# List of top-scoring protein chains for t2k-100-30-str2 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 4.01e-04 b.85.1.1 88466 1msi 70 1.14e-03 1msi b.85.1.1 28281 1hg7A 66 1.48e-03 1msi b.85.1.1 28280 1c89A 134 5.25e-02 1msi b.85.1.1 28314 b.85.1.1 28315 1pbp 321 6.02e-01 1ixh c.94.1.1 35768 1ixh 321 6.17e-01 1ixh c.94.1.1 35761 1mgtA 174 9.26e-01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1fr2B 134 1.12e+00 d.4.1.1 83257 1bxiB 134 1.25e+00 1bxiB d.4.1.1 37136 1emvB 134 1.29e+00 1bxiB d.4.1.1 37135 1vjeA 166 2.10e+00 d.185.1.2 -10261 1qdlB 195 2.30e+00 1qdlB c.23.16.1 31437 1t0bA 252 2.41e+00 1oaoA 674 2.50e+00 e.26.1.2 86744 1innA 166 2.50e+00 1j98A d.185.1.2 62608 1l6pA 125 2.63e+00 b.1.17.1 73626 1oxwA 373 2.64e+00 c.19.1.3 87539 1dujA 187 2.86e+00 1dujA d.135.1.1 41449 1jpeA 151 2.88e+00 b.1.17.1 77146 1nftA 329 3.09e+00 1nnt c.94.1.2 35881 1bgj 394 3.30e+00 1pbe c.3.1.2 30352 d.16.1.2 37883 1iejA 332 3.55e+00 1nnt c.94.1.2 62328 1go4A 205 3.71e+00 d.135.1.1 70292 1pne 140 3.72e+00 1pne d.110.1.1 40866 1ermA 263 4.34e+00 1btl e.3.1.1 42690 1cj3A 392 4.44e+00 1pbe c.3.1.2 30347 d.16.1.2 37878 1fqgA 263 4.50e+00 1btl e.3.1.1 42699 1btl 263 4.63e+00 1btl e.3.1.1 42691 1ml9A 302 4.64e+00 b.85.7.1 79282 1k5dC 386 4.69e+00 c.10.1.2 68170 1mai 131 4.70e+00 1mai b.55.1.1 26951 1m40A 263 4.95e+00 e.3.1.1 74437 1ozjA 144 5.26e+00 d.164.1.1 -11537 2phh 394 5.47e+00 1pbe c.3.1.2 30353 d.16.1.2 37884 1q4rA 112 5.53e+00 d.58.4.4 -9943 1pbe 394 5.54e+00 1pbe c.3.1.2 30338 d.16.1.2 37869 1gceA 364 5.55e+00 1gceA e.3.1.1 42738 1q53A 112 5.67e+00 d.58.4.4 -9944 1tfaA 329 5.80e+00 1nnt c.94.1.2 35880 1fuxA 166 5.82e+00 1fjjA b.17.1.2 60034 1onhA 364 6.04e+00 e.3.1.1 -11769 1klqA 197 6.24e+00 d.135.1.1 68689 1k0iA 394 6.38e+00 c.3.1.2 67942 d.16.1.2 67943 1i50F 155 6.47e+00 d.78.1.2 61760 1ubq 76 6.96e+00 1ubi d.15.1.1 37585 1d3zA 76 7.02e+00 1ubi d.15.1.1 37592 1qqtA 551 7.04e+00 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1ogwA 76 7.26e+00 d.15.1.1 87001 1ubi 76 7.39e+00 1ubi d.15.1.1 37584 1jqlB 140 7.54e+00 c.37.1.20 63234 1qz5A 375 7.73e+00 c.55.1.1 -7590 c.55.1.1 -7591 1dr8B 344 7.85e+00 1cnzA c.77.1.1 35052 1oahA 519 7.85e+00 a.138.1.3 86736 1ga0A 364 7.94e+00 1gceA e.3.1.1 60410 1nbfD 76 7.94e+00 d.15.1.1 80390 1g1eB 89 8.12e+00 1g1eB a.59.1.1 17931 1yrgB 385 8.55e+00 1yrgA c.10.1.2 30855 1r1dA 247 8.83e+00 unknown_sccs -8335 1tedA 393 8.93e+00 1jbuL 63 8.99e+00 1hcgB g.3.11.1 62857 1jr1A 514 9.09e+00 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1aim 215 9.12e+00 1cs8A d.3.1.1 37044 1fil 139 9.67e+00 1pne d.110.1.1 40869 1c7sA 858 1.01e+01 1qba b.1.18.2 21812 b.2.2.3 22408 c.1.8.6 29011 d.92.2.1 40410 1rgzA 363 1.05e+01 e.3.1.1 -11771 1theB 260 1.07e+01 1theB d.3.1.1 37057 1q9bA 43 1.10e+01 g.3.1.1 -12392 1kliL 69 1.12e+01 g.3.11.1 77436 1cvwL 55 1.12e+01 1hcgB g.3.11.1 44211 1vybA 238 1.13e+01 1rl2A 137 