvB 255 2.47e+00 1efvB c.29.1.1 31634 1drw 273 2.59e+00 1drw c.2.1.3 30057 d.81.1.3 39972 1f48A 589 2.68e+00 1f48A c.37.1.10 32280 c.37.1.10 32281 1bg4 302 2.71e+00 1taxA c.1.8.3 28806 1prxB 224 2.74e+00 1prxA c.47.1.10 33077 1h7wD 1025 2.77e+00 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1gt8C 1025 2.87e+00 1ia8A 289 3.15e+00 1ia8A d.144.1.1 62112 1gt8D 1025 3.35e+00 1h7xB 1025 3.41e+00 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1h7xA 1025 3.46e+00 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1h7wB 1025 3.49e+00 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1h7wA 1025 3.55e+00 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1gteA 1025 3.58e+00 1qj4A 257 3.60e+00 1qj4A c.69.1.20 34796 1jdpA 441 3.61e+00 c.93.1.1 62906 1c0nA 406 3.64e+00 1c0nA c.67.1.3 34433 1gthC 1025 3.66e+00 1gthA 1025 3.70e+00 1f28A 297 3.70e+00 1bkpA d.117.1.1 59608 1h7xC 1025 3.78e+00 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1gkuB 1054 3.89e+00 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1bib 321 3.98e+00 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1ewkA 490 4.11e+00 1ewkA c.93.1.1 35712 1d6jA 211 4.31e+00 1d6jA c.37.1.4 31940 1qdlA 422 4.32e+00 1qdlA d.161.1.1 42088 1jr3A 373 4.52e+00 a.80.1.1 63245 c.37.1.13 63246 1qmuA 380 4.57e+00 1qmuA b.3.2.1 22534 c.56.5.1 33827 2cmd 312 4.76e+00 2cmd c.2.1.5 30135 d.162.1.1 42102 1vid 221 4.81e+00 1vid c.66.1.1 34178 1gosA 520 4.92e+00 c.3.1.2 65425 d.16.1.5 65426 1dbfA 127 4.92e+00 2chsA d.79.1.2 39761 1g291 372 5.03e+00 1g291 1dih 273 5.16e+00 1drw c.2.1.3 30056 d.81.1.3 39971 1uok 558 5.50e+00 1uok b.71.1.1 27801 c.1.8.1 28788 1g60A 260 5.52e+00 1ej6A 1289 5.86e+00 i.7.1.1 45967 1ewqA 765 5.95e+00 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1gteD 1025 6.00e+00 1f6dA 376 6.04e+00 1f6dA c.87.1.3 35467 1thm 279 6.06e+00 1gci c.41.1.1 32544 1h7xD 1025 6.36e+00 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1dts 221 6.78e+00 1byi c.37.1.10 32200 1omp 370 6.97e+00 4mbp c.94.1.1 35778 1rthA 560 6.99e+00 1rthA c.55.3.1 33576 e.8.1.2 43028 1cf2O 337 7.04e+00 1b7gO c.2.1.3 29994 d.81.1.1 39909 1g8mA 593 7.06e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1lk5A 229 7.12e+00 1k6dA 220 7.22e+00 1ckmA 330 7.27e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1i4wA 353 7.31e+00 c.66.1.9 66028 1f2dA 341 7.31e+00 1f2dA c.79.1.1 35298 1dad 224 7.32e+00 1byi c.37.1.10 32204 1dbs 224 7.59e+00 1byi c.37.1.10 32209 1byi 224 7.70e+00 1byi c.37.1.10 32199 1jenA 267 8.18e+00 1jenA 1kwsA 261 8.26e+00 1fggA 261 8.26e+00 1fggA c.68.1.7 34576 1h54A 754 8.38e+00 a.102.1.4 60634 b.30.4.1 60635 1im2A 444 8.66e+00 1do0A c.37.1.13 62564 1dbiA 280 9.19e+00 1gci c.41.1.1 32543 1kfiA 572 9.25e+00 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1d7kA 421 9.27e+00 7odcA b.49.2.1 26486 c.1.6.1 28648 7odcA 424 9.40e+00 7odcA b.49.2.1 26488 c.1.6.1 28650 1bx4A 345 9.44e+00 1bx4A c.72.1.1 34935 1sesA 421 1.00e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 2hmiA 558 1.01e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1taq 832 1.05e+01 1taq a.60.7.1 18082 c.53.