# List of top-scoring protein chains for t04-100-30-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 1h2kA 349 8.07e-29 b.82.2.6 76572 1dgwA 178 1.37e-04 1dgwA b.82.1.2 28090 1fi2A 201 2.61e-04 1fi2A b.82.1.2 59845 2arcA 164 6.99e-04 2arcA b.82.4.1 28148 1o4tA 133 1.69e-03 b.82.1.9 86622 1j58A 385 1.79e-03 b.82.1.2 71531 1qwrA 319 2.49e-03 1lr5A 163 3.33e-03 b.82.1.2 74215 1qxrA 189 3.80e-03 1plzA 189 4.32e-03 b.82.1.7 88160 1e5rA 290 5.39e-03 1e5rA b.82.2.4 59276 1a8s 273 2.83e-02 1brt c.69.1.12 34710 1od5A 492 6.81e-02 b.82.1.2 86832 b.82.1.2 86833 2phlA 397 1.13e-01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1ko3A 230 1.28e-01 1hu4A 288 1.29e-01 1hu4A 1n5dA 288 1.48e-01 c.2.1.2 80030 1nrfA 262 2.16e-01 1dgwY 93 2.52e-01 1caxB 1jm6A 407 3.07e-01 a.29.5.1 66876 d.122.1.4 66877 1mrzA 293 3.12e-01 1htqA 477 3.76e-01 d.15.9.1 71035 d.128.1.1 71036 1az9 457 4.70e-01 1az9 c.55.2.1 33547 d.127.1.1 41164 1ofnA 205 4.85e-01 1knwA 425 4.93e-01 1dgwX 79 5.51e-01 1caxB b.82.1.2 28091 1nxmA 197 5.76e-01 b.82.1.1 86385 1oi6A 205 6.57e-01 1o5uA 101 7.61e-01 1g291 372 7.95e-01 1g291 1gx3A 284 8.96e-01 d.3.1.5 70678 1vpt 348 9.21e-01 3mag c.66.1.25 34207 1a53 247 1.24e+00 1a53 c.1.2.4 28564 1ojxA 263 1.24e+00 1uwvA 433 1.36e+00 1rthA 560 1.44e+00 1rthA c.55.3.1 33576 e.8.1.2 43028 1igs 248 1.56e+00 1a53 c.1.2.4 28565 1v39 322 1.64e+00 3mag c.66.1.25 34206 1rcf 169 1.64e+00 1rcf c.23.5.1 31170 1uok 558 1.70e+00 1uok b.71.1.1 27801 c.1.8.1 28788 1vp9 322 1.71e+00 3mag c.66.1.25 34210 1ly1A 181 1.71e+00 c.37.1.1 74334 1iupA 282 1.75e+00 c.69.1.10 76815 1j8fA 323 1.88e+00 1j8fA c.31.1.5 62738 1byqA 228 1.95e+00 1yer d.122.1.1 41100 1vrtA 560 2.33e+00 1rthA c.55.3.1 33574 e.8.1.2 43023 1o7tA 309 2.36e+00 c.94.1.1 86645 1ofdA 1520 2.38e+00 b.80.4.1 86935 c.1.4.1 86936 d.153.1.1 86937 1ui0A 205 2.45e+00 1o1yA 239 2.54e+00 c.23.16.1 86554 1mdbA 539 2.54e+00 e.23.1.1 79008 1amy 403 2.55e+00 1jdc b.71.1.1 27799 c.1.8.1 28786 1avaA 403 2.55e+00 1jdc b.71.1.1 27797 c.1.8.1 28784 1jqnA 883 2.78e+00 c.1.12.3 77159 1ptmA 329 2.81e+00 1f7uA 607 2.82e+00 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1pamA 686 3.01e+00 1cxlA b.1.18.2 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1n40A 396 3.05e+00 a.104.1.1 79977 1gsa 316 3.06e+00 1gsa c.30.1.3 31718 d.142.1.1 41477 1kyqA 274 3.25e+00 c.2.1.11 73281 e.37.1.1 73282 1d2eA 397 3.28e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1ne9A 335 3.46e+00 1fiy 883 3.47e+00 1fiy c.1.12.3 29307 1yacA 208 3.66e+00 1yacA c.33.1.2 31757 1j5sA 463 3.85e+00 c.1.9.8 71580 1g2bA 62 4.33e+00 1tud b.34.2.1 24488 1euwA 152 4.45e+00 1dupA b.85.4.1 28349 1v7nV 163 4.45e+00 1bqk 124 4.65e+00 1bqk b.6.1.1 22889 1dar 691 4.69e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 3mag 307 