# List of top-scoring protein chains for t2k-100-30-str 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 1c24A 263 2.30e-36 1c24A d.127.1.1 41148 1mat 264 2.56e-36 1c24A d.127.1.1 41152 2matA 264 2.93e-36 1c24A d.127.1.1 41146 1a16 440 2.88e-32 1az9 c.55.2.1 33548 d.127.1.1 41165 1az9 457 3.53e-32 1az9 c.55.2.1 33547 d.127.1.1 41164 1xgsA 295 8.27e-29 1bn5 a.4.5.25 16216 d.127.1.1 41153 1bn5 478 1.09e-27 1bn5 a.4.5.25 16224 d.127.1.1 41161 1b6a 478 1.17e-27 1bn5 a.4.5.25 16223 d.127.1.1 41160 1chmA 401 3.54e-26 1chmA c.55.2.1 33545 d.127.1.1 41142 1ayyA 151 4.48e-01 1apyA d.153.1.5 42016 1dar 691 4.99e-01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1f60A 458 5.37e-01 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1derA 547 1.11e+00 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1kcw 1046 1.24e+00 1kcw b.6.1.3 23151 b.6.1.3 23152 b.6.1.3 23153 b.6.1.3 23154 b.6.1.3 23155 b.6.1.3 23156 1tie 172 1.26e+00 1wba b.42.4.1 25592 1qexA 288 1.41e+00 1qexA b.32.1.1 24425 1cc1L 498 1.52e+00 1h2rL e.18.1.1 43301 1jhfA 202 1.54e+00 a.4.5.2 63057 b.87.1.1 63058 1f82A 424 1.85e+00 1f82A d.92.1.7 40307 1epwA 1290 1.88e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1ea7A 310 1.91e+00 1fliA 98 2.02e+00 1awcA a.4.5.21 16160 1kv8A 216 2.24e+00 1vdrA 162 2.47e+00 1vdrA c.71.1.1 34893 1bc8C 93 2.61e+00 1awcA a.4.5.21 16168 1gof 639 2.64e+00 1gof b.1.1.5 21807 b.18.1.1 23709 b.69.1.1 27631 1avwB 171 2.64e+00 1wba b.42.4.1 25599 1bf5A 545 3.03e+00 1bg1A a.47.1.1 17766 b.2.5.1 22460 d.93.1.1 40526 1e2tA 284 3.03e+00 1e2tA d.3.1.5 37121 2cmd 312 3.07e+00 2cmd c.2.1.5 30135 d.162.1.1 42102 1svq 114 3.09e+00 1svy d.109.1.1 40832 1svy 114 3.33e+00 1svy d.109.1.1 40831 1mgn 154 3.39e+00 1a6m a.1.1.2 15097 1hzgA 295 3.50e+00 1hzgA d.194.1.1 61436 1cskA 71 3.57e+00 1ckaA b.34.2.1 24513 2spo 154 3.79e+00 1a6m a.1.1.2 15053 1kbvA 327 3.80e+00 b.6.1.3 68395 b.6.1.3 68396 1f83A 425 3.96e+00 1f82A d.92.1.7 40306 1goh 639 4.02e+00 1gof b.1.1.5 21809 b.18.1.1 23711 b.69.1.1 27633 1je5A 206 4.08e+00 1je5A b.40.4.7 62909 1ifrA 121 4.17e+00 2mcm 112 4.20e+00 2mcm b.1.7.1 22207 1e0tA 470 4.27e+00 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1eylA 186 4.30e+00 1wba b.42.4.1 25593 1a49A 530 4.31e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1bbhA 131 4.74e+00 1bbhA a.24.3.2 16546 1guzA 310 4.76e+00 c.2.1.5 65586 d.162.1.1 65587 1hq0A 295 4.87e+00 1hzgA d.194.1.1 61122 1k3iA 656 4.96e+00 b.1.1.5 68113 b.18.1.1 68114 b.69.1.1 68115 2ezl 99 4.97e+00 2ezk a.4.1.2 16026 1a64A 97 5.02e+00 1cdcA b.1.1.1 19750 