1.13e+01 1rl2A b.34.5.3 24610 b.40.4.5 25342 1griA 217 1.14e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 2bltA 361 1.17e+01 1gceA e.3.1.1 42739 1q40B 219 1.19e+01 d.17.4.2 -9287 1pfvA 551 1.20e+01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1f4lA 551 1.20e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1gehA 444 1.20e+01 c.1.14.1 65181 d.58.9.1 65182 1qh0A 295 1.22e+01 b.43.4.2 68891 c.25.1.1 68892 1go2A 304 1.26e+01 b.43.4.2 76243 c.25.1.1 76244 1s5pA 235 1.26e+01 c.31.1.5 -6774 1b2rA 304 1.27e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1hev 43 1.31e+01 1hev g.3.1.1 44060 1f0xA 571 1.31e+01 1f0xA d.58.32.2 39483 d.145.1.1 41746 1theA 260 1.32e+01 1theB d.3.1.1 37056 1qwiA 143 1.33e+01 d.227.1.1 -11183 1ithA 141 1.33e+01 1ithA a.1.1.2 15623 1b71A 191 1.36e+01 1ryt a.25.1.1 16647 g.41.5.1 45246 1dvbA 191 1.37e+01 1ryt a.25.1.1 16645 g.41.5.1 45244 1ryt 190 1.38e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 1aqb 183 1.41e+01 1aqb b.60.1.1 27084 1lj5A 379 1.48e+01 e.1.1.1 73928 1amx 180 1.49e+01 1amx b.2.3.1 22410 1f37A 110 1.52e+01 1f37A c.47.1.11 33088 1rcqA 357 1.55e+01 1bpwA 503 1.55e+01 1bpwA c.82.1.1 35365 1mo9A 523 1.59e+01 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1nzoA 363 1.68e+01 b.105.1.1 -2933 e.3.1.1 -11784 1f8gA 384 1.70e+01 1sayA c.2.1.4 59695 c.23.12.2 59696 1yrgA 385 1.70e+01 1yrgA c.10.1.2 30854 1j6rA 214 1.73e+01 d.173.1.2 71598 1l7dA 384 1.76e+01 c.2.1.4 77774 c.23.12.2 77775 2reb 352 1.77e+01 2reb c.37.1.11 32282 d.48.1.1 38767 1sv6A 269 1.78e+01 1ji0A 240 1.79e+01 c.37.1.12 71665 1nj4A 363 1.81e+01 b.105.1.1 80545 e.3.1.1 80546 1wgtA 186 1.81e+01 9wgaA g.3.1.1 44008 g.3.1.1 44009 g.3.1.1 44010 g.3.1.1 44011 2btfA 375 1.82e+01 1yagA c.55.1.1 33429 c.55.1.1 33430 1vk4A 298 1.88e+01 c.72.1.1 -8414 1que 303 1.93e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1fnmA 691 1.94e+01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1i8nA 126 1.97e+01 1i8nA g.10.1.2 61976 1cuk 203 1.98e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1nd4A 264 2.09e+01 d.144.1.6 -11381 1f1uA 323 2.09e+01 d.32.1.3 83200 d.32.1.3 83201 1vj1A 363 2.18e+01 b.35.1.2 -3728 c.2.1.1 -5752 1ogiA 303 2.18e+01 b.43.4.2 -4042 c.25.1.1 -6587 1nnt 328 2.19e+01 1nnt c.94.1.2 35884 1fit 147 2.24e+01 1fit d.13.1.1 37499 1jeyB 565 2.25e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1m5sA 297 2.25e+01 d.58.33.1 74511 d.58.33.1 74512 1d4xA 375 2.25e+01 1yagA c.55.1.1 59107 c.55.1.1 59108 1di1A 300 2.26e+01 1di1A a.128.1.4 19446 1hd8A 363 2.28e+01 b.105.1.1 65803 e.3.1.1 65804 1m2bA 110 2.32e+01 c.47.1.11 78474 1m2aA 110 2.32e+01 c.47.1.11 78472 1m2dA 110 2.45e+01 c.47.1.11 78476 1ujnA 348 2.46e+01 e.22.1.1 -11998 1rqlA 267 2.49e+01 c.108.1.3 -6814 1mhdA 132 2.50e+01 1mhdA d.164.1.1 42175 1ejbA 168 2.59e+01 1rvv1 c.16.1.1 59417 1me4A 215 2.61e+01 d.3.1.1 79023 1r13A 148 2.62e+01 d.169.1.1 -11646 