# List of top-scoring protein chains for t2k-w0.5 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 1cozA 129 2.40e-22 1cozA c.26.1.2 31598 1od6A 160 8.48e-05 1h1tA 159 4.74e-04 1qjcA 158 5.45e-04 1b6tA c.26.1.3 63328 1mrzA 293 1.85e-02 1lw7A 365 1.06e-01 c.26.1.3 74295 c.37.1.1 74296 1f9aA 168 1.63e-01 1f9aA c.26.1.3 31602 1k4mA 213 2.92e-01 c.26.1.3 77258 1dgsA 667 3.92e-01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1nazA 154 5.99e-01 1j9aA 184 7.63e-01 1fcs 154 9.42e-01 1a6m a.1.1.2 15055 1ofj 154 9.78e-01 1a6m a.1.1.2 15065 2mge 154 1.20e+00 1a6m a.1.1.2 15056 2mgj 154 1.25e+00 1a6m a.1.1.2 15119 1ofk 154 1.47e+00 1a6m a.1.1.2 15061 1mgn 154 1.87e+00 1a6m a.1.1.2 15097 102m 154 2.07e+00 1a6m a.1.1.2 15073 1mod 154 2.09e+00 1a6m a.1.1.2 15107 1mcy 154 2.14e+00 1a6m a.1.1.2 15076 1mlu 154 2.28e+00 1a6m a.1.1.2 15093 2mgg 154 2.35e+00 1a6m a.1.1.2 15069 2mgb 154 2.39e+00 1a6m a.1.1.2 15102 1mnh 153 2.49e+00 1a6m a.1.1.2 15187 1ihoA 283 2.70e+00 1ihoA c.26.1.4 62390 1mnkA 153 2.81e+00 1a6m a.1.1.2 15181 1m8fA 181 2.82e+00 1mniA 153 2.85e+00 1a6m a.1.1.2 15173 1mnjA 153 3.08e+00 1a6m a.1.1.2 15179 1qb2A 109 3.39e+00 1qb2A a.36.1.1 17125 1kanA 253 3.43e+00 1knyA a.24.16.1 75878 d.218.1.1 75879 1mlg 154 3.43e+00 1a6m a.1.1.2 15104 1knyA 253 3.46e+00 1knyA a.24.16.1 75896 d.218.1.1 75897 1mfqC 129 3.48e+00 a.36.1.1 79046 1ml6A 221 3.52e+00 1m8jA 181 3.62e+00 1cikA 154 3.80e+00 1a6m a.1.1.2 15039 1irc 154 3.83e+00 1a6m a.1.1.2 15141 1dtiA 154 3.90e+00 1a6m a.1.1.2 15074 1n2eA 300 4.03e+00 1do1A 154 4.07e+00 1a6m a.1.1.2 15049 1ej2A 181 4.10e+00 1f9aA c.26.1.3 59414 1ch1A 154 4.12e+00 1a6m a.1.1.2 15094 1lht 153 4.15e+00 1a6m a.1.1.2 15205 1co9A 154 4.34e+00 1a6m a.1.1.2 15028 1cioA 154 4.43e+00 1a6m a.1.1.2 15029 2spl 154 4.46e+00 1a6m a.1.1.2 15047 2spo 154 4.56e+00 1a6m a.1.1.2 15053 1m8gA 181 4.73e+00 1jw8A 154 4.75e+00 a.1.1.2 67376 1myjA 153 4.84e+00 1a6m a.1.1.2 15171 1cp5A 154 4.85e+00 1a6m a.1.1.2 15123 1co8A 154 4.89e+00 1a6m a.1.1.2 15079 1ch3A 154 4.91e+00 1a6m a.1.1.2 15111 1cpwA 154 4.93e+00 1a6m a.1.1.2 15136 1ch9A 154 4.95e+00 