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1i9sA 210 1.05e+01 1i9sA c.45.1.1 62099 1etu 394 1.06e+01 1efcA c.37.1.8 64737 1cp2A 269 1.08e+01 1cp2A c.37.1.10 32269 1k8tA 510 1.12e+01 e.9.1.4 68316 1e2gA 215 1.14e+01 3tmkA c.37.1.1 59165 1f2tB 148 1.14e+01 1f2tB 1fx3B 169 1.16e+01 1fx3B d.33.1.1 38525 1uaaA 673 1.17e+01 1pjr c.37.1.13 32401 c.37.1.13 32402 1d5rA 324 1.17e+01 1d5rA b.7.1.1 23181 c.45.1.1 32697 1tux 301 1.21e+01 1taxA c.1.8.3 28907 1jr3E 334 1.25e+01 a.80.1.1 63253 c.37.1.13 63254 1fo8A 343 1.32e+01 1foaA c.68.1.10 59927 1e9eA 215 1.35e+01 c.37.1.1 64810 1auvA 311 1.36e+01 1auvA c.30.1.5 31723 d.142.1.3 41558 1e2fA 215 1.41e+01 3tmkA c.37.1.1 59164 2rslA 140 1.42e+01 2rslA c.53.1.1 33345 1i1nA 226 1.46e+01 1cknA 330 1.47e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1d8iA 311 1.48e+01 1d8iA d.63.1.1 39541 1g41A 444 1.50e+01 1do0A c.37.1.13 32450 1fyeA 229 1.52e+01 1fyeA c.23.16.4 31477 1fs0G 230 1.53e+01 1fs0G c.49.2.1 59999 1k6aA 303 1.53e+01 1jj2B 337 1.57e+01 1ffkB b.43.3.2 63086 1hyeA 313 1.59e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1k7cA 233 1.60e+01 c.23.10.4 68267 1d8hA 311 1.62e+01 1d8iA d.63.1.1 39544 1qhtA 775 1.67e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1ycqA 107 1.68e+01 1ycqA a.42.1.1 17419 1kr5A 226 1.72e+01 c.66.1.7 68847 1dp4A 435 1.73e+01 1dp4A c.93.1.1 35710 1pfkA 320 1.80e+01 3pfk c.89.1.1 35575 1h54B 754 1.81e+01 a.102.1.4 60636 b.30.4.1 60637 1g5qA 181 1.83e+01 1g5qA c.34.1.1 60288 1j5pA 253 1.86e+01 1jhdA 396 1.87e+01 b.58.1.2 66712 c.26.1.5 66713 1d0qA 103 1.91e+01 1d0qA g.41.3.2 45208 1jl0A 334 1.92e+01 1jenA d.156.1.1 63155 830cA 168 1.98e+01 1ck7A d.92.1.11 40400 1k30A 368 2.00e+01 c.112.1.1 68067 1jf9A 408 2.02e+01 1c0nA c.67.1.3 62931 1fpzA 212 2.04e+01 1fpzA c.45.1.1 59976 2tysA 268 2.07e+01 2tysA c.1.2.4 28572 2pfkA 320 2.11e+01 3pfk c.89.1.1 35577 1mldA 314 2.14e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1bg1A 722 2.15e+01 1bg1A a.47.1.1 17767 b.2.5.1 22461 d.93.1.1 40527 1b25A 619 2.16e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1jk3A 158 2.16e+01 d.92.1.11 66790 1b9zA 516 2.17e+01 1b9zA b.3.1.1 22528 c.1.8.2 28798 1bksA 268 2.21e+01 2tysA c.1.2.4 28585 1ib8A 164 2.29e+01 1abrA 251 2.29e+01 1mrj d.165.1.1 42196 1dctA 324 2.29e+01 6mhtA c.66.1.10 34244 1lci 550 2.30e+01 1lci e.23.1.1 43349 1brwA 433 2.31e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1eyeA 280 2.35e+01 1aj2 c.1.21.1 29672 1foaA 348 2.39e+01 1foaA c.68.1.10 59929 1b0nB 57 2.40e+01 1b0nB a.34.1.1 17002 1deoA 233 2.44e+01 