# List of top-scoring protein chains for t2k-100-30-bys 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 1ucsA 64 8.16e-05 b.85.1.1 88466 1msi 70 1.38e-04 1msi b.85.1.1 28281 1c89A 134 2.09e-04 1msi b.85.1.1 28314 b.85.1.1 28315 1hg7A 66 1.13e-03 1msi b.85.1.1 28280 1lfaA 187 3.96e-02 1ido c.62.1.1 34122 1mjnA 179 6.84e-02 c.62.1.1 79210 1dgqA 188 1.45e-01 1ido c.62.1.1 34131 2wrpR 107 1.62e-01 1jhgA a.4.12.1 19010 1trrA 107 1.98e-01 1jhgA a.4.12.1 19017 1jhgA 101 2.22e-01 1jhgA a.4.12.1 19009 1amx 180 4.05e-01 1amx b.2.3.1 22410 1ml9A 302 4.40e-01 b.85.7.1 79282 1a3aA 148 5.49e-01 1a3aA d.112.1.1 40917 1a3aC 148 7.52e-01 1a3aA d.112.1.1 40919 1n7kA 234 9.06e-01 c.1.10.1 85374 1io2A 213 9.26e-01 1ekeA c.55.3.1 62612 1n9lA 109 1.01e+00 d.110.3.6 85468 1vjeA 166 1.02e+00 d.185.1.2 -10261 1yprA 125 1.02e+00 3nul d.110.1.1 40888 1pcfA 66 1.06e+00 1pcfA d.18.1.1 38142 1bo4B 168 1.11e+00 1bo4A d.108.1.1 40799 1bo4A 168 1.19e+00 1bo4A d.108.1.1 40798 1o5oA 221 1.19e+00 c.61.1.1 -7954 1nnt 328 1.54e+00 1nnt c.94.1.2 35884 1tk1A 260 1.96e+00 1f4qA 165 2.09e+00 1alvA a.39.1.8 17360 1jsxA 207 2.15e+00 c.66.1.20 71846 1plr 258 2.19e+00 1plq d.131.1.2 41390 d.131.1.2 41391 1js8A 394 2.39e+00 a.86.1.1 67219 b.112.1.1 67220 1oo0A 147 2.42e+00 d.232.1.1 87182 1ba1 386 2.45e+00 1ba1 c.55.1.1 33387 c.55.1.1 33388 1bupA 386 2.46e+00 1ba1 c.55.1.1 33377 c.55.1.1 33378 1kblA 873 2.86e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1lgyA 269 2.97e+00 3tgl c.69.1.17 34758 1innA 166 3.02e+00 1j98A d.185.1.2 62608 1el6B 219 3.08e+00 1el6B d.182.1.1 42607 1dik 874 3.08e+00 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1nftA 329 3.13e+00 1nnt c.94.1.2 35881 1ido 192 3.25e+00 1ido c.62.1.1 34139 1iejA 332 3.40e+00 1nnt c.94.1.2 62328 1jlm 192 3.43e+00 1ido c.62.1.1 34140 1mf7A 194 3.44e+00 c.62.1.1 84937 1go4A 205 3.78e+00 d.135.1.1 70292 1jj2U 70 3.78e+00 1ffkS a.2.2.1 63106 1s72V 71 3.80e+00 1ao0A 459 4.02e+00 1ecfB c.61.1.1 34049 d.153.1.1 41816 1kay 381 4.07e+00 1ba1 c.55.1.1 33385 c.55.1.1 33386 1emvB 134 4.27e+00 1bxiB d.4.1.1 37135 1plq 258 4.27e+00 1plq d.131.1.2 41388 d.131.1.2 41389 1k94A 165 4.91e+00 a.39.1.8 68333 1el6A 219 5.11e+00 1el6B d.182.1.1 42606 1jpeA 151 5.14e+00 b.1.17.1 77146 1ujnA 348 5.16e+00 e.22.1.1 -11998 1kfuS 184 5.36e+00 a.39.1.8 68574 1rcsA 105 5.64e+00 1jhgA a.4.12.1 19025 1rh5B 74 6.07e+00 unknown_sccs -12198 1r13A 148 6.13e+00 d.169.1.1 -11646 h.1.1.1 -12895 1rl2A 137 6.51e+00 1rl2A b.34.5.3 24610 b.40.4.5 25342 1nq7A 244 6.54e+00 a.123.1.1 -1682 1s5pA 235 6.86e+00 c.31.1.5 -6774 1fr2B 134 7.00e+00 d.4.1.1 83257 1l6pA 125 7.04e+00 b.1.17.1 73626 1k4wA 252 7.32e+00 a.123.1.1 72068 1a8h 500 7.43e+00 1a8h a.27.1.1 16922 c.26.1.1 31589 1r1uA 106 7.84e+00 1bxiB 134 7.98e+00 1bxiB d.4.1.1 37136 1h1nA 305 8.11e+00 c.1.8.3 70855 2sas 185 8.12e+00 2sas a.39.1.5 17258 1d8iA 311 8.41e+00 1d8iA d.63.1.1 39541 1eljA 381 8.66e+00 4mbp c.94.1.1 35791 1mnaA 298 8.76e+00 c.69.1.22 79322 1yagA 375 8.85e+00 1yagA c.55.1.1 33449 c.55.1.1 33450 1f7wA 144 9.02e+00 1f46A d.129.4.1 59679 1tfaA 329 9.05e+00 1nnt c.94.1.2 35880 1lkoA 191 9.06e+00 a.25.1.1 78063 g.41.5.1 78064 1dvbA 191 1.00e+01 1ryt a.25.1.1 16645 g.41.5.1 45244 1jbaA 204 1.02e+01 1rec a.39.1.5 17330 1cnpA 90 1.04e+01 4icb a.39.1.2 17161 1ssn 136 1.07e+01 2sak d.15.5.1 37720 1ryt 190 1.08e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 1p5hA 428 1.09e+01 c.123.1.1 87802 1hy0A 466 1.10e+01 1auwA a.127.1.1 61392 1g5yA 238 1.14e+01 1lbd a.123.1.1 60294 1i8nA 126 1.14e+01 1i8nA g.10.1.2 61976 1qz5A 375 1.15e+01 c.55.1.1 -7590 c.55.1.1 -7591 1f1uA 323 1.17e+01 d.32.1.3 83200 d.32.1.3 83201 1o20A 427 1.21e+01 c.82.1.1 86556 3tgl 269 1.25e+01 3tgl c.69.1.17 34733 1olsB 342 1.25e+01 c.36.1.7 -6919 c.48.1.2 -7529 1b71A 191 1.28e+01 1ryt a.25.1.1 16647 g.41.5.1 45246 1nu4A 97 1.30e+01 d.58.7.1 80731 1fwrA 213 1.31e+01 1fwrA c.1.10.1 29164 1oaoA 674 1.32e+01 e.26.1.2 86744 1ns5A 155 1.34e+01 c.116.1.3 80705 1qhbA 596 1.41e+01 1qhbA a.111.1.2 19055 1tfe 145 1.42e+01 1tfe d.43.1.1 38680 1mhdA 132 1.45e+01 1mhdA d.164.1.1 42175 1lfb 99 1.47e+01 1lfb a.4.1.1 15989 1v4xB 146 1.49e+01 1kyqA 274 1.50e+01 c.2.1.11 73281 e.37.1.1 73282 1jbuL 63 1.51e+01 1hcgB g.3.11.1 62857 1jakA 512 1.52e+01 c.1.8.6 66472 d.92.2.1 66473 1kliL 69 1.53e+01 g.3.11.1 77436 1f46A 140 1.54e+01 1f46A d.129.4.1 59643 1duvG 333 1.54e+01 1othA c.78.1.1 35228 c.78.1.1 35229 1gp1A 198 1.58e+01 1gp1A c.47.1.10 33059 1o0xA 262 1.59e+01 d.127.1.1 80755 1euaA 213 1.60e+01 1fwrA c.1.10.1 29155 1c0pA 363 1.60e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1urnA 97 1.62e+01 1urnA d.58.7.1 39153 1kjqA 391 1.64e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1k8eA 345 1.67e+01 1o17A 345 1.67e+01 a.46.2.1 80765 c.27.1.1 80766 1lbd 282 1.69e+01 1lbd a.123.1.1 19279 1ejeA 192 1.71e+01 1ejeA b.45.1.2 25757 1mznA 240 1.76e+01 a.123.1.1 79704 1fslA 143 1.78e+01 2gdm a.1.1.2 15229 1xxaA 78 1.79e+01 1xxaA d.74.2.1 39700 1q4rA 112 1.80e+01 d.58.4.4 -9943 1fq0A 213 1.81e+01 1fwrA c.1.10.1 29161 1cvwL 55 1.82e+01 1hcgB g.3.11.1 44211 2dpg 485 1.83e+01 1dpgA c.2.1.3 30076 