4.75e+00 3mag c.66.1.25 34205 1d3cA 686 5.06e+00 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721 1qhoA 686 5.11e+00 1cxlA b.1.18.2 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1paz 123 5.18e+00 1bqk b.6.1.1 22878 1rc6A 261 5.25e+00 1hfoA 113 5.27e+00 d.80.1.3 61006 1ihkA 174 5.47e+00 1bfg b.42.1.1 62384 1e43A 483 5.49e+00 1bli b.71.1.1 59217 c.1.8.1 59218 1k1xA 659 5.76e+00 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1dp0A 1023 5.80e+00 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1mkeA 152 6.08e+00 b.55.1.4 79231 1ut7A 171 6.13e+00 1ht6A 405 6.37e+00 b.71.1.1 83629 c.1.8.1 83630 1d2nA 272 6.77e+00 1d2nA c.37.1.20 32428 1e8gA 560 6.78e+00 1qltA d.58.32.1 39455 d.145.1.1 41718 1g94A 448 6.80e+00 b.71.1.1 65169 c.1.8.1 65170 1cznA 169 6.80e+00 1rcf c.23.5.1 31181 1p4cA 380 6.81e+00 1oboA 169 6.90e+00 c.23.5.1 86776 1dyqA 234 6.97e+00 3seb b.40.2.2 59140 d.15.6.1 59141 1aqm 453 7.39e+00 1smd b.71.1.1 27717 c.1.8.1 28704 1tuc 63 7.47e+00 1tuc b.34.2.1 24492 1upiA 225 7.58e+00 1ra9 159 7.62e+00 1vdrA c.71.1.1 34820 1iwhA 141 7.67e+00 a.1.1.2 76882 1mzjA 339 7.79e+00 c.95.1.1 79700 c.95.1.1 79701 1dhr 241 7.83e+00 1dhr c.2.1.2 29832 1ppa 121 7.86e+00 1poa a.133.1.2 19550 1rl2A 137 7.87e+00 1rl2A b.34.5.3 24610 b.40.4.5 25342 1fsu 492 7.92e+00 1auk c.76.1.2 35032 1e7uA 961 7.97e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1s8iA 121 8.04e+00 1aohA 147 8.18e+00 1aohA b.2.2.2 22401 1uyrA 737 8.29e+00 1uumA 372 8.60e+00 1dqsA 393 8.94e+00 1dqsA e.22.1.1 43347 1aa8A 347 8.97e+00 1an9A c.4.1.2 30619 d.16.1.3 37906 1e8yA 966 9.17e+00 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 7odcA 424 9.30e+00 7odcA b.49.2.3 26488 c.1.6.1 28650 1m1nB 522 9.38e+00 c.92.2.3 78418 1ps9A 671 9.38e+00 1m6iA 493 9.50e+00 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1nnfA 309 9.81e+00 c.94.1.1 85903 1ve9A 347 9.87e+00 1ha3A 405 9.95e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1bf6A 291 9.96e+00 1pscA c.1.9.3 29065 1ad2 228 1.01e+01 1ad2 e.24.1.1 43353 1ktbA 405 1.08e+01 b.71.1.1 72960 c.1.8.1 72961 1o0xA 262 1.10e+01 d.127.1.1 80755 1adt 356 1.10e+01 1anv a.54.1.1 17887 g.51.1.1 45362 g.51.1.1 45368 1mrp 309 1.14e+01 1mrp c.94.1.1 35796 1id2A 106 1.15e+01 1aac b.6.1.1 62288 1jz8A 1023 1.15e+01 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.5.1 67833 c.1.8.3 67834 1oz9A 150 1.19e+01 1js8A 394 1.19e+01 a.86.1.1 67219 b.112.1.1 67220 1augA 215 1.22e+01 1a2zA c.56.4.1 33798 1m07A 111 1.24e+01 d.5.1.1 78328 1m2kA 249 1.26e+01 c.31.1.5 84754 2viuA 328 1.29e+01 1hgeA b.19.1.2 23797 1khbA 625 1.32e+01 c.91.1.1 68606 c.109.1.1 68607 1cb8A 678 1.32e+01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1pvvA 315 1.39e+01 1gpuA 680 1.44e+01 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1m7bA 