1kq4A 232 5.10e+00 d.207.1.1 68791 1qf8A 182 5.12e+00 1qf8A g.41.4.1 45212 1a3aC 148 5.18e+00 1a3aA d.112.1.1 40919 1a3aA 148 5.42e+00 1a3aA d.112.1.1 40917 1apyA 162 5.44e+00 1apyA d.153.1.5 42004 2ezk 99 5.89e+00 2ezk a.4.1.2 16027 1b9zA 516 6.07e+00 1b9zA b.3.1.1 22528 c.1.8.2 28798 1lldA 319 6.12e+00 3ldh c.2.1.5 30177 d.162.1.1 42144 1dupA 152 6.28e+00 1dupA b.85.4.1 28351 1euwA 152 6.28e+00 1dupA b.85.4.1 28349 9gafA 295 6.43e+00 1apyA d.153.1.5 42008 5bcaA 516 6.53e+00 1b9zA b.3.1.1 22529 c.1.8.2 28799 1hxvA 113 6.53e+00 1kv7A 488 6.87e+00 b.6.1.3 68873 b.6.1.3 68874 b.6.1.3 68875 3ncmA 92 7.01e+00 3ncmA b.1.1.4 21702 1gmlA 178 7.06e+00 1befA 181 7.19e+00 1befA b.47.1.3 26419 1svr 114 7.50e+00 1svy d.109.1.1 40833 1imdA 277 7.70e+00 1imbA e.7.1.1 42968 1gegA 256 7.71e+00 1ybvA c.2.1.2 29888 1jk3A 158 7.83e+00 d.92.1.11 66790 1e42A 258 8.00e+00 1e42A b.1.10.1 22316 d.105.1.1 40792 1fd9A 213 8.02e+00 1fd9A d.26.1.1 59771 1gpeA 587 8.11e+00 1gpeA c.3.1.2 30387 d.16.1.4 37951 1h91A 180 8.15e+00 b.60.1.1 60805 1pmy 123 8.29e+00 1bqk b.6.1.1 22888 1bdmA 327 8.33e+00 1bmdA c.2.1.5 30137 d.162.1.1 42104 1i4uA 181 8.38e+00 b.60.1.1 61732 1b4kA 337 8.40e+00 1b4kA c.1.10.3 29184 1rhoA 145 8.77e+00 1rhoA b.1.1.5 21899 1shg 62 8.87e+00 1ckaA b.34.2.1 24493 1jdpA 441 8.93e+00 c.93.1.1 62906 1pwt 61 9.05e+00 1tud b.34.2.1 24490 1cdcA 99 9.06e+00 1cdcA b.1.1.1 19746 1noa 113 9.15e+00 2mcm b.1.7.1 22208 1gjnA 153 9.20e+00 1cdcB 99 9.61e+00 1cdcA b.1.1.1 19747 1bzpA 153 9.97e+00 1a6m a.1.1.2 15020 1mbd 153 1.04e+01 1a6m a.1.1.2 15033 1bb9 115 1.06e+01 1bb9 b.34.2.1 24554 1rhoC 145 1.08e+01 1rhoA b.1.1.5 21901 1aozA 552 1.11e+01 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 1io1A 398 1.12e+01 1io1A e.32.1.1 62611 1xsm 390 1.13e+01 1xsm a.25.1.2 16804 1i6pA 220 1.14e+01 1ddzA c.53.2.1 61848 1oacA 727 1.18e+01 1oacA b.30.2.1 24390 d.17.2.1 38007 d.17.2.1 38008 d.82.1.1 40003 1qqjA 419 1.19e+01 1qcnA b.34.8.1 59034 d.177.1.1 59035 1abrA 251 1.22e+01 1mrj d.165.1.1 42196 1qcnA 421 1.24e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1d6zA 727 1.24e+01 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1exnA 290 1.25e+01 1exnA a.60.7.1 18088 c.53.1.2 33358 1ku2A 241 1.28e+01 1jkw 323 1.28e+01 1jkw a.74.1.1 18356 a.74.1.1 18357 1imbA 277 1.29e+01 1imbA e.7.1.1 42957 1bvqA 141 1.29e+01 1bvqA d.38.1.1 38542 1j8fA 323 1.30e+01 1j8fA c.31.1.5 62738 1hyoA 421 1.33e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1bmdA 327 1.34e+01 1bmdA c.2.1.5 30139 d.162.1.1 42106 1gguA 731 1.36e+01 1f13A b.1.1.5 21885 