d.81.1.5 39991 1yacA 208 1.85e+01 1yacA unknown_sccs 31757 1hxhA 253 1.85e+01 c.2.1.2 76725 1sctB 151 1.85e+01 3sdhA a.1.1.2 15003 1s4nA 348 1.88e+01 unknown_sccs -8262 2bdpA 580 1.89e+01 1xwl c.55.3.5 33709 e.8.1.1 43002 1eyzA 392 1.91e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1r26A 125 1.92e+01 c.47.1.1 -7389 1kxu 333 1.93e+01 1jkw a.74.1.1 18358 a.74.1.1 18359 1v7zA 260 1.96e+01 unknown_sccs -6353 1oiaA 95 1.96e+01 d.58.7.1 87051 1q53A 112 2.01e+01 d.58.4.4 -9944 1eriA 276 2.02e+01 1ckqA c.52.1.1 33231 1cpt 412 2.06e+01 1cpt a.104.1.1 18968 1ez1A 392 2.07e+01 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1l4uA 176 2.08e+01 c.37.1.2 73568 2bmhA 455 2.09e+01 1bu7A a.104.1.1 18941 1bw9A 356 2.13e+01 1bw9A c.2.1.7 30274 c.58.1.1 33922 1f47B 144 2.14e+01 1f46A d.129.4.1 59645 1rqlA 267 2.15e+01 c.108.1.3 -6814 1a76 326 2.16e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1ee8A 266 2.16e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1ithA 141 2.17e+01 1ithA a.1.1.2 15623 1kcqA 104 2.18e+01 d.109.1.1 68449 1jndA 420 2.19e+01 c.1.8.5 71757 d.26.3.1 71758 1hp5A 512 2.21e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 2bc2A 227 2.23e+01 1a7tA d.157.1.1 42031 1sv6A 269 2.23e+01 1iw7C 1119 2.24e+01 e.29.1.1 71474 2sak 121 2.26e+01 2sak d.15.5.1 37711 1hdhA 536 2.27e+01 c.76.1.2 65805 1d0qA 103 2.31e+01 1d0qA g.41.3.2 45208 1hp4A 512 2.32e+01 1hp4A c.1.8.6 61111 d.92.2.1 61112 3pvaA 335 2.36e+01 3pvaA d.153.1.3 41854 1v1rB 342 2.39e+01 1mqoA 227 2.41e+01 1c76A 136 2.42e+01 2sak d.15.5.1 37718 1ugiA 84 2.42e+01 1ugiA d.17.5.1 38125 1l3aA 228 2.46e+01 d.18.1.2 73531 1ab4 477 2.46e+01 1ab4 e.11.1.1 43251 1c1dA 355 2.47e+01 1bw9A c.2.1.7 30270 c.58.1.1 33918 1ji0A 240 2.49e+01 c.37.1.12 71665 1o0pA 104 2.49e+01 d.58.7.1 86535 1lvaA 258 2.49e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1scfA 273 2.50e+01 1exzA a.26.1.2 16873 1r62A 160 2.51e+01 1ughI 82 2.54e+01 1ugiA d.17.5.1 38133 1jqlB 140 2.55e+01 c.37.1.20 63234 1j6zA 376 2.56e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 1g5cA 170 2.58e+01 1g5cA c.53.2.1 60264 1pc6A 146 2.58e+01 unknown_sccs -11739 1q8fA 313 2.59e+01 c.70.1.1 -8358 1vi2A 300 2.59e+01 c.2.1.7 -5960 c.58.1.5 -6366 1dpgA 485 2.60e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1gjxA 81 2.61e+01 b.84.1.1 65222 1pmt 203 2.62e+01 1a0fA a.45.1.1 17740 c.47.1.5 33034 1dtwB 342 2.63e+01 1qs0B c.36.1.7 31828 c.48.1.2 33102 1mkeA 152 2.64e+01 b.55.1.4 79231 1vimA 200 2.66e+01 c.80.1.3 -8532 1btmA 252 2.68e+01 1amk c.1.1.1 28513 1qycA 308 2.69e+01 