# 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 1qsmA 152 2.99e-15 1qsmA d.108.1.1 40808 1i12A 160 3.14e-15 1i21A d.108.1.1 61515 1i1dA 161 3.15e-15 1i21A d.108.1.1 61526 1i21A 159 3.37e-15 1i21A d.108.1.1 61549 1qsoA 149 4.18e-15 1qsmA d.108.1.1 40812 1bo4A 168 1.82e-11 1bo4A d.108.1.1 40798 1bo4B 168 1.82e-11 1bo4A d.108.1.1 40799 1b87A 181 1.07e-08 1b87A d.108.1.1 40797 1b6bA 174 3.32e-07 1cjwA d.108.1.1 40819 1cjwA 166 3.38e-07 1cjwA d.108.1.1 40818 1ib1E 200 3.74e-07 1cjwA d.108.1.1 62137 1kuxA 207 3.78e-07 1qstA 160 7.02e-07 1yghA d.108.1.1 40804 1qsrA 162 7.16e-07 1yghA d.108.1.1 40805 5gcnA 166 7.26e-07 1yghA d.108.1.1 40807 1cm0A 168 1.51e-06 1yghA d.108.1.1 40800 1l0cA 207 1.60e-06 1yghA 164 5.02e-05 1yghA d.108.1.1 40802 1bob 320 3.73e-04 1bob d.108.1.1 40816 1fy7A 278 5.40e-03 1fy7A d.108.1.1 40817 1nmtA 392 9.81e-03 1nmtA d.108.1.2 40823 d.108.1.2 40824 1iicA 422 1.34e-01 1nmtA d.108.1.2 62422 d.108.1.2 62423 1h4yA 117 7.01e-01 1auz c.13.2.1 60628 1h4xA 117 1.17e+00 1auz c.13.2.1 60626 1h4zA 117 1.37e+00 1auz c.13.2.1 60630 1e3rA 131 1.66e+00 1opy d.17.4.3 59199 1c7hA 131 2.09e+00 1opy d.17.4.3 38117 1dmmA 131 2.27e+00 1opy d.17.4.3 38114 4tsuA 130 2.37e+00 1opy d.17.4.3 38118 1opy 131 2.38e+00 1opy d.17.4.3 38113 1ea2A 131 2.53e+00 d.17.4.3 64860 1dmnA 131 2.66e+00 1opy d.17.4.3 38115 1dmqA 131 2.80e+00 1opy d.17.4.3 38116 1e97A 131 2.86e+00 d.17.4.3 64803 1ko7A 314 3.22e+00 1dtzA 689 3.37e+00 1cb6A c.94.1.2 59134 c.94.1.2 59135 1i94H 138 5.95e+00 1seiA d.140.1.1 61999 1di1A 300 7.06e+00 1di1A a.128.1.4 19446 1i8kA 107 7.41e+00 1b9bB 255 7.68e+00 1amk c.1.1.1 28532 1kxjA 205 7.96e+00 1an7A 136 8.18e+00 1seiA d.140.1.1 41465 1eg0E 138 8.24e+00 1seiA i.1.1.1 45811 1aigH 260 8.37e+00 6prcH b.41.1.1 25473 f.2.1.2 43484 1ystH 260 8.51e+00 6prcH b.41.1.1 25482 f.2.1.2 43511 1qovH 260 8.51e+00 6prcH b.41.1.1 25464 f.2.1.2 43457 1havB 217 8.90e+00 1havA b.47.1.4 26424 1havA 217 9.51e+00 1havA b.47.1.4 26423 1quaA 197 9.56e+00 1atlA d.92.1.9 40330 1l8tA 263 9.88e+00 1j7lA 264 9.89e+00 d.144.1.6 62697 1j7iA 264 9.89e+00 1j7iA d.144.1.6 62694 1gpwB 201 1.06e+01 c.23.16.1 65461 1k9vF 201 1.06e+01 c.23.16.1 68365 1qa7A 215 1.10e+01 1havA b.47.1.4 26425 1hd8A 363 1.12e+01 b.105.1.1 65803 e.3.1.1 65804 1qa7B 219 1.13e+01 1havA b.47.1.4 26426 1buqA 125 1.17e+01 1opy d.17.4.3 38111 1eq2A 310 1.22e+01 1eq2A c.2.1.2 29814 1lh0A 213 1.25e+01 1opr 213 1.25e+01 1opr c.61.1.1 34091 1sto 213 1.26e+01 1opr c.61.1.1 34092 1qjgA 125 1.28e+01 1opy d.17.4.3 38102 1poy2 323 1.28e+01 1pot 1pot 325 1.29e+01 1pot c.94.1.1 35807 1j77A 209 1.33e+01 1j77A a.132.1.2 62674 1qjgE 125 1.34e+01 1opy d.17.4.3 38106 1i9zA 347 1.38e+01 1i9yA d.151.1.2 62102 1i9yA 347 1.38e+01 1i9yA d.151.1.2 62101 1yrgA 385 1.40e+01 1yrgA c.10.1.2 30854 1yrgB 385 1.40e+01 1yrgA c.10.1.2 30855 1k5dC 386 1.40e+01 c.10.1.2 68170 1i51B 105 1.41e+01 1qjgF 125 1.44e+01 1opy d.17.4.3 38107 1gdhA 320 1.45e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1oroA 213 1.58e+01 1opr c.61.1.1 34093 1mat 264 1.62e+01 1c24A d.127.1.1 41152 1gcjA 460 1.72e+01 1qgrA