# 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 1khhA 198 2.09e-01 c.66.1.16 68615 1lpuA 332 2.38e-01 1jj2M 186 1.44e+00 1ffkK c.55.4.1 63098 1ab4 477 2.02e+00 1ab4 e.11.1.1 43251 1ffkK 186 2.53e+00 1ffkK c.55.4.1 33731 3pmgA 561 2.74e+00 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1lxtA 561 3.22e+00 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1qnnA 191 3.27e+00 1avmA a.2.11.1 15792 d.44.1.1 38755 1jqsC 68 3.82e+00 i.1.1.1 63239 1howA 373 3.96e+00 1hcl d.144.1.1 41679 1f0yA 302 4.40e+00 2hdhA a.100.1.3 18793 c.2.1.6 30197 2hdhA 293 4.50e+00 2hdhA a.100.1.3 18795 c.2.1.6 30199 1jg5A 83 4.55e+00 d.205.1.1 66666 1qqvA 67 4.77e+00 1qqvA a.14.1.1 16379 1sknP 92 4.87e+00 1sknP a.37.1.1 17127 1a7tA 232 5.22e+00 1a7tA d.157.1.1 42041 3ygsP 97 5.24e+00 3ygsP a.77.1.1 18435 1eswA 500 5.59e+00 1cwyA c.1.8.1 59500 1jl5A 454 5.61e+00 c.10.2.6 66830 4lbd 267 5.64e+00 2lbd a.123.1.1 19289 1ihp 438 5.65e+00 1ihp c.60.1.3 33993 1vii 36 5.73e+00 1vii a.14.1.1 16378 1fcyA 236 5.75e+00 2lbd a.123.1.1 19282 1i2mA 216 5.99e+00 1byuA c.37.1.8 61568 1g9uA 454 6.27e+00 c.10.2.6 65172 1hv8A 367 6.54e+00 1hv8A c.37.1.13 32405 c.37.1.13 32406 1j7nA 776 7.04e+00 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1cwyA 500 7.10e+00 1cwyA c.1.8.1 28789 1aep 161 7.13e+00 1aep a.63.1.1 18139 1rypA 243 7.21e+00 1pmaA d.153.1.4 41932 1qh8B 519 7.34e+00 1qguB c.92.2.3 35634 1b00A 127 7.50e+00 3chy c.23.1.1 31122 2lbd 267 7.56e+00 2lbd a.123.1.1 19287 1qguB 519 7.62e+00 1qguB c.92.2.3 35626 1nar 290 7.75e+00 1nar c.1.8.5 28988 1euaA 213 8.29e+00 1fwrA c.1.10.1 29155 1a26 361 8.48e+00 1a26 a.41.1.1 17412 d.166.1.2 42274 3nodB 423 8.51e+00 1nseA d.174.1.1 42513 1smtB 122 8.56e+00 1smtA a.4.5.5 16110 1l0wA 580 8.57e+00 1ax4A 467 8.89e+00 1ax4A c.67.1.2 34391 1b3qA 379 9.22e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1smtA 122 9.33e+00 1smtA a.4.5.5 16109 1nbcA 155 9.96e+00 1nbcA b.2.2.2 22390 1jr8A 117 1.01e+01 a.24.15.1 67115 1jraA 117 1.02e+01 a.24.15.1 67117 1lkzA 219 1.02e+01 1fq0A 213 1.06e+01 1fwrA c.1.10.1 29161 1jjoC 261 1.12e+01 1uch 230 1.16e+01 1uch d.3.1.6 37129 1g99A 408 1.19e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1efyA 350 1.19e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1ffyA 917 1.24e+01 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 1.24e+01 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1qj4A 257 1.25e+01 1qj4A c.69.1.20 34796 1lr0A 129 1.30e+01 1i0hA 205 1.31e+01 1avmA a.2.11.1 15760 d.44.1.1 38685 1d5nA 205 1.33e+01 1avmA a.2.11.1 15762 d.44.1.1 38687 2cae 484 1.40e+01 1cf9A e.5.1.1 42810 2tysA 268 1.40e+01 2tysA c.1.2.4 28572 1yasA 257 1.42e+01 1qj4A c.69.1.20 34801 1fewA 184 1.43e+01 1fewA a.7.4.1 16334 1dar 691 1.45e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1ddt 535 1.46e+01 1ddt b.2.1.1 22379 d.166.1.1 42241 f.1.2.1 43384 1dc1A 323 1.52e+01 1dc1A c.52.1.11 33321 1aew 174 1.55e+01 2fha a.25.1.1 16676 1cc8A 73 1.58e+01 1cc8A d.58.17.1 39343 1g73A 162 1.61e+01 1fewA a.7.4.1 16332 1thv 207 1.63e+01 1thv b.25.1.1 23904 1ewaA 137 1.63e+01 1ewaA a.1.1.2 15639 1gsa 316 1.64e+01 1gsa c.30.1.3 31718 d.142.1.1 41477 1anxA 319 1.69e+01 1avc a.65.1.1 18161 1ew6A 137 1.69e+01 1ewaA a.1.1.2 15637 1zymA 258 