# 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 1b9kA 238 1.05e-02 1qtsA b.1.10.1 22315 d.105.1.1 40791 1qtsA 247 1.67e-02 1qtsA b.1.10.1 22313 d.105.1.1 40789 1kyfA 247 2.31e-02 1e42A 258 2.87e-02 1e42A b.1.10.1 22316 d.105.1.1 40792 1bhgA 613 3.99e-01 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 2ms2A 129 6.25e-01 1msc d.85.1.1 40049 1msc 129 8.09e-01 1msc d.85.1.1 40039 1rl6A 177 1.25e+00 1rl6A d.141.1.1 41473 d.141.1.1 41474 1uch 230 1.32e+00 1uch d.3.1.6 37129 1pii 452 1.45e+00 1pii c.1.2.4 28559 c.1.2.4 28563 1qhoA 686 1.75e+00 1cxlA b.1.1.5 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1bob 320 1.78e+00 1bob d.108.1.1 40816 2pil 159 2.04e+00 2pil d.24.1.1 38376 2prd 174 2.09e+00 2prd b.40.5.1 25435 1hetA 374 2.16e+00 2ohxA b.35.1.2 60975 c.2.1.1 60976 1b3qA 379 2.21e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 2ohxA 374 2.51e+00 2ohxA b.35.1.2 24669 c.2.1.1 29685 1g4mA 393 2.57e+00 b.1.1.5 65143 b.1.1.5 65144 1cwvA 492 2.59e+00 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1heuA 374 2.68e+00 2ohxA b.35.1.2 60979 c.2.1.1 60980 1fzyA 149 2.72e+00 d.20.1.1 65072 2arcB 164 3.19e+00 2arcA b.82.4.1 28149 1eut 605 3.49e+00 1eut b.1.1.5 21891 b.18.1.1 23712 b.68.1.1 27609 1euu 605 3.67e+00 1eut b.1.1.5 21892 b.18.1.1 23713 b.68.1.1 27610 1qlpA 394 3.82e+00 1ovaA e.1.1.1 42628 1hcqA 84 3.91e+00 2nllB g.39.1.2 45117 1lylA 504 3.94e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 1aogA 485 4.20e+00 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1ap8 213 4.34e+00 1ap8 d.86.1.1 40151 2arcA 164 4.36e+00 2arcA b.82.4.1 28148 1ay2 159 4.43e+00 2pil d.24.1.1 38377 1efuB 282 4.69e+00 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1ee2A 373 4.71e+00 2ohxA b.35.1.2 24663 c.2.1.1 29679 1e1oA 504 4.78e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 1krs 120 4.89e+00 1krs b.40.4.1 25256 1d4xG 126 5.20e+00 1d0nA d.109.1.1 59109 1ao0A 459 5.22e+00 1ecfB c.61.1.1 34049 d.153.1.1 41816 1e69B 322 5.29e+00 1e69B c.37.1.12 32377 1yagG 125 5.31e+00 1d0nA d.109.1.1 40846 1cvsC 225 5.69e+00 1cvsC b.1.1.4 21726 b.1.1.4 21727 1ckmA 330 6.35e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1j98A 157 6.40e+00 1j98A d.185.1.2 62755 1f1sA 814 6.43e+00 a.102.3.2 64928 b.1.1.5 64929 b.24.1.1 64930 b.30.3.1 64931 1a65A 504 6.67e+00 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1cknA 330 6.70e+00 1ckmA b.40.4.6 25360 d.142.2.3 41587 1kpf 126 7.08e+00 1kpf d.13.1.1 37507 1mypA 108 7.24e+00 1d2vA a.93.1.2 18701 1lox 662 7.27e+00 1lox a.119.1.2 19238 b.12.1.1 23638 1cl8A 276 7.39e+00 1ckqA c.52.1.1 33230 1qpsA 261 7.61e+00 1ckqA c.52.1.1 33234 1g7jA 107 7.63e+00 32c2A b.1.1.1 19932 8adh 374 7.68e+00 2ohxA b.35.1.2 24690 c.2.1.1 29706 1a2yA 107 7.72e+00 8fabA b.1.1.1 19926 1ckqA 276 7.77e+00 1ckqA c.52.1.1 33229 1tig 94 8.27e+00 1tig d.68.1.1 39566 1fb6A 105 8.29e+00 1thx c.47.1.1 32739 1bjx 110 8.48e+00 1bjx