184 1.45e+01 c.37.1.8 74572 1ebfA 358 1.47e+01 1ebuA c.2.1.3 30033 d.81.1.2 39948 1ja1A 622 1.50e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1n3lA 372 1.50e+01 c.26.1.1 79966 1pa1A 310 1.53e+01 1su4A 994 1.55e+01 1kjvA 284 1.61e+01 b.1.1.2 77421 d.19.1.1 77422 1orvA 728 1.62e+01 b.70.3.1 87354 c.69.1.24 87355 1rxxA 421 1.63e+01 1trkA 680 1.63e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1iy8A 267 1.64e+01 c.2.1.2 83774 1dlfL 113 1.65e+01 8fabA b.1.1.1 20382 1d8dB 437 1.65e+01 1ft1B a.102.4.3 18866 7a3hA 303 1.66e+01 7a3hA c.1.8.3 28817 1mh1 186 1.67e+01 1eesA c.37.1.8 32002 1tf4A 605 1.68e+01 1tf4A a.102.1.2 18827 b.2.2.2 22393 2pth 193 1.71e+01 2pth c.56.3.1 33793 1pvc3 238 1.73e+01 1aym3 1ezfA 340 1.74e+01 1ezfA a.128.1.2 19440 1bb9 115 1.75e+01 1bb9 b.34.2.1 24554 1g8sA 230 1.78e+01 1ble 163 1.79e+01 1ble c.38.1.1 32475 1ngvA 534 1.79e+01 c.111.1.2 85698 2ng1 293 1.80e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1dcs 311 1.80e+01 1dcs b.82.2.1 28124 1ifrA 121 1.81e+01 b.1.16.1 71203 1k8kD 300 1.84e+01 d.198.2.1 68309 d.198.2.1 68310 1nsf 273 1.84e+01 1d2nA c.37.1.20 32429 1ds1A 324 1.84e+01 1drtA b.82.2.2 28127 1qgtA 149 1.91e+01 1qgtA a.62.1.1 18135 1o2dA 371 1.94e+01 e.22.1.2 86591 1hurA 180 1.94e+01 1hurA c.37.1.8 32052 1ayl 541 1.95e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1i1qB 192 1.96e+01 1qdlB c.23.16.1 61544 1pht 85 1.99e+01 1ckaA b.34.2.1 24483 3seb 238 2.01e+01 3seb b.40.2.2 25184 d.15.6.1 37773 1mxgA 435 2.01e+01 b.71.1.1 85193 c.1.8.1 85194 1juhA 350 2.01e+01 b.82.1.5 71884 1vhcA 224 2.02e+01 1h0hB 214 2.03e+01 d.58.1.5 76437 1omzA 293 2.06e+01 c.68.1.15 87093 1b24A 188 2.08e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 1an9A 340 2.10e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1gttA 429 2.15e+01 d.177.1.1 70529 d.177.1.1 70530 1hf2A 210 2.16e+01 1hf2A b.80.3.1 60992 c.102.1.1 60993 1exmA 405 2.18e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1lzlA 323 2.18e+01 c.69.1.2 78306 1nktA 922 2.18e+01 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1d9uA 154 2.20e+01 1am7A d.2.1.4 59111 1qh8B 519 2.21e+01 1qguB c.92.2.3 35634 1pa2A 306 2.21e+01 1bgp a.93.1.1 18693 1kzfA 230 2.24e+01 d.108.1.3 73354 1evhA 112 2.26e+01 1evhA b.55.1.4 26997 1irdA 141 2.27e+01 a.1.1.2 66286 1iv8A 720 2.31e+01 b.71.1.1 76842 c.1.8.1 76843 1pzxA 289 2.33e+01 1pi1A 185 2.36e+01 2pii 112 2.38e+01 2pii d.58.5.1 39071 2aaa 484 2.40e+01 7taa b.71.1.1 27777 c.1.8.1 28764 1g7fA 298 2.45e+01 1pty c.45.1.2 60330 1squA 155 2.47e+01 1n6aA 259 2.47e+01 b.76.2.1 80121 b.85.7.1 80122 1d7oA 297 2.49e+01 1enp c.2.1.2 29907 1kjqA 391 2.51e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1vhnA 318 2.53e+01 1jjvA 206 2.58e+01 c.37.1.1 71698 1dfmA 223 2.61e+01 