# List of top-scoring protein chains for T0348.t04-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 1pft 50 2.46e-03 1pft g.41.3.1 45206 1tr9A 341 4.88e-01 1y65A 342 4.90e-01 2ct7A 86 1.42e+00 2aq6A 147 2.30e+00 2ct2A 88 2.47e+00 1wd2A 60 2.59e+00 g.44.1.1 109232 1e4uA 78 3.04e+00 1e4uA g.44.1.1 59231 1s72Z 73 3.27e+00 g.41.8.1 105345 1vqoZ 83 3.75e+00 1edyA 134 3.76e+00 1ayoA b.2.4.1 22428 2a62A 322 4.56e+00 1y88A 199 4.78e+00 1gnf 46 4.92e+00 1gatA g.39.1.1 45107 1ur6B 52 5.07e+00 g.44.1.1 99812 2avyS 91 5.80e+00 2ff0A 102 5.84e+00 1so2A 420 5.92e+00 a.211.1.2 98936 1sojI 420 5.93e+00 a.211.1.2 98950 2a66A 113 6.12e+00 1odhA 174 6.21e+00 d.239.1.1 86850 1r4mA 529 6.22e+00 c.111.1.2 96999 1tt5A 531 6.24e+00 c.111.1.2 107291 1yovA 537 6.28e+00 1zsqA 528 6.41e+00 1jm7A 112 6.66e+00 g.44.1.1 66880 1frfS 264 6.66e+00 2frvA e.19.1.1 43312 1yqwA 264 6.86e+00 1yrqA 264 6.91e+00 1us5A 314 7.01e+00 c.94.1.1 99856 1p91A 269 7.02e+00 c.66.1.33 94378 1n9dA 199 7.50e+00 a.26.1.1 85464 1bc8C 93 8.11e+00 1awcA a.4.5.21 16168 1fl2A 310 8.31e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 1vdwA 254 8.47e+00 e.7.1.1 100569 1reqA 727 9.30e+00 1reqA c.1.19.1,c.23.6.1 29620,31247 5reqA 727 9.31e+00 1reqA c.1.19.1,c.23.6.1 29632,31259 1e1cA 727 9.33e+00 1reqA c.1.19.1,c.23.6.1 29636,31263 1u79A 129 9.47e+00 d.26.1.1 107714 1lw3A 657 9.58e+00 b.55.1.8,c.45.1.3 91152,91153 2a1rA 430 1.03e+01 1ww8A 439 1.11e+01 1wfeA 86 1.15e+01 1dx8A 70 1.15e+01 1rb9 g.41.5.1 45243 1lm5A 214 1.20e+01 d.211.2.1 74029 1ffkW 73 1.28e+01 1ffkW g.41.8.1 45315 1p9rA 418 1.29e+01 c.37.1.11 94399 1yc5A 246 1.40e+01 1yqdA 366 1.42e+01 1hbxG 157 1.42e+01 1awcA a.4.5.21 60934 1ydfA 257 1.47e+01 1wiiA 85 1.47e+01 1ichA 112 1.47e+01 a.77.1.2 71182 1z6uA 150 1.50e+01 1zd9A 188 1.51e+01 1z1zA 131 1.52e+01 1vd4A 62 1.54e+01 1dsvA 31 1.54e+01 1dsvA g.40.1.1 45174 2h18A 193 1.56e+01 1l8dA 112 1.65e+01 h.4.12.1 73687 2al7A 186 1.67e+01 2fymB 18 1.69e+01 1h7vA 60 1.74e+01 g.41.5.1 65713 1f4dA 264 1.75e+01 1bkpA d.117.1.1 40972 2a8jA 420 1.77e+01 1rlyA 60 1.77e+01 g.41.3.1 104988 2a8mA 420 1.77e+01 1dl6A 58 1.78e+01 1dl6A g.41.3.1 45207 2a8lA 420 1.79e+01 2fqpA 97 1.85e+01 1fl1A 230 1.90e+01 1at3A b.57.1.1 27023 1hyuA 521 1.96e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1dfoA 417 2.02e+01 1bj4A c.67.1.4 34480 1eqbA 417 2.02e+01 1bj4A c.67.1.4 34484 1faq 52 2.05e+01 1far g.49.1.1 45352 1t9oA 54 2.07e+01 1sp1 29 2.09e+01 g.37.1.1 45051 1mm3A 61 2.12e+01 g.50.1.2 85016 1fiuA 286 2.16e+01 1fiuA c.52.1.10 33317 1hzwA 290 2.24e+01 1bkpA d.117.1.1 61464 1hvyA 288 2.26e+01 1bkpA d.117.1.1 41049 1v6eA 95 2.27e+01 1ju6A 313 2.29e+01 d.117.1.1 63289 1cqjA 286 2.30e+01 2scuA c.2.1.8,c.23.4.1 30305,31133 2scuA 288 