# 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 1jx7A 117 4.10e-03 c.114.1.1 77195 1ndk 155 1.20e-02 1npk d.58.6.1 39118 1f3fA 155 1.33e-02 1npk d.58.6.1 39101 1npk 154 1.34e-02 1npk d.58.6.1 39099 1m32A 366 2.07e-02 c.67.1.3 78508 1hdfA 102 3.57e-02 1ag4 b.11.1.1 23627 1bcpB 199 3.92e-02 1bcpB b.40.2.1 25120 d.169.1.2 42429 1d7yA 408 6.63e-02 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1r6xA 395 3.16e-01 1g8fA 511 4.06e-01 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 1gydB 315 5.35e-01 b.67.2.1 70751 1bia 321 5.70e-01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1h0cA 392 6.36e-01 c.67.1.3 83424 1ag4 103 6.70e-01 1ag4 b.11.1.1 23629 1f20A 435 7.08e-01 b.43.4.1 64932 c.25.1.4 64933 1ge8A 249 7.65e-01 1plq d.131.1.2 41398 d.131.1.2 41399 1plq 258 7.77e-01 1plq d.131.1.2 41388 d.131.1.2 41389 1iz5A 249 8.45e-01 d.131.1.2 83834 d.131.1.2 83835 1cauA 181 9.64e-01 1dgwA b.82.1.2 28102 1mjgM 729 1.01e+00 e.26.1.3 79204 1g6oA 330 1.04e+00 1g6oA c.37.1.11 32430 1bcpC 199 1.07e+00 1bcpB b.40.2.1 25121 d.169.1.2 42430 3sicI 107 1.07e+00 3ssi d.84.1.1 40028 1a2vA 655 1.09e+00 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 2bb2 181 1.12e+00 2bb2 b.11.1.1 23604 b.11.1.1 23605 1k3sA 113 1.18e+00 d.198.1.1 68120 1hh1A 143 1.18e+00 1gefA c.52.1.18 61036 1bib 321 1.26e+00 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1vj1A 363 1.28e+00 1dgrC 178 1.42e+00 1dgwA b.82.1.2 28100 1pls 113 1.44e+00 1pls b.55.1.1 26965 1cbf 285 1.44e+00 1cbf c.90.1.1 35587 2sicI 107 1.52e+00 3ssi d.84.1.1 40031 1gdtA 183 1.62e+00 2rslA a.4.1.2 16021 c.53.1.1 33348 1s3zA 165 1.63e+00 1jb9A 316 1.67e+00 1fnc b.43.4.2 62840 c.25.1.1 62841 1ogdA 131 1.70e+00 1dmr 823 1.74e+00 1dmr b.52.2.2 26904 c.81.1.1 35312 2ay1A 394 1.89e+00 1ajsA c.67.1.1 34357 1cl1A 395 1.96e+00 1cl2A c.67.1.3 34395 1rypG 244 1.97e+00 d.153.1.4 41938 1am2 199 1.98e+00 1am2 b.86.1.2 28381 2frvA 264 2.25e+00 2frvA e.19.1.1 43303 1aw8E 91 2.26e+00 1aw8B 1ghtA 105 2.35e+00 2rslA c.53.1.1 60526 1plr 258 2.44e+00 1plq d.131.1.2 41390 d.131.1.2 41391 1hgeA 328 2.47e+00 1hgeA b.19.1.2 23816 1h10A 125 2.53e+00 b.55.1.1 83446 1dgwA 178 2.56e+00 1dgwA b.82.1.2 28090 2cbf 234 2.63e+00 1cbf c.90.1.1 35588 1gc0A 398 2.65e+00 c.67.1.3 70168 1oaoC 729 2.84e+00 e.26.1.3 86746 3hmgA 328 2.87e+00 1hgeA b.19.1.2 23825 1of5B 184 3.03e+00 d.17.4.2 86934 2viuA 328 3.05e+00 1hgeA b.19.1.2 23797 1ufkA 254 3.05e+00 1k7cA 233 3.11e+00 c.23.10.4 68267 1ei5A 520 3.21e+00 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1deoA 233 3.25e+00 1deoA c.23.10.4 31345 1c7nA 399 3.26e+00 