1a6m a.1.1.2 15062 1ku0A 388 4.95e+00 c.69.1.18 72994 1ch5A 154 4.97e+00 1a6m a.1.1.2 15127 1duoA 153 5.05e+00 1a6m a.1.1.2 15137 1cp0A 154 5.33e+00 1a6m a.1.1.2 15109 1mlo 154 5.35e+00 1a6m a.1.1.2 15085 1jbwA 428 5.41e+00 c.59.1.2 62860 c.72.2.2 62861 1odbA 95 5.42e+00 1e8aA 91 5.55e+00 1b4cA a.39.1.2 17188 1rlr 761 5.56e+00 1rlr a.98.1.1 18753 c.7.1.2 30679 1ch2A 154 5.62e+00 1a6m a.1.1.2 15064 1bzpA 153 5.70e+00 1a6m a.1.1.2 15020 1ch7A 154 5.79e+00 1a6m a.1.1.2 15083 1a6m 151 5.80e+00 1a6m a.1.1.2 15018 1m6mA 153 5.94e+00 1a6m a.1.1.2 15163 1obm 154 5.96e+00 1a6m a.1.1.2 15091 1kamA 194 6.27e+00 c.26.1.3 72254 1a6g 151 6.37e+00 1a6m a.1.1.2 15021 1ufvA 276 6.41e+00 1yma 153 6.70e+00 1a6m a.1.1.2 15202 1baiA 124 6.93e+00 2rspB b.50.1.1 26773 1gdhA 320 7.06e+00 1gdhA c.2.1.4 30095 c.23.12.1 31355 1m2pA 325 7.23e+00 1m2rA 327 7.25e+00 1lpuA 332 7.40e+00 d.144.1.1 74177 1bje 153 7.43e+00 1a6m a.1.1.2 15197 1hruA 188 7.71e+00 1hruA d.115.1.1 40926 1mym 154 7.76e+00 1a6m a.1.1.2 15054 1pn3A 404 7.93e+00 1myhA 153 7.93e+00 1a6m a.1.1.2 15177 1gil 353 8.19e+00 1cipA a.66.1.1 18223 c.37.1.8 32106 1ev9A 221 8.22e+00 1pgtA a.45.1.1 17696 c.47.1.5 32990 1mwcA 153 8.32e+00 1a6m a.1.1.2 15157 1ev4A 221 8.32e+00 1pgtA a.45.1.1 17693 c.47.1.5 32987 4r1rA 761 8.56e+00 1rlr a.98.1.1 18772 c.7.1.2 30698 2r1rA 761 8.56e+00 1rlr a.98.1.1 18769 c.7.1.2 30695 1r1rA 761 8.56e+00 1rlr a.98.1.1 18754 c.7.1.2 30680 7r1rA 761 8.56e+00 1rlr a.98.1.1 18763 c.7.1.2 30689 5r1rA 761 8.57e+00 1rlr a.98.1.1 18757 c.7.1.2 30683 6r1rA 761 8.57e+00 1rlr a.98.1.1 18760 c.7.1.2 30686 1f3aA 222 9.13e+00 1pgtA a.45.1.1 17701 c.47.1.5 32995 1mls 154 9.39e+00 1a6m a.1.1.2 15058 1b5l 172 1.13e+01 1b5l a.26.1.3 16900 1mti 154 1.19e+01 1a6m a.1.1.2 15114 1rse 153 1.23e+01 1a6m a.1.1.2 15196 1e94A 175 1.39e+01 1nedA d.153.1.4 41977 1gjnA 153 1.41e+01 a.1.1.2 70191 1fsz 372 1.42e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1nedA 183 1.47e+01 1nedA d.153.1.4 41974 1xch 153 1.51e+01 1a6m a.1.1.2 15194 1hrm 153 1.56e+01 1a6m a.1.1.2 15193 1reqB 637 1.57e+01 1reqB c.1.19.1 29621 c.23.6.1 