c.47.1.2 32774 2bjxA 110 8.48e+00 1bjx c.47.1.2 32776 1hfuA 503 8.62e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1kwaB 88 8.69e+00 1kwaA b.36.1.1 24773 1fi2A 201 8.72e+00 1fi2A b.82.1.2 59845 1thx 115 8.81e+00 1thx c.47.1.1 32732 1smlA 269 8.95e+00 1smlA d.157.1.1 42053 1ebaA 215 9.08e+00 1eerB b.1.2.1 22015 b.1.2.1 22016 1jjtA 228 9.13e+00 1a7tA d.157.1.1 63139 2pth 193 9.39e+00 2pth c.56.3.1 33793 1qoxN 449 9.42e+00 1qoxN c.1.8.4 28978 1hyeA 313 9.43e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1a8d 452 9.48e+00 1a8d b.29.1.6 24262 b.42.4.2 25607 1vfbA 107 9.96e+00 8fabA b.1.1.1 19930 1eriA 276 1.04e+01 1ckqA c.52.1.1 33231 1jmrA 249 1.11e+01 1f0lA 535 1.12e+01 1ddt b.2.1.1 22377 d.166.1.1 42239 f.1.2.1 43382 1dt9A 437 1.14e+01 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1d2vA 104 1.14e+01 1d2vA a.93.1.2 18697 1dgwA 178 1.15e+01 1dgwA b.82.1.2 28090 1i2sA 282 1.16e+01 1f5wA 126 1.18e+01 1f5wA b.1.1.1 19705 1tf4A 605 1.20e+01 1tf4A a.102.1.2 18827 b.2.2.2 22393 2i1b 153 1.20e+01 2i1b b.42.1.2 25538 1eajA 126 1.26e+01 1f5wA b.1.1.1 59401 1dq3A 454 1.29e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1f13A 731 1.30e+01 1f13A b.1.1.5 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1k8kA 418 1.31e+01 c.55.1.1 68305 c.55.1.1 68306 1cf1A 404 1.33e+01 1cf1A b.1.1.5 21907 b.1.1.5 21908 1ci3M 249 1.39e+01 1hcz b.2.6.1 22480 b.84.2.2 28266 1bwwA 109 1.39e+01 8fabA b.1.1.1 20518 2mev1 277 1.40e+01 2mev1 1e4iA 447 1.41e+01 1e70M c.1.8.4 59225 1dd6A 228 1.44e+01 1a7tA d.157.1.1 42054 1tnm 100 1.44e+01 1wit b.1.1.4 21710 1k32A 1045 1.46e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 4sli 679 1.46e+01 2sli b.29.1.9 24275 b.68.1.1 27612 1kwaA 88 1.47e+01 1kwaA b.36.1.1 24772 1ipaA 274 1.52e+01 2cavA 445 1.53e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1kypA 237 1.54e+01 1dqwA 267 1.55e+01 1dqwA c.1.2.3 28551 1cauA 181 1.58e+01 1dgwA b.82.1.2 28102 1hxxA 340 1.60e+01 2omf f.4.3.1 61385 3grx 82 1.63e+01 1aba c.47.1.1 32769 1dgrC 178 1.66e+01 1dgwA b.82.1.2 28100 1lnh 857 1.68e+01 1yge a.119.1.1 19237 b.12.1.1 23637 1mhlA 108 1.71e+01 1d2vA a.93.1.2 18699 1qc9A 276 1.72e+01 1ckqA c.52.1.1 33235 1hynP 379 1.76e+01 1hynP d.112.1.2 61408 1ryp2 233 1.78e+01 1ryp2 1i8kA 107 1.80e+01 1ebfA 358 1.81e+01 1ebuA c.2.1.3 30033 d.81.1.2 39948 1cgt 684 1.84e+01 1cxlA b.1.1.5 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 1f7cA 231 1.88e+01 1f7cA a.116.1.1 19107 1k2yX 463 1.91e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 c.84.1.1 68066 1qtnB 95 1.92e+01 1pauB 1cxpA 104 1.97e+01 1d2vA a.93.1.2 18695 1i58A 189 1.98e+01 1b3qA d.122.1.3 61773 9apiA 347 2.00e+01 1ovaA e.1.1.1 42630 1bpv 112 2.07e+01 1bpv b.1.2.1 22071 1gw5S 142 2.14e+01 1bkzA 135 2.20e+01 1a3k b.29.1.3 24202 1j58A 385 2.21e+01 2sli 679 2.31e+01 2sli b.29.1.9 24274 b.68.1.1 27611 1exg 110 2.33e+01 1exg b.2.2.1 22387 2trxA 108 2.34e+01 1thx c.47.1.1 