# 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 1mwsA 646 7.48e-02 d.17.4.5 79592 d.175.1.1 79593 e.3.1.1 79594 1phk 298 9.81e-02 1cdkA d.144.1.7 41635 1mwxA 646 2.82e-01 d.17.4.5 79610 d.175.1.1 79611 e.3.1.1 79612 1byqA 228 3.40e-01 1yer d.122.1.1 41100 1cjtA 217 5.56e-01 1azsA d.58.29.1 39419 1azsA 220 6.75e-01 1azsA d.58.29.1 39416 1yer 228 8.42e-01 1yer d.122.1.1 41101 1j5eE 161 8.66e-01 d.14.1.1 71547 d.50.1.2 71548 1o0pA 104 9.04e-01 d.58.7.1 86535 1mai 131 1.21e+00 1mai b.55.1.1 26951 1mwrA 646 1.25e+00 d.17.4.5 79586 d.175.1.1 79587 e.3.1.1 79588 1gwmA 153 1.46e+00 b.18.1.19 83348 1kzlA 208 1.56e+00 b.43.4.3 77635 b.43.4.3 77636 1culA 217 1.96e+00 1azsA d.58.29.1 39417 1ayl 541 2.28e+00 1ayl c.91.1.1 64718 c.109.1.1 64719 1ep0A 185 2.31e+00 1dzrA b.82.1.1 28080 1fnoA 417 2.44e+00 c.56.5.4 75841 d.58.19.1 70145 1ukkA 142 2.47e+00 d.227.1.1 -11206 1nnhA 294 2.49e+00 d.104.1.1 -10772 1rgxA 114 2.58e+00 1t62A 166 2.61e+00 1qy5A 269 2.78e+00 d.122.1.1 -10958 1e87A 118 2.90e+00 1b6e d.169.1.1 42327 1jc7A 131 3.01e+00 1jc7A b.40.3.2 62873 1fm5A 199 3.30e+00 1fm5A d.169.1.1 42330 1jb3A 131 3.60e+00 1jc7A b.40.3.2 62833 1gmiA 136 3.87e+00 b.7.1.1 65309 1adr 76 3.99e+00 1r69 a.35.1.2 17042 1faeA 629 4.10e+00 1fce a.102.1.2 18837 1nslA 184 4.13e+00 d.108.1.1 86137 1qaxA 428 4.18e+00 1qaxA d.58.20.1 39376 d.179.1.1 42597 1g9gA 629 4.42e+00 a.102.1.2 83279 1d2gA 292 4.60e+00 1xvaA c.66.1.5 34187 1r31A 428 4.61e+00 d.58.20.1 -10108 d.179.1.1 -11716 1hyeA 313 4.94e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1i8dA 213 4.94e+00 b.43.4.3 61953 b.43.4.3 61954 1fce 629 5.00e+00 1fce a.102.1.2 18836 1eg2A 319 5.51e+00 1eg2A c.66.1.11 34249 1a8vA 121 6.03e+00 1a62 a.140.3.1 64712 b.40.4.5 64713 1qwlA 505 6.08e+00 e.5.1.1 -11823 1lplA 95 6.08e+00 b.34.10.1 74173 1g59A 468 6.13e+00 a.97.1.1 60257 c.26.1.1 60258 1bhjA 292 6.30e+00 1xvaA c.66.1.5 34189 1r0wA 286 7.20e+00 c.37.1.12 -7158 1ew4A 106 7.21e+00 1ew4A d.82.2.1 40023 1ezoA 370 7.22e+00 4mbp c.94.1.1 59539 1vkbA 161 7.32e+00 1d7qA 143 7.36e+00 1d7qA b.40.4.5 25331 1t1dA 100 7.55e+00 1t1dA d.42.1.2 38637 1xvaA 292 7.70e+00 1xvaA c.66.1.5 34183 2cyp 294 7.76e+00 1ryc a.93.1.1 18600 1g6oA 330 7.82e+00 1g6oA c.37.1.11 32430 1ryc 294 7.85e+00 1ryc a.93.1.1 18601 1yghA 164 7.94e+00 1yghA d.108.1.1 40802 1j09A 468 8.02e+00 a.97.1.1 77025 c.26.1.1 77026 1nw8A 319 8.47e+00 c.66.1.11 86292 1dctA 324 8.49e+00 6mhtA c.66.1.26 34244 6pfkA 319 8.59e+00 3pfk c.89.1.1 35583 3pfk 319 8.63e+00 3pfk c.89.1.1 35581 1k8kD 300 8.64e+00 d.198.2.1 68309 d.198.2.1 68310 1gv3A 248 8.91e+00 a.2.11.1 70585 d.44.1.1 70586 1ds4A 292 9.14e+00 1ryc a.93.1.1 59129 1l1oC 181 9.38e+00 b.40.4.3 73480 1faoA 126 9.45e+00 