31248 2mm1 153 1.61e+01 1a6m a.1.1.2 15203 1mtcA 217 1.61e+01 1bh2 315 1.63e+01 1cipA a.66.1.1 18214 c.37.1.8 32097 1mgpA 313 1.69e+01 c.119.1.1 79098 1ji3A 388 1.75e+01 c.69.1.18 77115 1oioA 178 1.79e+01 1cnuA 137 1.83e+01 1cof d.109.1.2 40862 1nz2A 153 1.87e+01 1h7eA 245 1.95e+01 c.68.1.13 60717 1j71A 334 2.01e+01 1eagA b.50.1.2 62669 1l8tA 263 2.01e+01 d.144.1.6 73702 1j7lA 264 2.02e+01 d.144.1.6 62697 1nz3A 153 2.06e+01 1h0cA 392 2.12e+01 1kjyA 325 2.13e+01 a.66.1.1 72624 c.37.1.8 72625 1nogA 177 2.20e+01 1qi5A 429 2.31e+01 1jdc b.71.1.1 27792 c.1.8.1 28779 6gsuA 217 2.42e+01 1b8xA a.45.1.1 17635 c.47.1.5 32929 6gsvA 217 2.43e+01 1b8xA a.45.1.1 17633 c.47.1.5 32925 2gstA 217 2.43e+01 1b8xA a.45.1.1 17629 c.47.1.5 32923 6gsxA 217 2.46e+01 1b8xA a.45.1.1 17641 c.47.1.5 32935 6gswA 217 2.48e+01 1b8xA a.45.1.1 17631 c.47.1.5 32927 1blp 257 2.61e+01 1btl e.3.1.1 42716 1o9zA 177 2.66e+01 1schA 294 2.74e+01 1bgp a.93.1.1 18685 1o9wA 177 2.85e+01 2amg 418 2.88e+01 1jdc b.71.1.1 27796 c.1.8.1 28783 1qpkA 418 2.88e+01 1jdc b.71.1.1 27793 c.1.8.1 28780 1mll 154 2.91e+01 1a6m a.1.1.2 15057 1mkmA 249 3.08e+01 a.4.5.33 79242 d.110.2.2 79243 1myiA 153 3.21e+01 1a6m a.1.1.2 15175 1m9hA 278 3.21e+01 1g1xC 88 3.21e+01 1fjfR a.4.8.1 16249 1oi7A 288 3.22e+01 1bkcI 256 3.23e+01 1bkcA d.92.1.10 40334 1emy 153 3.23e+01 1a6m a.1.1.2 15204 1g20E 289 3.29e+01 1cp2A c.37.1.10 32247 1i94R 87 3.33e+01 1fjfR a.4.8.1 62009 1jdc 429 3.34e+01 1jdc b.71.1.1 27789 c.1.8.1 28776 1qi4A 429 3.34e+01 1jdc b.71.1.1 27791 c.1.8.1 28778 1qi3A 429 3.34e+01 1jdc b.71.1.1 27794 c.1.8.1 28781 1j9lA 247 3.35e+01 c.106.1.1 62762 1ireA 204 3.49e+01 d.149.1.1 76769 1iruB 233 3.50e+01 d.153.1.4 71353 1bkcC 254 3.51e+01 1bkcA d.92.1.10 40332 1bkcA 255 3.55e+01 1bkcA d.92.1.10 40331 1pea 385 3.61e+01 1pea c.93.1.1 35662 1akz 223 3.63e+01 3eugA c.18.1.1 31007 2sspE 223 3.67e+01 3eugA c.18.1.1 31012 1hw6A 278 3.71e+01 1frb c.1.7.1 61296 1a80 277 3.74e+01 1frb c.1.7.1 28700 1qnlA 385 3.76e+01 1pea c.93.1.1 35665 1omeA 258 3.83e+01 1btl e.3.1.1 42717 3blm 257 3.86e+01 1btl e.3.1.1 42709 1h3gA 601 3.89e+01