# 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 1j2gA 319 1.26e-01 1gbg 214 8.28e-01 1axkA b.29.1.2 24171 2ayh 214 1.38e+00 1axkA b.29.1.2 24172 1cpn 208 1.74e+00 1axkA b.29.1.2 24175 1axkA 394 2.24e+00 1axkA b.29.1.2 24181 b.29.1.11 24315 5nn9 388 2.27e+00 2qwc b.68.1.1 27563 2qwc 388 2.38e+00 2qwc b.68.1.1 27547 1bywA 110 2.81e+00 1bywA d.110.3.6 40912 1f8eA 388 3.01e+00 2qwc b.68.1.1 59694 3nn9 388 3.19e+00 2qwc b.68.1.1 27566 1qs8A 329 3.60e+00 1smrA b.50.1.2 26887 1s14A 194 3.72e+00 d.122.1.2 -10973 1vzoA 355 4.26e+00 1j5wA 298 5.08e+00 d.104.1.1 71589 1vcaA 202 6.94e+00 1vcaA b.1.1.3 21649 b.1.1.4 21685 1tuhA 156 7.64e+00 1roaA 122 8.50e+00 1k5wA 152 8.54e+00 b.7.1.2 68212 1r2zA 274 9.12e+00 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1l1zA 274 9.18e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1d3bA 75 9.81e+00 1d3bA b.38.1.1 24798 1ge8A 249 1.01e+01 1plq d.131.1.2 41398 d.131.1.2 41399 1fsoA 139 1.02e+01 1rhoA b.1.18.8 60007 1qlmA 316 1.08e+01 1qlmA d.147.1.1 41765 1ivwA 638 1.09e+01 b.30.2.1 71456 d.17.2.1 71457 d.17.2.1 71458 1jhjA 171 1.18e+01 b.18.1.9 66714 1ivg 388 1.24e+01 2qwc b.68.1.1 27578 1viwB 198 1.36e+01 1led b.29.1.1 24170 1ivd 388 1.39e+01 2qwc b.68.1.1 27568 1smvA 260 1.40e+01 1smvA b.121.4.7 23288 1ui7A 638 1.41e+01 b.30.2.1 -3523 d.17.2.1 -9268 d.17.2.1 -9269 1lnrI 134 1.43e+01 1iqyA 638 1.47e+01 b.30.2.1 76763 d.17.2.1 76764 d.17.2.1 76765 1phm 310 1.49e+01 1phm b.121.1.2 59015 b.121.1.2 59016 1miqA 375 1.55e+01 b.50.1.2 79151 1nscA 390 1.55e+01 2qwc b.68.1.1 27591 1i7nA 309 1.56e+01 c.30.1.5 83681 d.142.1.3 83682 1ha1 184 1.59e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1sixA 174 1.62e+01 b.85.4.1 -5030 1ystH 260 1.73e+01 6prcH b.41.1.1 25482 f.23.10.1 43511 1j1tA 233 1.79e+01 unknown_sccs -3462 1pvl 301 1.81e+01 1pvl f.6.1.1 43819 1ui8A 638 1.89e+01 b.30.2.1 -3525 d.17.2.1 -9272 d.17.2.1 -9273 1at0 145 1.93e+01 1at0 b.86.1.1 28374 1ngvA 534 1.93e+01 c.111.1.2 85698 1nr0A 611 1.95e+01 b.69.4.1 86078 b.69.4.1 86079 1s5aA 150 2.02e+01 unknown_sccs -9300 1gy6A 127 2.09e+01 d.17.4.2 70736 1ar0A 127 2.10e+01 1ounA d.17.4.2 38092 1gwmA 153 2.15e+01 b.18.1.19 83348 1uhvA 500 2.20e+01 b.71.1.2 -4683 c.1.8.3 -5354 1pfzA 380 2.26e+01 1smrA b.50.1.2 26881 1h2vZ 156 2.28e+01 d.58.7.1 76595 1pz4A 116 2.29e+01 