1faoA b.55.1.1 26974 1o7kA 131 9.57e+00 d.189.1.1 81144 1c52 131 9.57e+00 1c52 a.3.1.1 15810 1gln 468 9.80e+00 1gln a.97.1.1 18752 c.26.1.1 31588 1gjwA 637 1.01e+01 b.71.1.1 60582 c.1.8.1 60583 1r0vA 305 1.04e+01 c.52.2.1 -7572 c.52.2.1 -7573 d.75.1.1 -10344 1pfkA 320 1.07e+01 3pfk c.89.1.1 35575 1kutA 230 1.08e+01 d.143.1.1 73017 1pk6A 133 1.10e+01 b.22.1.1 -3287 1eaxA 241 1.12e+01 b.47.1.2 64889 1rot 149 1.14e+01 1fkj d.26.1.1 38429 1lqtA 456 1.15e+01 c.3.1.1 74198 c.4.1.1 74199 1ahsA 126 1.16e+01 1ahsA b.19.1.1 23794 1j58A 385 1.17e+01 b.82.1.2 71531 1j6wA 175 1.17e+01 1j98A d.185.1.2 62663 1mvfD 82 1.19e+01 b.129.1.1 85143 1k75A 434 1.21e+01 c.82.1.2 68253 1d5mB 192 1.22e+01 1iakB b.1.1.2 21618 d.19.1.1 38192 1v8fA 276 1.24e+01 c.26.1.4 -6618 1ig3A 263 1.27e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1qayA 428 1.28e+01 1qaxA d.58.20.1 39378 d.179.1.1 42599 1f7lA 121 1.28e+01 1f7lA d.150.1.2 59666 1lea 84 1.30e+01 1lea a.4.5.2 16085 1a62 130 1.31e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1mw7A 240 1.32e+01 e.39.1.1 79557 1gjuA 637 1.33e+01 b.71.1.1 60580 c.1.8.1 60581 1v3wA 173 1.34e+01 b.81.1.5 -4815 1kaeA 434 1.36e+01 c.82.1.2 72247 1g3p 217 1.37e+01 1g3p b.37.1.1 24788 b.37.1.1 24789 1rpyA 114 1.39e+01 d.93.1.1 -10636 2gar 212 1.40e+01 2gar c.65.1.1 34161 1bf8 205 1.40e+01 1qpxA b.1.11.1 22332 b.7.2.1 23214 1hqz1 141 1.44e+01 1d5yA 292 1.49e+01 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1v7oA 165 1.50e+01 unknown_sccs -10249 1itg 166 1.50e+01 1b9dA c.55.3.2 33661 1uj2A 252 1.51e+01 c.37.1.6 -7061 1vixA 420 1.52e+01 c.56.5.4 -7866 d.58.19.1 -10090 1l4iA 206 1.52e+01 b.1.11.1 73564 b.7.2.1 73565 1l8bA 190 1.52e+01 d.86.1.1 73683 1f42A 306 1.56e+01 1f42A b.1.1.4 59636 b.1.2.1 59637 b.1.2.1 59638 1d6zA 727 1.59e+01 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1r5rA 119 1.59e+01 a.39.2.1 -893 1kk6A 209 1.60e+01 b.81.1.3 68657 1ndk 155 1.61e+01 1npk d.58.6.1 39118 1ccg 291 1.62e+01 1ryc a.93.1.1 18627 1fjrA 195 1.67e+01 1fjrA b.102.1.1 59855 1qmhA 347 1.71e+01 1qmhA c.47.2.1 33082 d.68.2.1 39568 1k3eA 156 1.76e+01 d.198.1.1 68103 1qgvA 142 1.77e+01 1qgvA c.47.1.8 33056 1dseA 292 1.81e+01 1ryc a.93.1.1 59130 1hdp 63 1.81e+01 1au7A a.4.1.1 15998 1nf3C 128 1.81e+01 b.36.1.1 85596 1mroC 247 1.82e+01 1mroC d.58.31.1 39437 1jdw 423 1.82e+01 1jdw d.126.1.2 41129 1ln1A 214 1.84e+01 d.129.3.2 74038 1gtmA 419 1.84e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1b43A 340 1.84e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1hr6B 443 1.87e+01 1be3A d.185.1.1 61166 d.185.1.1 61167 1fgjA 546 1.92e+01 1fgjA a.138.1.3 19679 1qk9A 92 1.92e+01 1qk9A d.10.1.3 37485 1oh0A 131 1.93e+01 d.17.4.3 87004 1rl6A 177 