1d2fA c.67.1.3 34413 1gyhA 318 3.30e+00 b.67.2.1 70757 1pt1A 143 3.33e+00 1cl2A 395 3.43e+00 1cl2A c.67.1.3 34397 1nykA 165 3.46e+00 b.33.1.1 86408 1ik6A 369 3.47e+00 c.36.1.7 66174 c.48.1.2 66175 1bw0A 416 3.49e+00 1bw0A c.67.1.1 34385 1jxhA 288 3.62e+00 c.72.1.2 67415 1jj2N 115 3.66e+00 1ffkL c.12.1.1 63099 1cfyA 143 3.67e+00 1cof d.109.1.2 40858 3psg 370 4.14e+00 1smrA b.50.1.2 26841 1fjgB 256 4.40e+00 1fjfB c.23.15.1 31400 1j5eB 256 4.46e+00 c.23.15.1 71543 1jsmA 325 4.56e+00 b.19.1.2 63264 1pqhA 143 4.62e+00 1dqwA 267 4.69e+00 1dqwA c.1.2.3 28551 1qjcA 158 4.70e+00 1b6tA c.26.1.3 63328 1h80A 464 4.76e+00 b.80.1.8 65714 3ssi 113 5.06e+00 3ssi d.84.1.1 40032 1pnsB 234 5.09e+00 i.1.1.1 88169 1eu1A 780 5.16e+00 1dmr b.52.2.2 26903 c.81.1.1 35311 1qzzA 374 5.21e+00 1l1sA 113 5.39e+00 c.114.1.1 73484 1nrjB 218 5.41e+00 c.37.1.8 86125 1m4iA 181 5.46e+00 d.108.1.1 74457 1m5q1 130 5.77e+00 1ypcI 64 6.18e+00 2sniI d.40.1.1 38570 2admA 421 6.23e+00 2admA c.66.1.27 34238 1t9kA 347 6.72e+00 1hymA 45 6.79e+00 1hymA d.40.1.1 38581 1cxyA 90 6.80e+00 1cyo d.120.1.1 41085 1hnnA 282 6.97e+00 c.66.1.15 65895 1oruA 195 7.35e+00 1ne8A 117 7.36e+00 b.34.6.2 80424 1ffkL 115 7.39e+00 1ffkL c.12.1.1 30881 1jotA 133 7.45e+00 1jotA 1s98A 107 7.82e+00 1jtdB 273 8.22e+00 b.69.5.2 67265 1qauA 112 8.32e+00 1qauA b.36.1.1 24779 1l1qA 186 8.38e+00 c.61.1.1 77653 1qnoA 344 8.38e+00 1qnoA c.1.8.3 28838 1php 394 8.42e+00 16pk c.86.1.1 35452 1ebpA 211 8.62e+00 1eerB b.1.2.1 22023 b.1.2.1 22024 1mplA 349 8.84e+00 e.3.1.1 79387 1fjrA 195 8.90e+00 1fjrA b.102.1.1 59855 1g4yR 148 9.16e+00 1cll a.39.1.5 60252 1qnrA 344 9.32e+00 1qnoA c.1.8.3 28834 1oz7A 131 9.37e+00 2sniI 83 9.37e+00 2sniI d.40.1.1 38573 1rthA 560 9.49e+00 1rthA c.55.3.1 33576 e.8.1.2 43028 1o1xA 155 9.70e+00 c.121.1.1 86553 1mj4A 82 9.74e+00 d.120.1.1 79189 1ikoP 178 9.78e+00 b.6.1.5 71243 1okiA 210 1.00e+01 1fdr 248 1.04e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1ndh 272 1.04e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1qavB 115 1.08e+01 1qauA b.36.1.1 24780 1p0hA 318 1.09e+01 1jtgB 165 1.13e+01 d.98.1.1 67267 1lxjA 104 1.16e+01 d.58.48.1 84736 1b5pA 385 1.18e+01 1fukA 165 1.19e+01 1fukA c.37.1.19 32409 1o12A 376 1.19e+01 b.92.1.5 80758 c.1.9.10 80759 1aw8B 91 1.20e+01 1aw8B 4pep 326 1.20e+01 1smrA b.50.1.2 26843 1k9uA 78 1.21e+01 a.39.1.10 84348 1o4sA 389 1.21e+01 c.67.1.1 86620 1jacC 133 1.22e+01 1jotA 2blsA 358 1.25e+01 1gceA e.3.1.1 42747 1coaI 64 1.25e+01 2sniI d.40.1.1 38574 1f6bA 198 1.26e+01 c.37.1.8 64986 1b2pA 119 1.27e+01 1b2pA b.78.1.1 27998 3pte 349 1.27e+01 3pte