32719 1ckeA 227 2.36e+01 1ckeA c.37.1.1 31846 1l4iA 206 2.39e+01 1bmv2 374 2.40e+01 1bmv2 1knqA 175 2.42e+01 1ggtB 731 2.52e+01 1f13A b.1.1.5 21882 b.1.5.1 22173 b.1.5.1 22174 d.3.1.4 37112 1prxB 224 2.53e+01 1prxA c.47.1.10 33077 1ag9A 175 2.55e+01 1rcf c.23.5.1 31178 2pcdM 238 2.55e+01 3pchM b.3.6.1 22760 1dykA 394 2.60e+01 1dykA b.29.1.4 24223 b.29.1.4 24224 2fibA 269 2.68e+01 3fib d.171.1.1 42457 2rspB 124 2.68e+01 2rspB b.50.1.1 26772 1tr1A 447 2.73e+01 1e70M c.1.8.4 28957 1ayyA 151 2.77e+01 1apyA d.153.1.5 42016 1k8wA 327 2.79e+01 d.58.35.2 68317 d.58.35.2 68318 1gefA 123 2.79e+01 1gefA c.52.1.18 60465 1prxA 224 2.80e+01 1prxA c.47.1.10 33076 31bi 153 2.81e+01 2i1b b.42.1.2 25541 1l0bA 229 2.85e+01 1yge 839 2.85e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1srvA 145 2.86e+01 1derA c.8.5.1 30817 1i40A 175 2.87e+01 b.40.5.1 66024 1c44A 123 2.89e+01 1qndA d.106.1.1 40795 1ghhA 81 2.95e+01 1ghhA d.57.1.1 38940 1qj2A 166 2.99e+01 1qj2A a.56.1.1 17913 d.15.4.2 37698 2cgpA 210 3.02e+01 2cgpA a.4.5.4 16102 b.82.3.2 28141 1f3yA 165 3.06e+01 d.113.1.1 59635 3fib 249 3.08e+01 3fib d.171.1.1 42455 1mfa 247 3.09e+01 1mfa b.1.1.1 19888 b.1.1.1 19889 1je5A 206 3.09e+01 1je5A b.40.4.7 62909 21bi 153 3.09e+01 2i1b b.42.1.2 25542 1i8dA 213 3.14e+01 b.43.4.3 61953 b.43.4.3 61954 1a1w 91 3.15e+01 1a1z a.77.1.1 18425 1fib 269 3.15e+01 3fib d.171.1.1 42456 1l5wA 796 3.15e+01 1qo0D 196 3.17e+01 1qo0D c.23.1.3 31125 1gguA 731 3.18e+01 1f13A b.1.1.5 21885 b.1.5.1 22179 b.1.5.1 22180 d.3.1.4 37115 1kpeA 126 3.20e+01 1kpf d.13.1.1 37508 1gatA 60 3.21e+01 1gatA g.39.1.1 45106 1thtA 305 3.22e+01 1thtA c.69.1.13 34711 1bgf 124 3.26e+01 1bgf a.90.1.1 18537 1hw5A 210 3.31e+01 2cgpA a.4.5.4 16098 b.82.3.2 28137 1hn2A 159 3.32e+01 b.60.1.1 65890 1a1z 91 3.33e+01 1a1z a.77.1.1 18427 1evuA 731 3.38e+01 1f13A b.1.1.5 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 3pcgM 238 3.41e+01 3pchM b.3.6.1 22742 6gsvA 217 3.42e+01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1qc5A 192 3.43e+01 1aoxA c.62.1.1 34147 1kid 203 3.44e+01 1derA c.8.5.1 30771 1ema 236 3.45e+01 1ema d.22.1.1 38339 1ejrB 101 3.45e+01 1ubpB b.85.3.1 28320 1i1b 153 3.48e+01 2i1b b.42.1.2 25537 1ifrA 121 3.49e+01 1gg6B 131 3.49e+01 5ptp 1k6zA 141 3.49e+01 d.198.1.1 68247 1ep0A 185 3.49e+01 1dzrA b.82.1.1 28080 1pdkB 157 3.52e+01 1pdkB b.2.3.2 22427 1jyaA 130 3.55e+01 d.198.1.1 67453 1obwA 175 3.58e+01 2prd b.40.5.1 25416 1mcpL 220 3.66e+01 8fabA b.1.1.1 19858 b.1.1.2 20958 1c5cL 214 3.68e+01 32c2A b.1.1.1 20474 b.1.1.2 21438 1aqb 183 3.74e+01 1aqb b.60.1.1 27084 1b3tA 147 3.74e+01 1b3tA d.58.8.1 39228 1a8l 226 3.76e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1ev2E 220 3.78e+01 1cvsC b.1.1.4 21738 b.1.1.4 21739 1jwiB 125 3.87e+01 d.169.1.1 67384 1obpA 159 3.88e+01 1obpA b.60.1.1 27092 2kauB 106 3.89e+01 1ubpB b.85.3.1 28328 1ajqB 557 3.90e+01 1ajqB 3pchM 238 3.96e+01 3pchM b.3.6.1 22748