# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 2matA 264 1.72e-49 1c24A d.127.1.1 41146 1c24A 263 1.72e-49 1c24A d.127.1.1 41148 1mat 264 5.69e-49 1c24A d.127.1.1 41152 1a16 440 7.06e-42 1az9 c.55.2.1 33548 d.127.1.1 41165 1az9 457 7.07e-42 1az9 c.55.2.1 33547 d.127.1.1 41164 1xgsA 295 6.26e-37 1bn5 a.4.5.25 16216 d.127.1.1 41153 1b6a 478 3.13e-36 1bn5 a.4.5.25 16223 d.127.1.1 41160 1bn5 478 7.37e-36 1bn5 a.4.5.25 16224 d.127.1.1 41161 1chmA 401 6.43e-33 1chmA c.55.2.1 33545 d.127.1.1 41142 1gmlA 178 5.93e-01 1hzgA 295 1.16e+00 1hzgA d.194.1.1 61436 1e2tA 284 2.22e+00 1e2tA d.3.1.5 37121 1ekfA 365 2.76e+00 1ekfA e.17.1.1 59445 1a64A 97 2.89e+00 1cdcA b.1.1.1 19750 1qexA 288 2.92e+00 1qexA b.32.1.1 24425 1hq0A 295 2.94e+00 1hzgA d.194.1.1 61122 1i1kA 309 3.31e+00 1daaA e.17.1.1 61533 1guzA 310 3.36e+00 c.2.1.5 65586 d.162.1.1 65587 1b04A 318 3.40e+00 1b04A d.142.2.2 41579 1cdcA 99 3.57e+00 1cdcA b.1.1.1 19746 1cdcB 99 3.57e+00 1cdcA b.1.1.1 19747 1tkiA 321 3.68e+00 1tkiA d.144.1.1 41638 2jhbA 143 3.75e+00 2jhbA b.54.1.1 26950 1f60A 458 3.80e+00 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1gdeA 389 4.57e+00 c.67.1.1 60456 1ea7A 310 4.92e+00 1euwA 152 5.12e+00 1dupA b.85.4.1 28349 1a8o 70 5.40e+00 1a8o a.28.3.1 16953 1tie 172 5.42e+00 1wba b.42.4.1 25592 1dar 691 5.65e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1befA 181 5.86e+00 1befA b.47.1.3 26419 1dupA 152 5.99e+00 1dupA b.85.4.1 28351 1hyeA 313 6.19e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1bc8C 93 6.28e+00 1awcA a.4.5.21 16168 1epwA 1290 6.66e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1avwB 171 6.94e+00 1wba b.42.4.1 25599 1derA 547 7.02e+00 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1gpeA 587 7.42e+00 1gpeA c.3.1.2 30387 d.16.1.4 37951 1kcw 1046 7.71e+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 1oacA 727 8.47e+00 1oacA b.30.2.1 24390 d.17.2.1 38007 d.17.2.1 38008 d.82.1.1 40003 1fd9A 213 8.67e+00 1fd9A d.26.1.1 59771 1cskA 71 8.84e+00 1ckaA b.34.2.1 24513 1k59A 123 8.86e+00 1e42A 258 9.13e+00 1e42A b.1.10.1 22316 d.105.1.1 40792 1shg 62 9.26e+00 1ckaA b.34.2.1 24493 1pwt 61 9.27e+00 1tud b.34.2.1 24490 1bf5A 545 9.48e+00 1bg1A a.47.1.1 17766 b.2.5.1 22460 d.93.1.1 40526 1lr0A 129 9.51e+00 1seiA 130 9.51e+00 1seiA d.140.1.1 41463 1fliA 98 9.70e+00 1awcA a.4.5.21 16160 1h9dB 134 9.76e+00 2jhbA b.54.1.1 60822 1abrA 251 9.96e+00 1mrj d.165.1.1 42196 1f82A 424 1.01e+01 1f82A d.92.1.7 40307 1cmiA 85 1.08e+01 1cmiA d.39.1.1 38551 1ji1A 637 1.14e+01 1hbyA 123 1.16e+01 7rsa d.5.1.1 60936 