e.3.1.1 42687 1jacA 133 1.30e+01 1jotA 1kebA 108 1.31e+01 c.47.1.1 77341 1bc5A 269 1.31e+01 1af7 a.58.1.1 17929 c.66.1.8 34204 1jsqA 582 1.33e+01 i.13.1.1 63270 1o7fA 469 1.34e+01 a.4.5.31 81131 b.82.3.2 81132 b.82.3.2 81133 1uag 437 1.34e+01 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1m6sA 347 1.35e+01 c.67.1.1 78701 1nfiC 301 1.35e+01 b.1.18.1 21943 b.2.5.3 22456 1jg8A 347 1.37e+01 1jg8A c.67.1.1 62946 1bjwA 382 1.38e+01 1bjwA c.67.1.1 34349 1dfoA 417 1.40e+01 1bj4A c.67.1.4 34480 3ncmA 92 1.41e+01 3ncmA b.1.1.4 21702 1efcA 393 1.41e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1lw6I 64 1.43e+01 d.40.1.1 74294 1on3A 523 1.43e+01 c.14.1.4 87107 c.14.1.4 87108 1m2oB 190 1.44e+01 c.37.1.8 78485 1fxzA 476 1.46e+01 b.82.1.2 65059 b.82.1.2 65060 2pil 159 1.47e+01 2pil d.24.1.1 38376 1ku8A 133 1.48e+01 1nfiA 301 1.49e+01 1a3qA b.1.18.1 21942 b.2.5.3 22455 1ru4A 400 1.49e+01 3uagA 437 1.50e+01 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 1epxA 370 1.50e+01 1fbaA c.1.10.1 29150 1bftA 101 1.51e+01 1a3qA b.1.18.1 21934 1ponB 36 1.52e+01 1ponB 1fzcA 87 1.52e+01 1fzcA h.1.8.1 45590 1kf6B 243 1.53e+01 a.1.2.1 72397 d.15.4.2 72398 1spa 396 1.59e+01 1ajsA c.67.1.1 34291 1j71A 334 1.63e+01 1eagA b.50.1.2 62669 1my7A 114 1.63e+01 b.1.18.1 79675 1rypC 244 1.63e+01 1rypC d.153.1.4 41934 2cavA 445 1.64e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1uf2A 1019 1.65e+01 1m5yA 408 1.66e+01 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 1fl0A 171 1.68e+01 1eujA b.40.4.4 25315 1oheA 348 1.72e+01 c.45.1.1 87013 c.45.1.1 87014 1pk6C 129 1.72e+01 1mugA 168 1.74e+01 1mugA c.18.1.2 31030 1rc6A 261 1.76e+01 1ugxA 133 1.77e+01 1a8rA 221 1.78e+01 1a8rA d.96.1.1 40587 1e19A 314 1.79e+01 1b7bA c.73.1.1 34967 1kvlA 358 1.80e+01 e.3.1.1 73062 1gnuA 117 1.80e+01 d.15.1.3 65403 1rgyA 360 1.81e+01 3ullA 132 1.82e+01 3ullA b.40.4.3 25282 1bt4A 362 1.83e+01 1bjnA c.67.1.4 34468 1e4cP 215 1.84e+01 2fua c.74.1.1 34969 1jtkA 136 1.85e+01 c.97.1.1 71862 1bev1 281 1.86e+01 1aym1 2arcA 164 1.90e+01 2arcA b.82.4.1 28148 1l8rA 101 1.90e+01 a.6.1.4 73700 1c9fA 90 1.93e+01 1c9fA d.15.2.1 37639 1jnyA 435 1.94e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1mbmA 198 1.95e+01 b.47.1.3 78916 1b74A 254 1.96e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 2bltA 361 2.00e+01 1gceA e.3.1.1 42739 2aacA 177 2.01e+01 2arcA b.82.4.1 28150 1ohzB 60 2.03e+01 1m26A 133 2.03e+01 1pv0A 46 2.05e+01 1ga0A 364 2.06e+01 1gceA e.3.1.1 60410 2arcB 164 2.06e+01 2arcA b.82.4.1 28149 1kfuS 184 2.06e+01 a.39.1.8 68574 1my5A 114 2.07e+01 b.1.18.1 79673 