b.1.5.1 22179 b.1.5.1 22180 d.3.1.4 37115 1g4uS 383 1.38e+01 1g4uS a.24.11.1 16643 c.45.1.2 32691 1exnB 290 1.38e+01 1exnA a.60.7.1 18089 c.53.1.2 33359 1ggtB 731 1.40e+01 1f13A b.1.1.5 21882 b.1.5.1 22173 b.1.5.1 22174 d.3.1.4 37112 1g4wR 383 1.41e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 2hhmA 276 1.44e+01 1imbA e.7.1.1 42955 1jnyA 435 1.45e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1jg1A 235 1.46e+01 c.66.1.7 66661 1gzgA 337 1.46e+01 1k59A 123 1.46e+01 1spuB 727 1.48e+01 1oacA b.30.2.1 24399 d.17.2.1 38025 d.17.2.1 38026 d.82.1.1 40012 1kcqA 104 1.49e+01 d.109.1.1 68449 1g59A 468 1.50e+01 a.97.1.1 60257 c.26.1.1 60258 1gnlA 544 1.51e+01 1brmA 367 1.52e+01 1brmA c.2.1.3 30030 d.81.1.1 39945 1e6yC 247 1.56e+01 1mroC d.58.31.1 39441 1jgtA 513 1.57e+01 c.26.2.1 66684 d.153.1.1 66685 1dcs 311 1.66e+01 1dcs b.82.2.1 28124 1lo7A 141 1.67e+01 1evuA 731 1.67e+01 1f13A b.1.1.5 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 1aru 344 1.69e+01 1arv a.93.1.1 18589 1hbyA 123 1.69e+01 7rsa d.5.1.1 60936 1ew6A 137 1.69e+01 1ewaA a.1.1.2 15637 1ewaA 137 1.69e+01 1ewaA a.1.1.2 15639 1volA 204 1.71e+01 1tfb a.74.1.2 18370 a.74.1.2 18371 1i0dA 332 1.73e+01 1pscA c.1.9.3 61487 1arv 344 1.74e+01 1arv a.93.1.1 18590 1jdiA 231 1.74e+01 c.74.1.1 66551 1hzyA 332 1.74e+01 1pscA c.1.9.3 61468 6ldh 330 1.76e+01 3ldh c.2.1.5 30161 d.162.1.1 42128 1efyA 350 1.76e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1cd8 114 1.77e+01 1cd8 b.1.1.1 19714 1hyeA 313 1.77e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1dwtA 153 1.82e+01 1a6m a.1.1.2 15190 1pscA 365 1.84e+01 1pscA c.1.9.3 29058 1a6m 151 1.90e+01 1a6m a.1.1.2 15018 1a8o 70 1.91e+01 1a8o a.28.3.1 16953 1lycA 343 1.91e+01 1eywA 331 1.91e+01 1pscA c.1.9.3 29057 1gzcA 239 1.92e+01 1jv2B 692 1.97e+01 b.1.15.1 67338 c.62.1.1 67339 d.200.1.1 67340 g.3.11.6 67341 g.3.11.6 67342 1hcz 252 1.98e+01 1hcz b.2.6.1 22464 b.84.2.2 28250 1bsjA 168 2.02e+01 1bs4A d.167.1.1 42302 1bdmB 327 2.02e+01 1bmdA c.2.1.5 30138 d.162.1.1 42105 1ji1A 637 2.02e+01 1kk1A 410 2.05e+01 1iirA 415 2.05e+01 1iirA c.87.1.5 62453 1i1kA 309 2.07e+01 1daaA e.17.1.1 61533 1jpnA 296 2.08e+01 a.24.13.1 67039 c.37.1.10 67040 1ihoA 283 2.08e+01 1ihoA c.26.1.4 62390 1tud 62 2.10e+01 1tud b.34.2.1 24489 1kxu 333 2.11e+01 1jkw a.74.1.1 18358 a.74.1.1 18359 1sro 76 2.11e+01 1sro b.40.4.5 25327 1g2bA 62 2.11e+01 1tud b.34.2.1 24488 3ssi 113 2.11e+01 3ssi d.84.1.1 40032 1gesA 450 2.14e+01 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1eut 605 2.16e+01 1eut b.1.1.5 21891 b.18.1.1 