2.31e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1m1qA 91 2.35e+01 a.138.1.3 74419 1ypvA 313 2.41e+01 1c0fA 368 2.48e+01 1yagA c.55.1.1,c.55.1.1 33447,33448 2awpA 198 2.50e+01 1sur 215 2.52e+01 1sur c.26.2.2 31620 2d8iA 114 2.53e+01 1bor 56 2.55e+01 1bor g.44.1.1 45324 1vzv 221 2.57e+01 1at3A b.57.1.1 27025 1mm2A 61 2.57e+01 g.50.1.2 85015 1jagA 241 2.62e+01 c.37.1.1 66463 1uucA 55 2.63e+01 g.68.1.2 108045 2a4eA 215 2.77e+01 1q35A 320 2.80e+01 c.94.1.1 95661 1hw4A 355 2.82e+01 1bkpA d.117.1.1 41054 1h7kA 483 2.94e+01 e.5.1.1 90624 1spwA 39 2.94e+01 8rxnA 52 2.99e+01 1rb9 g.41.5.1 45215 1rb9 53 3.03e+01 1rb9 g.41.5.1 45214 1jj2Y 73 3.04e+01 1ffkW g.41.8.1 63110 1g4mA 393 3.07e+01 b.1.18.11,b.1.18.11 65143,65144 2gf0A 199 3.07e+01 1x4wA 67 3.15e+01 1t9pA 54 3.15e+01 1ctl 85 3.15e+01 g.39.1.3,g.39.1.3 45133,45134 2aq4A 434 3.26e+01 1jsyA 418 3.30e+01 b.1.18.11,b.1.18.11 71847,71848 1uufA 369 3.30e+01 b.35.1.2,c.2.1.1 100006,100007 2cjsC 62 3.32e+01 1yagA 375 3.37e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 1yvnA 375 3.41e+01 1yagA c.55.1.1,c.55.1.1 33451,33452 2a6hD 1524 3.44e+01 1erd 40 3.45e+01 1erd a.10.1.1 16362 1yk4A 52 3.50e+01 1vckA 115 3.53e+01 1cteA 254 3.53e+01 1theB d.3.1.1 37058 1theA 260 3.57e+01 1theB d.3.1.1 37056 2cbnA 306 3.66e+01 1sezA 504 3.75e+01 c.3.1.2,d.16.1.5 98822,98823 1ile 821 3.75e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1wjvA 79 3.77e+01 2cu8A 76 3.83e+01 1vor2 58 3.98e+01 1nwyZ 59 4.04e+01 i.1.1.2 86369 1yl35 60 4.10e+01 1rikA 31 4.14e+01 k.12.1.1 104952 1c0gA 375 4.16e+01 1yagA c.55.1.1,c.55.1.1 33443,33444 1g25A 65 4.16e+01 1g25A g.44.1.1 45325 1ynjD 1524 4.19e+01 1iq3A 110 4.19e+01 1iq3A a.39.1.6 62640 1pt4A 29 4.26e+01 g.3.3.1 104306 2g2kA 170 4.29e+01 1iml 76 4.30e+01 1iml g.39.1.3,g.39.1.3 45145,45146 2gpyA 233 4.30e+01 1xi6A 262 4.38e+01 1rjwA 339 4.40e+01 b.35.1.2,c.2.1.1 97582,97583 2a03A 206 4.42e+01 1wijA 140 4.44e+01 1ifqA 138 4.48e+01 1ifqA d.110.4.1 62350 1yk5A 53 4.49e+01 1ng0A 253 4.52e+01 b.121.4.7 80475 1xwhA 66 4.55e+01 1mirA 322 4.63e+01 1theB d.3.1.1 37062 1dejA 375 4.66e+01 1yagA c.55.1.1,c.55.1.1 33445,33446 1jcoB 30 4.66e+01 g.1.1.1 66503 1jbjA 186 4.75e+01 b.1.1.4,b.1.1.4 66482,66483 1sjxA 122 4.88e+01 1xtqA 177 4.90e+01 1brfA 53 4.90e+01 1rb9 g.41.5.1 45236 1a90 108 4.92e+01 1cewI d.17.1.2 38001 2agqA 341 4.93e+01 1bq8A 54 4.93e+01 1rb9 g.41.5.1 45237 1jx4A 352 5.03e+01 d.240.1.1,e.8.1.7 90378,90379 1inp 400 5.06e+01 1inp e.7.1.1 42972 2bq3A 358 5.09e+01 1xfkA 336 5.09e+01 2aw2B 108 5.10e+01 1ywzA 175 5.11e+01 1ek9A 428 5.11e+01 1ek9A f.5.1.1 43809 1rimA 35 5.12e+01 k.12.1.1 104953 1durA 55 5.15e+01 2fdn d.58.1.1 38943 2asdA 360 5.19e+01 1zyoA 191 5.22e+01 1ee0A 402 5.23e+01 1bi5A