1ay2 159 2.08e+01 2pil d.24.1.1 38377 1vkfA 188 2.08e+01 1fqtA 112 2.09e+01 1fqtA b.33.1.1 24441 1hvbA 349 2.11e+01 3pte e.3.1.1 42686 1cc1S 283 2.12e+01 2frvA e.19.1.1 43313 1onxA 390 2.13e+01 b.92.1.7 87176 c.1.9.13 87177 1fsyA 358 2.13e+01 1gceA e.3.1.1 60016 1k0gA 453 2.14e+01 d.161.1.1 67940 1sek 378 2.16e+01 1sek e.1.1.1 42675 1onwA 390 2.16e+01 b.92.1.7 87172 c.1.9.13 87173 1vrtA 560 2.17e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1onhA 364 2.17e+01 1psrA 100 2.18e+01 1psrA a.39.1.2 17180 1p9rA 418 2.18e+01 1fhdA 312 2.20e+01 1taxA c.1.8.3 28915 2hir 65 2.21e+01 4htcI g.3.15.2 44372 1qn2A 100 2.21e+01 1ycc a.3.1.1 15882 2his 312 2.22e+01 1taxA c.1.8.3 28918 1gceA 364 2.23e+01 1gceA e.3.1.1 42738 1chuA 540 2.24e+01 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1ej1A 190 2.25e+01 1ejhA d.86.1.1 40144 1eujA 166 2.25e+01 1eujA b.40.4.4 25316 1ordA 730 2.29e+01 1ordA c.23.1.4 31274 c.67.1.5 34503 d.125.1.1 41124 1a62 130 2.30e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1m2aA 110 2.32e+01 c.47.1.11 78472 1srvA 145 2.34e+01 1derA c.8.5.1 30817 2rslA 140 2.35e+01 2rslA c.53.1.1 33345 1ebdC 41 2.35e+01 1ebdC a.9.1.1 16355 1rwzA 245 2.36e+01 1vmoA 163 2.37e+01 1vmoA b.77.1.1 27974 1rgzA 363 2.37e+01 1m2bA 110 2.37e+01 c.47.1.11 78474 2pspA 106 2.38e+01 2pspA g.16.1.1 44730 g.16.1.1 44731 1fnhA 271 2.38e+01 1fnhA b.1.2.1 21976 b.1.2.1 21977 b.1.2.1 21978 1fh9A 312 2.41e+01 1taxA c.1.8.3 28913 1o54A 277 2.41e+01 1cof 143 2.42e+01 1cof d.109.1.2 40860 1s29A 92 2.45e+01 1gheA 177 2.47e+01 d.108.1.1 76222 1kq3A 376 2.47e+01 e.22.1.2 68790 1o5nA 126 2.48e+01 1vj2A 126 2.48e+01 1umdB 324 2.49e+01 1r94A 118 2.49e+01 4uagA 437 2.50e+01 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1a8vA 121 2.53e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1whtB 153 2.56e+01 1whtB 1fmb 104 2.58e+01 1fmb b.50.1.1 26777 1gdoB 240 2.62e+01 1gdoA d.153.1.1 41805 1har 216 2.65e+01 1rthA e.8.1.2 43025 1sfp 114 2.71e+01 1sfp b.23.1.1 23895 1l0oA 150 2.75e+01 d.122.1.3 73403 2trxA 108 2.75e+01 1thx c.47.1.1 32719 1vjpA 394 2.75e+01 1fr1A 361 2.76e+01 1gceA e.3.1.1 42734 1bhe 376 2.78e+01 1bhe b.80.1.3 28030 1booA 323 2.79e+01 1booA c.66.1.11 34248 1af7 274 2.81e+01 1af7 a.58.1.1 17928 c.66.1.8 34203 1bfi 112 2.81e+01 1qadA d.93.1.1 40499 1f37A 110 2.85e+01 1f37A c.47.1.11 33088 1n5dA 288 2.86e+01 c.2.1.2 80030 1uwzA 136 2.86e+01 1b6tA 159 2.86e+01 1b6tA c.26.1.3 31600 1p9bA 442 2.88e+01 1tin 69 2.88e+01 2sniI d.40.1.1 38580 1b73A 254 2.88e+01 1b74A c.78.2.1 35266 c.78.2.1 35267 1pi4A 358 2.89e+01 1knwA 425 2.90e+01 1rxxA 421 