1deoA c.23.10.4 31345 1jkvA 266 2.44e+01 1kwmA 402 2.44e+01 2rusB 490 2.44e+01 1burA c.1.14.1 29385 d.58.9.1 39291 1j6nA 303 2.45e+01 1g7tA 594 2.45e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 2chsA 127 2.45e+01 2chsA d.79.1.2 39764 1dl5A 317 2.51e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 5bcaA 516 2.52e+01 1b9zA b.3.1.1 22529 c.1.8.2 28799 1gqpA 221 2.60e+01 1fds 327 2.60e+01 1fds c.2.1.2 29838 1ad1A 266 2.62e+01 1aj2 c.1.21.1 29668 1jx2B 315 2.62e+01 c.37.1.8 67404 1jnrA 643 2.63e+01 a.7.3.1 66966 c.3.1.4 66967 d.168.1.1 66968 1gpmA 525 2.64e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1ekjB 221 2.65e+01 1ekjB c.53.2.1 33365 1preB 470 2.73e+01 1preA d.169.1.2 42438 f.8.1.1 43825 1bwzA 274 2.75e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1a27 289 2.75e+01 1fds c.2.1.2 29839 1ihuA 589 2.76e+01 c.37.1.10 62394 c.37.1.10 62395 1fdt 327 2.78e+01 1fds c.2.1.2 29841 2cb5A 453 2.82e+01 3gcb d.3.1.1 37035 1mml 265 2.88e+01 1mml e.8.1.2 43015 1rkd 309 2.88e+01 1rkd c.72.1.1 34928 1dttA 560 2.94e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1anf 370 2.99e+01 4mbp c.94.1.1 35776 1qamA 244 3.00e+01 2ercA c.66.1.9 34220 1iatA 557 3.01e+01 1dqrA c.80.1.2 62123 1kimA 366 3.02e+01 1qhiA c.37.1.1 31864 1hqcA 324 3.03e+01 1hqcA a.4.5.11 16127 c.37.1.13 32424 1ipiA 123 3.08e+01 c.52.1.18 66255 1h6fA 193 3.11e+01 1h6kA 757 3.13e+01 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 1vom 762 3.13e+01 1lvk b.34.3.1 24577 c.37.1.9 32174 1ia9A 280 3.18e+01 1ia9A d.144.1.5 62113 3tmkA 216 3.19e+01 3tmkA c.37.1.1 31920 1g4wR 383 3.19e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1mpyA 307 3.25e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1vrtA 560 3.27e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1fnnA 389 3.29e+01 1fnnA a.4.5.11 16129 c.37.1.13 32426 1etxA 98 3.31e+01 1fipA a.105.1.1 18978 1dqrA 557 3.33e+01 1dqrA c.80.1.2 35305 1nipA 289 3.36e+01 1cp2A c.37.1.10 32263 1kzhA 555 3.36e+01 1lx7A 253 3.36e+01 1i88A 389 3.40e+01 c.95.1.2 66070 c.95.1.2 66071 1xbrA 184 3.42e+01 1xbrA b.2.5.1 22458 1gefA 123 3.49e+01 1gefA c.52.1.18 60465 1cr0A 296 3.54e+01 1cr1A c.37.1.11 32287 1b78A 193 3.54e+01 1b78A c.51.4.1 33221 1i52A 236 3.60e+01 1i52A c.68.1.13 61767 1d2sA 170 3.63e+01 1d2sA b.29.1.4 24221 1mat 264 3.66e+01 1c24A d.127.1.1 41152 1k3fA 253 3.70e+01 c.56.2.1 68105 1qh5A 260 3.70e+01 1qh5A d.157.1.2 42057 1lqvA 193 3.72e+01 1rusA 490 3.72e+01 1burA c.1.14.1 29388 d.58.9.1 39294 1c3oE 1073 3.81e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1ax4A 467 3.82e+01 1ax4A c.67.1.2 34391 1ekjA 221 3.83e+01 1ekjB c.53.2.1 33364 1g2hA 61 3.84e+01 1g2hA a.4.1.10 60224 1uteA 313 3.86e+01 1uteA d.159.1.1 42078 1gm5A 780 3.89e+01 a.29.4.1 65298 b.40.4.9 65299 c.37.1.13 65300 c.37.1.13 65301 1hnuA 280 3.90e+01 1hnoA c.14.1.3 61096