d.106.1.1 -10780 1my7A 114 2.34e+01 b.1.18.1 79675 1avk 638 2.37e+01 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1dynA 125 2.51e+01 1dynA b.55.1.1 26955 1dhkB 223 2.52e+01 1led b.29.1.1 24157 1mq7A 154 2.52e+01 b.85.4.1 79404 1d2gA 292 2.66e+01 1xvaA c.66.1.5 34187 1lr0A 129 2.67e+01 d.212.1.1 74213 1k4jA 230 2.68e+01 d.108.1.3 72057 1miuA 738 2.68e+01 a.170.1.1 79153 a.171.1.1 79154 b.40.4.3 79155 b.40.4.3 79156 b.40.4.3 79157 1ei5A 520 2.68e+01 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1jz8A 1023 2.81e+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 2dynA 122 2.81e+01 1dynA b.55.1.1 26957 1dp0A 1023 2.86e+01 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 1ic7H 114 2.87e+01 1f3rB b.1.1.1 62258 1jb2A 127 2.88e+01 d.17.4.2 71624 1iz5A 249 2.89e+01 d.131.1.2 83834 d.131.1.2 83835 1ryp2 233 2.99e+01 1ryp2 1rhoA 145 3.11e+01 1rhoA b.1.18.8 21899 1ah9 71 3.15e+01 1ah9 b.40.4.5 25330 1g4mA 393 3.25e+01 b.1.18.11 65143 b.1.18.11 65144 1jmmA 377 3.25e+01 b.30.6.1 71749 1e8nA 710 3.27e+01 1qfmA b.69.7.1 27675 c.69.1.4 34643 1gw5M 435 3.29e+01 b.2.7.1 70631 d.110.4.2 70632 1jd0A 263 3.30e+01 2cba b.74.1.1 62888 1rypH 205 3.32e+01 d.153.1.4 41876 1qovH 260 3.38e+01 6prcH b.41.1.1 25464 f.23.10.1 43457 1kn9A 249 3.42e+01 b.87.1.2 68699 1ounA 127 3.43e+01 1ounA d.17.4.2 38090 3sicI 107 3.44e+01 3ssi d.84.1.1 40028 1dtgA 334 3.44e+01 1nnt c.94.1.2 35896 1o59A 355 3.49e+01 unknown_sccs -3132 unknown_sccs -3133 1g0u1 266 3.51e+01 1i3uA 127 3.57e+01 1gc1H b.1.1.1 61636 1nox 205 3.59e+01 1nox d.90.1.1 40242 1i31A 314 3.62e+01 1bw8A b.2.7.1 22481 1dun 134 3.64e+01 1dun b.85.4.1 28371 1hmt 132 3.64e+01 1hmt b.60.1.2 27169 1mm4A 170 3.67e+01 f.4.1.2 79294 1hms 132 3.68e+01 1hmt b.60.1.2 27168 1hmr 132 3.68e+01 1hmt b.60.1.2 27170 1f9zA 135 3.72e+01 1qipA d.32.1.1 38484 1gv3A 248 3.73e+01 a.2.11.1 70585 d.44.1.1 70586 1q4uA 151 3.77e+01 d.38.1.5 -9701 1fr9A 194 3.86e+01 1fr9A c.68.1.8 34579 1pjxA 314 3.88e+01 1rhoC 145 3.88e+01 1rhoA b.1.18.8 21901 4sbvA 261 3.89e+01 1smvA b.121.4.7 23299 1n1mA 728 3.89e+01 b.70.3.1 79815 c.69.1.24 79816 1bv8A 138 3.93e+01 1ayoA b.2.4.1 22430 1udvA 89 3.94e+01 d.68.6.1 -10280 1q9uA 130 3.95e+01 unknown_sccs -11025 1e4fT 419 3.98e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1lqbC 162 3.99e+01 b.3.3.1 74186