c.95.1.2,c.95.1.2 36007,36008 1rdg 53 5.31e+01 1rb9 g.41.5.1 45221 1g0dA 695 5.36e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 1pkhA 204 5.41e+01 b.85.4.1 94832 1c09A 54 5.42e+01 1rb9 g.41.5.1 45228 1mea 28 5.57e+01 g.41.1.1 45176 1e8jA 52 5.57e+01 g.41.5.1 64796 1tqqA 471 5.57e+01 f.5.1.1 107242 1qxfA 66 5.72e+01 g.41.8.4 96527 1fiqB 350 5.79e+01 1fiqB d.87.2.1,d.145.1.3 40229,41760 1qyp 57 5.80e+01 1qyp g.41.3.1 45205 1ee8A 266 5.91e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1d4xA 375 5.95e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1qamA 244 5.96e+01 2ercA c.66.1.24 34220 1nigA 152 5.96e+01 a.25.2.1 85740 1gvzA 237 6.00e+01 b.47.1.2 76360 2rdvA 52 6.00e+01 1rb9 g.41.5.1 45217 1jmaB 167 6.06e+01 g.24.1.1,g.24.1.1 63178,63179 1h6nA 484 6.06e+01 e.5.1.1 90623 1e93A 484 6.09e+01 e.5.1.1 64802 1m85A 484 6.11e+01 e.5.1.1 74578 1f62A 51 6.24e+01 1f62A g.50.1.2 45360 2btfA 375 6.27e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 2g1uA 155 6.29e+01 2bx9A 53 6.33e+01 1cewI 108 6.38e+01 1cewI d.17.1.2 37999 1poiA 317 6.40e+01 1poiA c.124.1.2 34153 1b8tA 192 6.44e+01 1b8tA g.39.1.3,g.39.1.3,g.39.1.3,g.39.1.3 45135,45136,45137,45138 1nypA 66 6.50e+01 g.39.1.3,g.39.1.3 86411,86412 1jm1A 204 6.58e+01 b.33.1.1 71745 1ku1A 230 6.65e+01 a.118.3.1 72996 1fujA 221 6.69e+01 1a7s b.47.1.2 26349 1yvbI 111 6.70e+01 1v87A 114 6.89e+01 g.44.1.1 108422 1r6lA 239 6.97e+01 d.14.1.4,d.101.1.1 97153,97154 1zpuA 534 7.12e+01 2flgA 49 7.15e+01 1ob1C 99 7.16e+01 g.3.11.4,g.3.11.4 86752,86753 2bqzA 161 7.18e+01 1y9wA 140 7.22e+01 1cejA 96 7.23e+01 1b9wA g.3.11.4,g.3.11.4 44336,44337 1p9hA 226 7.27e+01 b.81.3.1 94389 1oy0A 281 7.39e+01 c.1.12.8 87543 1xmwA 178 7.42e+01 1zkkA 167 7.42e+01 5rxn 54 7.50e+01 1rb9 g.41.5.1 45225 1o6bA 169 7.50e+01 c.26.1.3 92564 1exkA 79 7.53e+01 1exkA g.54.1.1 45384 1zxzA 197 7.57e+01 1g47A 77 7.78e+01 1g47A g.39.1.3,g.39.1.3 45147,45148 1fp2A 352 7.81e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1cokA 68 7.81e+01 1cokA a.60.1.2 17945 1nm1A 375 7.91e+01 c.55.1.1,c.55.1.1 80651,80652 1p7aA 37 8.01e+01 g.37.1.1 94216 1iu5A 53 8.02e+01 g.41.5.1 71434 1x75A 132 8.20e+01 1ma9B 376 8.26e+01 c.55.1.1,c.55.1.1 78890,78891 1ajw 145 8.31e+01 1rhoA b.1.18.8 21905 1jm7B 117 8.36e+01 g.44.1.1 66881 1ejxA 100 8.38e+01 d.8.1.1 83182 1s7bA 110 8.45e+01 f.39.1.1 98634 1chc 68 8.53e+01 1chc g.44.1.1 45323 1nbwA 607 8.67e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 2f2mA 113 8.70e+01 1t1jA 125 8.74e+01 c.137.1.1 106249 1iro 54 8.88e+01 1rb9 g.41.5.1 45223 2cuqA 80 8.90e+01 2g8yA 385 8.96e+01 1mo2A 294 8.97e+01 c.69.1.22 79331 2tsrA 307 8.97e+01 1bkpA d.117.1.1 41043 1gqpA 221 8.97e+01 b.18.1.9 70372 1pw4A 451 8.98e+01 f.38.1.1 95198