23712 b.68.1.1 27609 1ktjA 129 2.17e+01 1qorA 327 2.19e+01 1qorA b.35.1.2 24766 c.2.1.1 29782 1rvaA 244 2.25e+01 1rvaA c.52.1.2 33240 1dun 134 2.25e+01 1dun b.85.4.1 28371 1f13A 731 2.26e+01 1f13A b.1.1.5 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1a3gA 308 2.27e+01 1daaA e.17.1.1 43286 1eonA 245 2.27e+01 1rvaA c.52.1.2 33238 1brwA 433 2.39e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1e85A 127 2.42e+01 1bbhA a.24.3.2 16549 1mroC 247 2.42e+01 1mroC d.58.31.1 39437 1hbnC 248 2.43e+01 1mroC d.58.31.1 60902 1d1gA 168 2.43e+01 1d1gA c.71.1.1 34889 1bg1A 722 2.44e+01 1bg1A a.47.1.1 17767 b.2.5.1 22461 d.93.1.1 40527 1jj2P 95 2.46e+01 1ffkN b.34.5.1 63101 1a3h 300 2.46e+01 7a3hA c.1.8.3 28819 1ffkN 95 2.48e+01 1ffkN b.34.5.1 24606 7a3hA 303 2.48e+01 7a3hA c.1.8.3 28817 1gln 468 2.48e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1hsr 344 2.50e+01 1arv a.93.1.1 18592 1goiA 499 2.51e+01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1qlaB 239 2.52e+01 1qlaB a.1.2.1 15679 d.15.4.2 37707 1e15A 499 2.52e+01 1e15A b.72.2.1 27810 c.1.8.5 29006 d.26.3.1 38440 1lxtA 561 2.52e+01 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1cgo 127 2.55e+01 1cpq a.24.3.2 16550 1bv1 159 2.60e+01 1bv1 d.129.3.1 41313 1vppV 102 2.61e+01 1vpfA g.17.1.1 44753 1smd 496 2.62e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1d9tA 289 2.63e+01 1deaA c.35.1.1 31767 1g8lA 411 2.64e+01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1ihfB 94 2.64e+01 1huuA a.55.1.1 17894 2pviA 157 2.65e+01 3pviA c.52.1.6 33302 1sig 339 2.65e+01 1sig a.112.1.1 19068 1fs7A 485 2.67e+01 1qdbA a.138.1.3 19691 1tkiA 321 2.68e+01 1tkiA d.144.1.1 41638 1a26 361 2.69e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 3tdt 274 2.70e+01 3tdt b.81.1.2 28053 1semA 58 2.71e+01 1ckaA b.34.2.1 24544 2rusB 490 2.72e+01 1burA c.1.14.1 29385 d.58.9.1 39291 1icjA 168 2.72e+01 1bs4A d.167.1.1 42284 1e6pA 499 2.73e+01 1e15A b.72.2.1 59314 c.1.8.5 59315 d.26.3.1 59316 1glaF 168 2.73e+01 1gpr b.84.3.1 28274 2tdt 274 2.73e+01 3tdt b.81.1.2 28054 1bqk 124 2.76e+01 1bqk b.6.1.1 22889 1cvrA 435 2.78e+01 1cvrA b.1.1.5 21949 c.17.1.2 31006 1ae7 119 2.80e+01 1poa a.133.1.2 19553 1e2uA 553 2.81e+01 1e1dA e.26.1.1 43362 1fsoA 139 2.81e+01 1rhoA b.1.1.5 60007 1gntA 553 2.82e+01 1seiA 130 2.82e+01 1seiA d.140.1.1 41463 1ekbB 235 2.84e+01 5ptp b.47.1.2 26282 1g2aA 168 2.84e+01 d.167.1.1 65109 6prcH 258 2.90e+01 6prcH b.41.1.1 25457 f.2.1.2 43436 1bywA 110 2.94e+01 1bywA d.110.3.3 40912 1c9oA 66 2.96e+01 1mjc b.40.4.5 25325 1ckaA 57 2.98e+01 1ckaA