1.93e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1suuA 312 1.95e+01 unknown_sccs -4610 1cw0A 155 1.98e+01 1vsrA c.52.1.15 33333 1bl3A 160 2.00e+01 1b9dA c.55.3.2 33655 1isaA 192 2.00e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1shwA 138 2.02e+01 4pfk 319 2.06e+01 3pfk c.89.1.1 35582 1mpp 361 2.06e+01 2rmpA b.50.1.2 26856 1krhA 338 2.07e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1j96A 323 2.10e+01 c.1.7.1 71616 1exqA 154 2.15e+01 1b9dA c.55.3.2 33646 1ggrA 168 2.23e+01 1gpr b.84.3.1 28279 1h72C 296 2.24e+01 d.14.1.5 60712 d.58.26.1 60713 1o8bA 219 2.26e+01 unknown_sccs 81180 d.58.40.1 81181 1i4fA 275 2.26e+01 1agdA b.1.1.2 61687 d.19.1.1 61688 1gg6B 131 2.26e+01 5ptp 1g5vA 88 2.27e+01 1g5vA b.34.9.1 60292 1mr7A 209 2.28e+01 b.81.1.3 -4798 1b3qA 379 2.29e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1mdaH 368 2.31e+01 2bbkH b.69.2.1 27637 1hsbA 270 2.31e+01 1agdA b.1.1.2 20736 d.19.1.1 38257 1jh2A 99 2.33e+01 1uag 437 2.34e+01 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1dlc 584 2.35e+01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1khiA 176 2.37e+01 b.34.5.2 77408 b.40.4.5 77409 1ks2A 219 2.37e+01 unknown_sccs 72908 d.58.40.1 72909 1bgp 309 2.37e+01 1bgp a.93.1.1 18690 1ndbA 596 2.38e+01 c.43.1.3 80411 c.43.1.3 80412 1d1nA 99 2.39e+01 1d1nA b.43.3.1 25718 2kinA 238 2.40e+01 1bg2 c.37.1.9 32190 1f3fA 155 2.41e+01 1npk d.58.6.1 39101 1jotA 133 2.45e+01 1jotA 1npk 154 2.47e+01 1npk d.58.6.1 39099 1kzfA 230 2.47e+01 d.108.1.3 73354 1jeqA 609 2.50e+01 1jeqA a.140.2.1 64748 unknown_sccs -4427 unknown_sccs -7991 1g8sA 230 2.53e+01 c.66.1.3 -8047 1bowA 159 2.54e+01 1bowA d.60.1.1 39528 1avk 638 2.55e+01 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1nv8A 284 2.55e+01 c.66.1.30 86224 4uagA 437 2.57e+01 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1o5zA 442 2.63e+01 c.59.1.2 -7939 c.72.2.2 -8418 1pt1A 143 2.65e+01 b.52.2.1 -4322 1s4kA 120 2.65e+01 1p97A 114 2.69e+01 unknown_sccs -10844 1qqeA 292 2.70e+01 1qqeA a.118.8.1 19210 1aly 146 2.70e+01 1aly b.22.1.1 23856 1vsrA 136 2.75e+01 1vsrA c.52.1.15 33332 1od5A 492 2.76e+01 b.82.1.2 86832 b.82.1.2 86833 1f5mB 180 2.78e+01 1f5mB d.110.2.1 40896 1hzdA 272 2.82e+01 c.14.1.3 65969 1dqaC 467 2.83e+01 1dqaA d.58.20.1 39366 d.179.1.1 42587 1d1rA 116 2.83e+01 1d1rA d.64.1.1 39548 1jwiA 131 2.84e+01 d.169.1.1 67383 1hyvA 166 2.85e+01 1b9dA c.55.3.2 61424 1hqz9 141 2.86e+01 1n71A 180 2.87e+01 d.108.1.1 85370 1oghA 204 2.88e+01 b.85.4.1 86994 5croA 66 2.91e+01 1orc a.35.1.2 17044 1r69 69 2.91e+01 1r69 a.35.1.2 17028 1f5mA 180 2.92e+01 1f5mB d.110.2.1 40895 2btvA 901 2.93e+01 2btvA e.28.1.1 43376 1repC 251 2.94e+01 1repC a.4.5.10 16125 a.4.5.10 16126 1uanA 