h.1.1.1 -12895 1ew3A 159 2.66e+01 1mup b.60.1.1 27114 1f2aA 215 2.68e+01 1cs8A d.3.1.1 37040 1me3A 215 2.70e+01 d.3.1.1 79022 9wgaA 171 2.70e+01 9wgaA g.3.1.1 44000 g.3.1.1 44001 g.3.1.1 44002 g.3.1.1 44003 1a4sA 503 2.71e+01 1bpwA c.82.1.1 35361 1xxaA 78 2.78e+01 1xxaA d.74.2.1 39700 1prxA 224 2.79e+01 1prxA c.47.1.10 33076 1j6zA 376 2.81e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 1jeqB 565 2.81e+01 1jeqB unknown_sccs -4432 unknown_sccs -7996 1kfuS 184 2.81e+01 a.39.1.8 68574 1jsqA 582 2.90e+01 i.13.1.1 63270 1f1xA 322 2.90e+01 d.32.1.3 83208 d.32.1.3 83209 1hjp 203 2.97e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1r53A 382 3.01e+01 unknown_sccs -11177 1qpsA 261 3.01e+01 1ckqA c.52.1.1 33234 1vns 609 3.08e+01 1vns a.111.1.3 19061 2sas 185 3.09e+01 2sas a.39.1.5 17258 1awcB 153 3.14e+01 1bd8 d.211.1.1 19156 1ej6A 1289 3.20e+01 i.7.1.1 45967 1egiA 147 3.20e+01 1eggA d.169.1.1 42331 1fezA 256 3.20e+01 1fezA c.108.1.3 43343 1tqyA 424 3.25e+01 1qba 858 3.26e+01 1qba b.1.18.2 21810 b.2.2.3 22406 c.1.8.6 29009 d.92.2.1 40408 1dlc 584 3.27e+01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1ihfA 99 3.33e+01 1huuA a.55.1.1 17893 1cl8A 276 3.34e+01 1ckqA c.52.1.1 33230 1n3jA 119 3.34e+01 b.85.7.2 79963 1rusA 490 3.35e+01 1burA c.1.14.1 29388 d.58.9.1 39294 1jraA 117 3.36e+01 a.24.15.1 67117 1i6aA 219 3.38e+01 c.94.1.1 61827 1a7cA 379 3.39e+01 1sek e.1.1.1 42660 1ljoA 77 3.41e+01 b.38.1.1 73941 1ggzA 148 3.41e+01 a.39.1.5 70176 2fhi 147 3.43e+01 1fit d.13.1.1 37505 1ft1B 437 3.44e+01 1ft1B a.102.4.3 18867 1udzA 182 3.45e+01 b.51.1.1 -4307 3ullA 132 3.49e+01 3ullA b.40.4.3 25282 1ckqA 276 3.49e+01 1ckqA c.52.1.1 33229 1owfA 99 3.50e+01 a.55.1.1 87487 1vnc 609 3.51e+01 1vns a.111.1.3 19065 1p9yA 121 3.52e+01 unknown_sccs -8996 1kvlA 358 3.57e+01 e.3.1.1 73062 1ile 821 3.57e+01 1ile a.27.1.1 16924 b.51.1.1 26889 c.26.1.1 31591 1iyu 79 3.62e+01 1iyu b.84.1.1 28227 1d8dB 437 3.63e+01 1ft1B a.102.4.3 18866 1jr8A 117 3.65e+01 a.24.15.1 67115 1ohuA 175 3.66e+01 f.1.4.1 -12058 2bnh 457 3.66e+01 1a4yA c.10.1.1 30850 1fmk 452 3.66e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.7 41690 1mpgA 282 3.67e+01 1mpgA a.96.1.3 18747 d.129.1.2 41296 1xyzA 347 3.69e+01 1taxA c.1.8.3 28804 1mkeA 152 3.70e+01 b.55.1.4 79231 1l0gA 358 3.70e+01 e.3.1.1 73400 1fr1A 361 3.74e+01 1gceA e.3.1.1 42734 1idm 343 3.75e+01 1cnzA c.77.1.1 35035 1copD 66 3.75e+01 1orc a.35.1.2 17058 1fwcA 100 3.78e+01 1ubpA d.8.1.1 37331 1ejxA 100 3.78e+01 d.8.1.1 83182 2kauA 100 3.81e+01 1ubpA d.8.1.1 37335 1gkkA 297 3.81e+01 c.69.1.2 65248 1jvwA 167 3.85e+01 d.26.1.1 71907 1eggA 147 3.87e+01 1eggA d.169.1.1 42333 1eayC 74 3.91e+01 1eayC d.58.24.1 39386 1v5xA 203 3.91e+01 c.1.2.4 -5169 1bw9A 356 3.91e+01 1bw9A c.2.1.7 30274 c.58.1.1 33922 1ipd 345 3.94e+01 1cnzA c.77.1.1 35038 1yagA 375 3.97e+01 1yagA c.55.1.1 33449 c.55.1.1 33450 1gklA 297 3.98e+01 c.69.1.2 65250