b.34.2.1 24459 1nkl 78 2.99e+01 1nkl a.64.1.1 18140 1ekfA 365 3.00e+01 1ekfA e.17.1.1 59445 1fxkC 133 3.03e+01 1fxkC a.2.5.1 15702 5eat 548 3.03e+01 5eat a.102.4.1 18853 a.128.1.3 19445 1lr0A 129 3.04e+01 1bs4A 168 3.05e+01 1bs4A d.167.1.1 42287 1b57A 358 3.05e+01 1dosA c.1.10.2 29177 1ipwA 175 3.07e+01 2prd b.40.5.1 25427 1tuc 63 3.07e+01 1tuc b.34.2.1 24492 1jbwA 428 3.08e+01 c.59.1.2 62860 c.72.2.2 62861 1frb 315 3.08e+01 1frb c.1.7.1 28665 1fmcA 255 3.13e+01 1cydA c.2.1.2 29856 2cbp 96 3.13e+01 2cbp b.6.1.1 22895 1vpfA 102 3.17e+01 1vpfA g.17.1.1 44767 1ah9 71 3.20e+01 1ah9 b.40.4.5 25330 1prxA 224 3.21e+01 1prxA c.47.1.10 33076 1octC 156 3.21e+01 1au7A a.4.1.1 15991 a.35.1.1 17017 1qg6A 261 3.23e+01 1eny c.2.1.2 29919 1reqA 727 3.24e+01 1reqA c.1.19.1 29620 c.23.6.1 31247 1bt0A 76 3.27e+01 1ubi d.15.1.1 37607 1hskA 326 3.27e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1pou 71 3.28e+01 1au7A a.35.1.1 17020 1dxrH 258 3.31e+01 6prcH b.41.1.1 25456 f.2.1.2 43433 1ig8A 486 3.32e+01 2yhx c.55.1.3 64746 c.55.1.3 64747 1enfA 212 3.39e+01 3seb b.40.2.2 25198 d.15.6.1 37787 1gcqC 70 3.43e+01 1gcpA b.34.2.1 60436 1a9v 129 3.45e+01 1a9v b.1.1.5 21946 1gdeA 389 3.45e+01 c.67.1.1 60456 3vtk 343 3.46e+01 1qhiA c.37.1.1 31884 2mysB 166 3.52e+01 1wdcB a.39.1.5 17308 1ng1 294 3.54e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1rdr 461 3.55e+01 1rdr e.8.1.4 43116 1apxA 249 3.55e+01 1ryc a.93.1.1 18669 1hyhA 309 3.56e+01 1hyhA c.2.1.5 30150 d.162.1.1 42117 1iatA 557 3.61e+01 1dqrA c.80.1.2 62123 1euu 605 3.61e+01 1eut b.1.1.5 21892 b.18.1.1 23713 b.68.1.1 27610 1ytfB 53 3.62e+01 1ytfB a.32.1.1 16997 1ew6B 137 3.65e+01 1ewaA a.1.1.2 15638 1jae 471 3.65e+01 1smd b.71.1.1 27773 c.1.8.1 28760 1umuB 116 3.66e+01 1umuA b.87.1.1 28383 1lk5A 229 3.75e+01 1e1dA 553 3.75e+01 1e1dA e.26.1.1 43363 3cox 507 3.76e+01 1b8sA c.3.1.2 30332 d.16.1.1 37863 1dmhA 311 3.78e+01 1dmhA b.3.6.1 22633 1c0aA 585 3.78e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1pta 318 3.79e+01 1pscA c.1.9.3 29064 1e3oC 160 3.82e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1gwcA 230 3.83e+01 1eaf 243 3.86e+01 1eaf c.43.1.1 32617 1f3z 161 3.86e+01 1gpr b.84.3.1 28273 2cb5A 453 3.89e+01 3gcb d.3.1.1 37035 1bag 425 3.91e+01 1bag b.71.1.1 27720 c.1.8.1 28707 1e2wA 251 3.92e+01 1hcz b.2.6.1 22466 b.84.2.2 28252 1fgs 428 3.93e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1ig3A 263 3.95e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1qsgA 265 3.99e+01 1eny c.2.1.2 29935 1ycsB 239 3.99e+01 1ycsB a.118.2.1 19155 b.34.2.1 24553