2.91e+01 1bjoA 360 2.91e+01 1bjnA c.67.1.4 34471 1dgzA 37 2.91e+01 1dfeA g.42.1.1 45319 2kauA 100 2.92e+01 1ubpA d.8.1.1 37335 1hu4A 288 2.93e+01 1hu4A 1e1oA 504 2.94e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1umzA 278 2.96e+01 1iweA 457 2.97e+01 c.37.1.10 71486 1pvtA 238 2.97e+01 2pdd 43 3.00e+01 1ebdC a.9.1.1 16358 1h05A 146 3.02e+01 c.23.13.1 76433 1c4kA 730 3.02e+01 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1l0gA 358 3.03e+01 e.3.1.1 73400 1qm4A 396 3.03e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1fwcA 100 3.04e+01 1ubpA d.8.1.1 37331 1pmaP 211 3.04e+01 1pmaP d.153.1.4 41863 1pcl 355 3.05e+01 1pcl b.80.1.1 28021 1bcsB 160 3.16e+01 1whtB 1iz0A 302 3.21e+01 b.35.1.2 83821 c.2.1.1 83822 1lylA 504 3.22e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1ars 396 3.22e+01 1ajsA c.67.1.1 34287 1a8y 367 3.23e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1qpcA 279 3.23e+01 1fgkA d.144.1.7 41685 1avsA 90 3.24e+01 1cll a.39.1.5 17226 1dfaA 454 3.30e+01 1vdeA b.86.1.2 28375 d.95.2.2 40575 d.95.2.2 40576 1dttA 560 3.32e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1ex1A 605 3.33e+01 1ex1A c.1.8.7 29013 c.23.11.1 31347 1pms 136 3.34e+01 1awe b.55.1.1 26966 1l4zB 136 3.36e+01 d.15.5.1 77704 1cozA 129 3.38e+01 1cozA c.26.1.2 31598 1p3dA 475 3.38e+01 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1iow 306 3.39e+01 1iow c.30.1.2 31713 d.142.1.1 41481 1hm6A 346 3.39e+01 1avc a.65.1.1 18147 1im3D 95 3.40e+01 1im3D b.1.18.5 62568 1vdeA 454 3.41e+01 1vdeA b.86.1.2 28378 d.95.2.2 40581 d.95.2.2 40582 1g38A 393 3.42e+01 2admA c.66.1.27 60235 1du9A 28 3.48e+01 g.3.7.2 44148 1l3rI 20 3.49e+01 1b8qA 127 3.49e+01 1qauA b.36.1.1 24781 1oe0A 230 3.52e+01 1inlA 296 3.52e+01 c.66.1.17 66220 1art 396 3.54e+01 1ajsA c.67.1.1 34285 1ejhA 190 3.55e+01 1ejhA d.86.1.1 40147 1qjvA 342 3.66e+01 1qjvA b.80.1.5 28035 1pvdA 537 3.68e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1rz3A 201 3.69e+01 8ohm 435 3.69e+01 1heiA c.37.1.14 32469 c.37.1.14 32470 1fua 215 3.70e+01 2fua c.74.1.1 34973 1ejxA 100 3.71e+01 d.8.1.1 83182 1h0bA 256 3.74e+01 b.29.1.11 83422 1hv8A 367 3.74e+01 1hv8A c.37.1.19 32405 c.37.1.19 32406 1whsB 153 3.75e+01 1whtB 1bfd 528 3.78e+01 1bfd c.31.1.3 31745 c.36.1.5 31801 c.36.1.9 31802 1bxwA 172 3.79e+01 1bxwA f.4.1.1 43743 1m2dA 110 3.80e+01 c.47.1.11 78476 1gg6C 97 3.84e+01 5ptp 1jg1A 235 3.90e+01 c.66.1.7 66661 1gkpA 458 3.91e+01 b.92.1.3 70231 c.1.9.6 70232 1qpbA 563 3.93e+01 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1ow1A 195 3.95e+01 1g57A 217 3.95e+01 1g57A d.115.1.2 60253