227 3.00e+01 unknown_sccs -8129 1jdrA 294 3.01e+01 1ryc a.93.1.1 62908 2or1L 69 3.03e+01 1r69 a.35.1.2 17031 1duzA 275 3.03e+01 1agdA b.1.1.2 20670 d.19.1.1 38224 1hbnC 248 3.03e+01 1mroC d.58.31.1 60902 1js8A 394 3.04e+01 a.86.1.1 67219 b.112.1.1 67220 1tmcA 175 3.05e+01 1agdA d.19.1.1 38258 1g4yR 148 3.08e+01 1cll a.39.1.5 60252 1bn6A 294 3.08e+01 1bn6A c.69.1.8 34678 1i58A 189 3.10e+01 1b3qA d.122.1.3 61773 1qyaA 307 3.11e+01 1ey4A 149 3.11e+01 1snc b.40.1.1 24815 1iomA 377 3.12e+01 a.103.1.1 83698 1fxjA 331 3.16e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1fxxA 482 3.17e+01 1fxxA c.55.3.5 33726 1dqaA 467 3.20e+01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1bx2B 191 3.21e+01 1iakB b.1.1.2 21610 d.19.1.1 38184 1pytA 94 3.22e+01 1pytA d.58.3.1 39064 1iscA 192 3.23e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1qtnA 164 3.25e+01 1pauA c.17.1.1 30999 1ry9A 145 3.25e+01 d.198.1.1 -9020 9ldtA 332 3.26e+01 3ldh c.2.1.5 30154 d.162.1.1 42121 1cxc 124 3.27e+01 1ycc a.3.1.1 15890 1jepA 222 3.27e+01 d.36.1.1 66612 1cqwA 295 3.27e+01 1b6g c.69.1.8 34679 1sbxA 106 3.33e+01 1ji8A 111 3.34e+01 d.203.1.1 66733 1uvqB 198 3.34e+01 b.1.1.2 -2659 d.19.1.1 -9348 1upkA 341 3.35e+01 unknown_sccs -1565 1jeyA 609 3.49e+01 1jeqA unknown_sccs -4426 unknown_sccs -7990 1eypA 222 3.54e+01 1eypA d.36.1.1 38536 2mjpA 193 3.56e+01 1b78A c.51.4.1 33223 1caxB 184 3.58e+01 1caxB b.82.1.2 28105 2madH 373 3.58e+01 2bbkH b.69.2.1 27639 1jeyB 565 3.61e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1n99A 166 3.62e+01 b.36.1.1 85459 b.36.1.1 85460 1nnvA 110 3.63e+01 unknown_sccs -9309 1giqA 413 3.65e+01 d.166.1.1 76224 d.166.1.1 76225 1vhxA 150 3.67e+01 unknown_sccs -7663 1fkd 107 3.68e+01 1fkj d.26.1.1 38383 1i7kA 179 3.68e+01 1u9aA d.20.1.1 61889 1qs1A 462 3.71e+01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1nm8A 616 3.71e+01 c.43.1.3 85872 c.43.1.3 85873 1eijA 80 3.72e+01 1eijA a.5.6.1 16298 1i18A 97 3.73e+01 b.43.4.3 61520 1du6A 64 3.75e+01 1akhA a.4.1.1 16002 1lfo 128 3.75e+01 1hmt b.60.1.2 27223 1qddA 144 3.78e+01 1qddA d.169.1.1 42324 2sas 185 3.79e+01 2sas a.39.1.5 17258 1bc8C 93 3.80e+01 1awcA a.4.5.21 16168 1mjc 69 3.80e+01 1mjc b.40.4.5 25319 1b9dA 163 3.80e+01 1b9dA c.55.3.2 33649 1h7mA 102 3.82e+01 d.79.3.1 83485 1agdA 276 3.83e+01 1agdA b.1.1.2 20741 d.19.1.1 38260 1mmoB 384 3.83e+01 1mtyB a.25.1.2 16768 1cmbA 104 3.83e+01 1cmbA unknown_sccs 17460 1djrD 103 3.85e+01 3chbD b.40.2.1 24865 1eyqA 222 3.85e+01 1eypA d.36.1.1 38534 1pg5A 299 3.86e+01 1gr8A 412 3.87e+01 1ockA 412 3.87e+01 c.117.1.1 86802 1on0A 158 3.92e+01 d.108.1.1 87095 1fbnA 230 3.97e+01 1fbnA c.66.1.3 34181 1axkA 394 3.98e+01 1axkA b.29.1.2 24181 b.29.1.11 24315