c.2.1.2 -5782 1g8iA 190 2.70e+01 1rec a.39.1.5 60363 1wdcC 156 2.71e+01 1wdcC a.39.1.5 17317 1oh0A 131 2.71e+01 d.17.4.3 87004 1oaqH 121 2.72e+01 b.1.1.1 -2287 1spgA 144 2.75e+01 1abwA a.1.1.2 15409 1jfvA 131 2.78e+01 c.44.1.1 66654 1up8A 598 2.79e+01 a.111.1.2 -1480 1oahA 519 2.82e+01 a.138.1.3 86736 1qc9A 276 2.82e+01 1ckqA c.52.1.1 33235 1fl0A 171 2.84e+01 1eujA b.40.4.4 25315 1kjs 74 2.84e+01 1kjs a.50.1.1 17792 1mkaA 171 2.87e+01 1mkaA d.38.1.2 38543 1d4xA 375 2.88e+01 1yagA c.55.1.1 59107 c.55.1.1 59108 1qgeE 97 2.93e+01 1cvl 1dvjA 246 2.94e+01 1dvjA c.1.2.3 28546 1udiI 83 2.95e+01 1ugiA d.17.5.1 38124 1ga8A 311 2.98e+01 1ga8A c.68.1.4 34516 1rypK 198 2.98e+01 d.153.1.4 41879 1k0eA 453 3.00e+01 d.161.1.1 67938 1p8xA 344 3.03e+01 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1l7dA 384 3.04e+01 c.2.1.4 77774 c.23.12.2 77775 2pvaA 345 3.06e+01 3pvaA d.153.1.3 41850 1g9rA 311 3.08e+01 1ga8A c.68.1.4 34517 1vhmA 195 3.08e+01 d.110.2.1 -10828 1vi9A 299 3.10e+01 c.72.1.5 -8393 1g2rA 100 3.14e+01 1g2rA d.192.1.1 60231 1h2xA 710 3.17e+01 b.69.7.1 76598 c.69.1.4 76599 1k0gA 453 3.19e+01 d.161.1.1 67940 1xxbA 78 3.19e+01 1xxaA d.74.2.1 39706 1d3bA 75 3.21e+01 1d3bA b.38.1.1 24798 1n4kA 381 3.22e+01 unknown_sccs 79992 b.42.6.1 79993 2lfb 100 3.26e+01 1lfb a.4.1.1 15990 1o7bT 98 3.27e+01 d.169.1.4 -11647 1fit 147 3.29e+01 1fit d.13.1.1 37499 1yrgA 385 3.29e+01 1yrgA c.10.1.2 30854 1dkxA 219 3.40e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 1ejxA 100 3.41e+01 d.8.1.1 83182 2bc2B 227 3.44e+01 1a7tA d.157.1.1 42032 1i1iP 681 3.44e+01 1i1iP d.92.1.5 40297 1d7yA 408 3.45e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1s96A 219 3.51e+01 c.37.1.1 -6972 1opy 131 3.55e+01 1opy d.17.4.3 38113 2hgsA 474 3.55e+01 2hgsA c.30.1.4 31722 d.142.1.6 75997 1hkkA 364 3.58e+01 c.1.8.5 -5384 d.26.3.1 -9506 1gq2A 555 3.58e+01 c.2.1.7 70308 c.58.1.3 70309 1lg2A 365 3.62e+01 c.1.8.5 77950 d.26.3.1 77951 1cll 148 3.62e+01 1cll a.39.1.5 17263 1jf8A 131 3.62e+01 c.44.1.1 66621 1dryA 324 3.65e+01 1drtA b.82.2.2 28128 1jmeA 455 3.66e+01 a.104.1.1 66885 1m5sA 297 3.67e+01 d.58.33.1 74511 d.58.33.1 74512 1uw6A 211 3.67e+01 b.96.1.1 -3077 1npdA 288 3.67e+01 c.2.1.7 80681 c.58.1.5 80682 1ds1A 324 3.69e+01 1drtA b.82.2.2 28127 1dcnD 436 3.70e+01 1auwA a.127.1.1 19423 1eujA 166 3.72e+01 1eujA b.40.4.4 25316 1m0wA 491 3.73e+01 c.30.1.4 78363 d.142.1.6 78364 1a6wH 120 3.75e+01 1mfa b.1.1.1 20253 1kjvA 284 3.84e+01 b.1.1.2 77421 d.19.1.1 77422 1f9yA 158 3.87e+01 d.58.30.1 83249 1seiA 130 3.94e+01 1seiA d.140.1.1 41463