1a3aA 148 1.18e+01 1a3aA d.112.1.1 40917 2mysB 166 1.19e+01 1wdcB a.39.1.5 17308 1spuB 727 1.25e+01 1oacA b.30.2.1 24399 d.17.2.1 38025 d.17.2.1 38026 d.82.1.1 40012 1jh2A 99 1.29e+01 b.35.1.1 63038 1d6zA 727 1.29e+01 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1rdr 461 1.33e+01 1rdr e.8.1.4 43116 1gof 639 1.33e+01 1gof b.1.1.5 21807 b.18.1.1 23709 b.69.1.1 27631 1svr 114 1.36e+01 1svy d.109.1.1 40833 1qrkA 731 1.38e+01 1f13A b.1.1.5 21889 b.1.5.1 22187 b.1.5.1 22188 d.3.1.4 37119 1qltA 560 1.38e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1semA 58 1.42e+01 1ckaA b.34.2.1 24544 1f83A 425 1.45e+01 1f82A d.92.1.7 40306 1vdrA 162 1.48e+01 1vdrA c.71.1.1 34893 1taq 832 1.49e+01 1taq a.60.7.1 18082 c.53.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1k3iA 656 1.50e+01 b.1.1.5 68113 b.18.1.1 68114 b.69.1.1 68115 1jbwA 428 1.51e+01 c.59.1.2 62860 c.72.2.2 62861 1gx3A 284 1.51e+01 1svq 114 1.58e+01 1svy d.109.1.1 40832 1ej6A 1289 1.58e+01 i.7.1.1 45967 1gqwA 283 1.59e+01 1eylA 186 1.63e+01 1wba b.42.4.1 25593 1a3aC 148 1.64e+01 1a3aA d.112.1.1 40919 1e2wA 251 1.67e+01 1hcz b.2.6.1 22466 b.84.2.2 28252 1qf8A 182 1.70e+01 1qf8A g.41.4.1 45212 1ihfB 94 1.70e+01 1huuA a.55.1.1 17894 1ckaA 57 1.71e+01 1ckaA b.34.2.1 24459 1g5gB 481 1.72e+01 f.12.1.1 65157 h.3.2.1 65158 1hmpA 217 1.72e+01 1qk3A c.61.1.1 34075 1g2bA 62 1.72e+01 1tud b.34.2.1 24488 1tud 62 1.74e+01 1tud b.34.2.1 24489 1vaoA 560 1.75e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1fgs 428 1.79e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1io1A 398 1.80e+01 1io1A e.32.1.1 62611 1vppV 102 1.81e+01 1vpfA g.17.1.1 44753 1svy 114 1.82e+01 1svy d.109.1.1 40831 1a49A 530 1.83e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1kxu 333 1.83e+01 1jkw a.74.1.1 18358 a.74.1.1 18359 1bsjA 168 1.86e+01 1bs4A d.167.1.1 42302 1gwcA 230 1.86e+01 1bncA 449 1.97e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1cc1L 498 2.07e+01 1h2rL e.18.1.1 43301 1jenA 267 2.11e+01 1jenA 1jhfA 202 2.12e+01 a.4.5.2 63057 b.87.1.1 63058 1a6jA 163 2.14e+01 1a6jA d.112.1.1 40915 1ycqA 107 2.15e+01 1ycqA a.42.1.1 17419 1ggtB 731 2.21e+01 1f13A b.1.1.5 21882 b.1.5.1 22173 b.1.5.1 22174 d.3.1.4 37112 1gguA 731 2.25e+01 1f13A b.1.1.5 21885 b.1.5.1 22179 b.1.5.1 22180 d.3.1.4 37115 1jkw 323 2.28e+01 1jkw a.74.1.1 18356 a.74.1.1 18357 1qmuA 380 2.30e+01 1qmuA b.3.2.1 22534 c.56.5.1 33827 2pviA 157 2.31e+01 3pviA c.52.1.6 33302 1goh 639 2.31e+01 1gof b.1.1.5 21809 b.18.1.1 23711 b.69.1.1 27633 1evuA 731 2.32e+01 1f13A b.1.1.5 