1d2iA c.52.1.5 33295 1sb8A 352 2.62e+01 1tafA 68 2.64e+01 1tafA a.22.1.3 16481 1e2uA 553 2.65e+01 1e1dA e.26.1.1 43362 1d2fA 390 2.67e+01 1d2fA c.67.1.3 34411 1lk2A 274 2.67e+01 1zpdA 568 2.70e+01 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1g7sA 594 2.73e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1gvfA 286 2.76e+01 c.1.10.2 70599 1jsdA 319 2.77e+01 b.19.1.2 63258 1k4mA 213 2.78e+01 c.26.1.3 77258 1hdr 244 2.80e+01 1dhr c.2.1.2 29837 1pbjA 125 2.81e+01 1aerA 205 2.83e+01 1aerA d.166.1.1 42249 1i7oA 429 2.83e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 2cb5A 453 2.83e+01 3gcb d.3.1.1 37035 1gntA 553 2.83e+01 e.26.1.1 70290 1jykA 254 2.83e+01 c.68.1.13 67458 1kgsA 225 2.90e+01 a.4.6.1 68596 c.23.1.1 68597 1o04A 500 2.90e+01 c.82.1.1 86508 1oivA 191 2.99e+01 1enp 312 2.99e+01 1enp c.2.1.2 29906 1it2A 146 3.00e+01 a.1.1.2 66365 1g63A 181 3.01e+01 1g5qA c.34.1.1 60299 1cqqA 180 3.03e+01 1cqqA b.47.1.4 26422 1xo1A 291 3.04e+01 1exnA a.60.7.1 18086 c.120.1.2 33356 1egaA 301 3.05e+01 1egaA c.37.1.8 32150 d.52.3.1 38836 1fbnA 230 3.07e+01 1fbnA c.66.1.3 34181 1a4mA 349 3.11e+01 1a4mA c.1.9.1 29014 8dfr 189 3.14e+01 1aoeA c.71.1.1 34895 1f42A 306 3.16e+01 1f42A b.1.1.4 59636 b.1.2.1 59637 b.1.2.1 59638 1nmeA 146 3.18e+01 c.17.1.1 85874 1ptvA 321 3.19e+01 1pty c.45.1.2 32665 1t0gA 109 3.20e+01 1qqp1 213 3.21e+01 1qqp1 1g5aA 628 3.22e+01 b.71.1.1 65152 c.1.8.1 65153 1tml 286 3.22e+01 1tml c.6.1.1 30656 1ax4A 467 3.23e+01 1ax4A c.67.1.2 34391 1ji7A 89 3.24e+01 a.60.1.1 71682 1php 394 3.27e+01 16pk c.86.1.1 35452 1tetL 216 3.30e+01 32c2A b.1.1.1 19902 b.1.1.2 20996 1e5kA 201 3.32e+01 1fr9A c.68.1.8 34578 2rslA 140 3.33e+01 2rslA c.53.1.1 33345 1pyoA 167 3.35e+01 1b9hA 388 3.36e+01 1b9hA c.67.1.4 34488 1ep0A 185 3.39e+01 1dzrA b.82.1.1 28080 1ld8B 437 3.42e+01 a.102.4.3 73839 1c7gA 456 3.43e+01 1kr4A 125 3.49e+01 d.58.5.2 72889 1l7aA 318 3.50e+01 c.69.1.25 77772 1p9bA 442 3.52e+01 1l8nA 679 3.54e+01 c.1.8.10 84564 d.92.2.2 84565 1v33A 366 3.54e+01 1lv7A 257 3.57e+01 c.37.1.20 78232 1jlnA 297 3.60e+01 1pty c.45.1.2 63172 1lcyA 325 3.60e+01 b.36.1.4 73834 b.47.1.1 73835 1msc 129 3.63e+01 1msc d.85.1.1 40039 1a8q 274 3.66e+01 1brt c.69.1.12 34702 1j9qA 341 3.69e+01 1nif b.6.1.3 62765 b.6.1.3 62766 1okrA 123 3.72e+01 1phm 310 3.75e+01 1phm b.121.1.2 59015 b.121.1.2 59016 1fzoA 274 3.75e+01 1agdA b.1.1.2 60155 d.19.1.1 60156 1kl1A 419 3.78e+01 c.67.1.4 72663 1fkx 349 3.80e+01 1a4mA c.1.9.1 29018 1hynP 379 3.80e+01 1hynP d.112.1.2 61408 1o3yA 166 3.81e+01 c.37.1.8 86618 1n8nA 212 3.81e+01 1ui8A 638 3.82e+01 1pgl2 370 3.83e+01 1o70A 324 3.87e+01 b.118.1.1 81115 b.118.1.1 81116 1bo1A 416 3.88e+01 1bo1A d.143.1.2 41591 1olrA 224 3.95e+01 1l1lA 739 3.96e+01 c.7.1.4 73470 1mvoA 136 3.96e+01 c.23.1.1 79513