1.71e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1byuA 216 1.71e+01 1byuA c.37.1.8 32032 1uag 437 1.74e+01 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1kdxA 81 1.83e+01 1kdxA a.12.1.1 16375 1eemA 241 1.90e+01 1eemA a.45.1.1 17717 c.47.1.5 33011 1ca1 370 1.91e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1jp3A 253 1.92e+01 1f75A c.101.1.1 63221 1floA 422 1.96e+01 1floA a.60.9.1 18106 d.163.1.1 42166 1a28A 256 1.96e+01 1a28A a.123.1.1 19290 1ew6B 137 2.01e+01 1ewaA a.1.1.2 15638 1gm5A 780 2.03e+01 a.29.4.1 65298 b.40.4.9 65299 c.37.1.13 65300 c.37.1.13 65301 1tdj 514 2.04e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 3uagA 437 2.14e+01 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 1jygA 69 2.15e+01 a.60.11.1 67457 1hekA 131 2.17e+01 a.61.1.5 65818 4uagA 437 2.17e+01 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 16pk 415 2.18e+01 16pk c.86.1.1 35454 1a16 440 2.20e+01 1az9 c.55.2.1 33548 d.127.1.1 41165 1efdN 266 2.22e+01 1efdN c.92.2.1 35597 1xwl 580 2.27e+01 1xwl c.55.3.5 33708 e.8.1.1 43001 1qnrA 344 2.28e+01 1qnoA c.1.8.3 28834 1cx8A 639 2.29e+01 1cx8B a.48.2.1 17782 c.8.4.1 30763 c.56.5.5 33851 1qnoA 344 2.30e+01 1qnoA c.1.8.3 28838 4pfk 319 2.32e+01 3pfk c.89.1.1 35582 1jmtA 104 2.33e+01 d.58.7.3 63180 1jvr 137 2.35e+01 1jvr a.61.1.2 18132 1szt 68 2.37e+01 1aikN h.3.2.1 45725 1cx8B 639 2.40e+01 1cx8B a.48.2.1 17783 c.8.4.1 30764 c.56.5.5 33852 1jilA 420 2.43e+01 c.26.1.1 66745 1j4wA 174 2.48e+01 1im4A 221 2.50e+01 e.8.1.5 62581 1dat 174 2.54e+01 2fha a.25.1.1 16677 1jhdA 396 2.56e+01 b.58.1.2 66712 c.26.1.5 66713 1cec 343 2.65e+01 1ceo c.1.8.3 28809 6pfkA 319 2.66e+01 3pfk c.89.1.1 35583 1gh8A 89 2.70e+01 1gh8A d.58.12.1 39309 1f2vA 219 2.75e+01 1f2vA c.23.17.1 59627 1f0lA 535 2.77e+01 1ddt b.2.1.1 22377 d.166.1.1 42239 f.1.2.1 43382 1g8mA 593 2.84e+01 1g8mA c.24.1.3 60371 c.97.2.1 60372 1bag 425 2.87e+01 1bag b.71.1.1 27720 c.1.8.1 28707 1ceo 343 2.90e+01 1ceo c.1.8.3 28808 2end 138 2.90e+01 2end a.18.1.1 16400 1blxA 326 3.01e+01 1hcl d.144.1.1 41596 3fib 249 3.08e+01 3fib d.171.1.1 42455 1edt 271 3.10e+01 2ebn c.1.8.5 28993 1envA 123 3.12e+01 1envA h.3.2.1 45726 1jr3E 334 3.12e+01 a.80.1.1 63253 c.37.1.13 63254 1idsA 207 3.13e+01 1avmA a.2.11.1 15722 d.44.1.1 38730 1dxrH 258 3.21e+01 6prcH b.41.1.1 25456 f.2.1.2 43433 1g5tA 196 3.25e+01 1g5rA c.37.1.11 32366 1vasA 137 3.26e+01 2end a.18.1.1 16404 1thw 207 3.33e+01 1thv b.25.1.1 23903 1trrA 107 3.33e+01 1jhgA a.107.1.1 19017 1ktgA 138 3.36e+01 1fwrA 213 3.42e+01 1fwrA c.1.10.1 29164 3bdpA 580 3.45e+01 1xwl c.55.3.5 33711 e.8.1.1 43004 1i1hA 219 3.48e+01 1f2vA c.23.17.1 61530 1c20A 128 3.51e+01 1c20A a.4.3.1 16079 1i58A 189 3.55e+01 1b3qA d.122.1.3 61773 1apa 266 3.63e+01 1qi7A d.165.1.1 42205 1hsbA 270 3.63e+01 1agdA b.1.1.2 20736 d.19.1.1 38257 2bdpA 580 3.65e+01 1xwl c.55.3.5 33709 e.8.1.1 43002 3pfk 319 3.68e+01 3pfk c.89.1.1 35581 1qtwA 285 3.68e+01 1qumA c.1.15.1 29392 1qovH 260 3.72e+01 6prcH b.41.1.1 25464 f.2.1.2 43457 1ae9A 179 3.72e+01 1ae9A d.163.1.1 42153 2minB 522 3.73e+01 1qguB c.92.2.3 35610 1kskA 234 3.76e+01 1g5rA 196 3.86e+01 1g5rA c.37.1.11 32367 1fib 269 3.90e+01 3fib d.171.1.1 42456 1qumA 285 3.94e+01 1qumA c.1.15.1 29393 1knvA 293 3.97e+01 c.52.1.7 68707 1eg7A 557 3.99e+01 1eg7A c.37.1.10 32241