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 1enfA 212 2.33e+01 3seb b.40.2.2 25198 d.15.6.1 37787 1jh5A 144 2.34e+01 b.22.1.1 66697 1jdiA 231 2.36e+01 c.74.1.1 66551 1g4wR 383 2.45e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1gmuA 143 2.53e+01 b.107.1.1 65335 d.58.38.1 65336 1ycsB 239 2.56e+01 1ycsB a.118.2.1 19155 b.34.2.1 24553 1rlr 761 2.58e+01 1rlr a.98.1.1 18753 c.7.1.2 30679 1mgn 154 2.58e+01 1a6m a.1.1.2 15097 1nkl 78 2.60e+01 1nkl a.64.1.1 18140 1ktjA 129 2.61e+01 1iq3A 110 2.64e+01 1iq3A a.39.1.6 62640 1qlpA 394 2.66e+01 1ovaA e.1.1.1 42628 1qorA 327 2.66e+01 1qorA b.35.1.2 24766 c.2.1.1 29782 1c14A 262 2.67e+01 1eny c.2.1.2 29927 1ipwA 175 2.70e+01 2prd b.40.5.1 25427 1je5A 206 2.73e+01 1je5A b.40.4.7 62909 1a3gA 308 2.75e+01 1daaA e.17.1.1 43286 1lmhA 184 2.77e+01 1dcs 311 2.84e+01 1dcs b.82.2.1 28124 1gegA 256 2.89e+01 1ybvA c.2.1.2 29888 1eywA 331 2.90e+01 1pscA c.1.9.3 29057 1hzyA 332 2.92e+01 1pscA c.1.9.3 61468 1dmhA 311 2.93e+01 1dmhA b.3.6.1 22633 3pviA 157 2.94e+01 3pviA c.52.1.6 33300 1a3h 300 3.04e+01 7a3hA c.1.8.3 28819 1fj7A 101 3.09e+01 1fj7A d.58.7.1 39209 1volA 204 3.09e+01 1tfb a.74.1.2 18370 a.74.1.2 18371 1griA 217 3.10e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 1qdeA 224 3.11e+01 1qvaA c.37.1.13 32410 1kiuB 279 3.20e+01 1f8yA 157 3.23e+01 1f8xA c.23.14.1 31395 1f13A 731 3.23e+01 1f13A b.1.1.5 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1hxvA 113 3.24e+01 2spo 154 3.24e+01 1a6m a.1.1.2 15053 1obwA 175 3.33e+01 2prd b.40.5.1 25416 1hskA 326 3.34e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1noa 113 3.34e+01 2mcm b.1.7.1 22208 1f8xA 157 3.37e+01 1f8xA c.23.14.1 31397 9apiA 347 3.38e+01 1ovaA e.1.1.1 42630 1i7oA 429 3.40e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1ayyA 151 3.44e+01 1apyA d.153.1.5 42016 1ffkN 95 3.51e+01 1ffkN b.34.5.1 24606 1i40A 175 3.57e+01 b.40.5.1 66024 1aipE 405 3.62e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1ihoA 283 3.67e+01 1ihoA c.26.1.4 62390 1ew6B 137 3.72e+01 1ewaA a.1.1.2 15638 7a3hA 303 3.73e+01 7a3hA c.1.8.3 28817 1d5mB 192 3.74e+01 1iakB b.1.1.2 21618 d.19.1.1 38192 5hvpA 99 3.76e+01 1fmb b.50.1.1 26605 9gafA 295 3.79e+01 1apyA d.153.1.5 42008 1ew6A 137 3.80e+01 1ewaA a.1.1.2 15637 1g2aA 168 3.82e+01 d.167.1.1 65109 1eemA 241 3.84e+01 1eemA a.45.1.1 17717 c.47.1.5 33011 1ewaA 137 3.85e+01 1ewaA a.1.1.2 15639 1pta 318 3.88e+01 1pscA c.1.9.3 29064 1ae7 119 3.96e+01 1poa a.133.1.2 19553 1bs4A 168 3.97e+01 1bs4A d.167.1.1 42287 1icjA 168 3.97e+01 1bs4A d.167.1.1 42284 1g4yR 148 3.99e+01 1cll a.39.1.5 60252