a.118.1.1 19125 1jxjA 496 1.77e+01 b.71.1.1 63314 c.1.8.1 63315 1eysH 259 1.78e+01 6prcH b.41.1.1 25484 f.2.1.2 43517 8cho 125 1.84e+01 1opy d.17.4.3 38108 1cvjB 190 1.86e+01 1cvjB d.58.7.1 39193 d.58.7.1 39194 1kgwA 496 1.90e+01 b.71.1.1 68600 c.1.8.1 68601 1cwxA 44 2.02e+01 1cwxA j.54.1.1 46338 1kguA 496 2.08e+01 b.71.1.1 68598 c.1.8.1 68599 1kgxA 496 2.09e+01 b.71.1.1 68602 c.1.8.1 68603 1kbkA 496 2.11e+01 1kbbA 496 2.12e+01 1hny 496 2.12e+01 1smd b.71.1.1 27769 c.1.8.1 28756 1b2yA 496 2.12e+01 1smd b.71.1.1 27772 c.1.8.1 28759 1c07A 95 2.13e+01 1eh2 a.39.1.6 17337 1dtyA 429 2.13e+01 1dtyA c.67.1.4 34495 1kb3A 496 2.14e+01 1e8xA 961 2.19e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1e7uA 961 2.19e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 3cpuA 496 2.21e+01 1smd b.71.1.1 63336 c.1.8.1 63337 1smd 496 2.22e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1pssH 237 2.28e+01 6prcH b.41.1.1 25479 f.2.1.2 43502 1ecfB 504 2.30e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1ecfA 504 2.30e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 6stdA 164 2.34e+01 3stdA d.17.4.1 38076 1iskA 125 2.34e+01 1opy d.17.4.3 38109 3stdA 165 2.38e+01 3stdA d.17.4.1 38073 1g4sA 226 2.43e+01 c.1.3.1 60247 1g67A 225 2.43e+01 c.1.3.1 60311 1g6cB 227 2.44e+01 c.1.3.1 60316 1g69B 228 2.44e+01 c.1.3.1 60314 1he8A 965 2.45e+01 1e8xA a.118.1.6 19154 b.7.1.1 23189 d.15.1.5 37637 d.144.1.4 41717 1hm9A 468 2.46e+01 b.81.1.4 65866 c.68.1.5 65867 1l3wA 546 2.48e+01 1fjjA 159 2.50e+01 1fjjA b.17.1.2 59852 1e8yA 966 2.55e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 2tpsA 227 2.56e+01 2tpsA c.1.3.1 28591 1jxkA 491 2.57e+01 b.71.1.1 63316 c.1.8.1 63317 1seiA 130 2.66e+01 1seiA d.140.1.1 41463 1g97A 459 2.69e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1std 172 2.75e+01 3stdA d.17.4.1 38089 2std 172 2.75e+01 3stdA d.17.4.1 38085 1eiwA 111 2.75e+01 1eiwA c.23.3.1 31130 2matA 264 2.78e+01 1c24A d.127.1.1 41146 3matA 265 2.80e+01 1c24A d.127.1.1 41149 1cr5A 189 2.89e+01 1cr5A b.52.2.3 26931 d.31.1.1 38465 3btaA 1295 2.91e+01 b.29.1.6 24268 b.42.4.2 25613 d.92.1.7 40304 h.4.2.1 45784 4matA 278 2.96e+01 1c24A d.127.1.1 41150 1qf7A 753 3.03e+01 1cf9A c.23.16.3 31461 e.5.1.1 42835 1k86A 253 3.09e+01 c.17.1.1 68288 1gqfA 265 3.11e+01 c.17.1.1 65470 1kpeA 126 3.14e+01 1kpf d.13.1.1 37508 1kpf 126 3.14e+01 1kpf d.13.1.1 37507 1ewiA 114 3.27e+01 1ewiA b.40.4.3 25302 1dtwA 400 3.34e+01 1qs0A c.36.1.3 31827 1k88B 253 3.41e+01 c.17.1.1 68291 1gnmA 99 3.48e+01 1hvc b.50.1.1 26672 1c24A 263 3.48e+01 1c24A d.127.1.1 41148 1c6xA 99 3.60e+01 1hvc b.50.1.1 26694 1ggkA 753 3.68e+01 1cf9A c.23.16.3 31453 e.5.1.1 42827 1ggjA 753 3.68e+01 1cf9A c.23.16.3 31457 e.5.1.1 42831 1cf9A 753 3.71e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1gghA 753 3.75e+01 1cf9A c.23.16.3 31465 e.5.1.1 42839 1gg9A 753 3.75e+01 1cf9A c.23.16.3 31445 e.5.1.1 42819 1ggeA 753 3.75e+01 1cf9A c.23.16.3 31449 e.5.1.1 42823 1jj2G 348 3.75e+01 j.84.1.1 63092 1cvrA 435 3.86e+01 1cvrA b.1.1.5 21949 c.17.1.2 31006 1f95A 89 3.89e+01 1cmiA d.39.1.1 38555