# 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 1eo1A 124 2.32e-18 1eo1A c.55.5.1 33739 1kv8A 216 5.08e-01 1g5cA 170 5.98e-01 1g5cA c.53.2.1 60264 1auoA 218 6.07e-01 1auoA c.69.1.14 34716 1aurA 218 6.07e-01 1auoA c.69.1.14 34718 1jvkA 216 8.78e-01 1qorA 327 8.81e-01 1qorA b.35.1.2 24766 c.2.1.1 29782 1g8lA 411 1.33e+00 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1iodA 129 1.33e+00 1ixxB d.169.1.1 62622 1dclA 216 1.33e+00 8fabA b.1.1.1 20565 b.1.1.2 21472 1fc5A 411 1.36e+00 1g8lA b.85.6.1 59762 b.103.1.1 59763 c.57.1.2 59764 1mcsA 216 1.49e+00 8fabA b.1.1.1 20585 b.1.1.2 21492 2mcg1 216 1.49e+00 8fabA 1mcoL 216 1.59e+00 8fabA b.1.1.1 20563 b.1.1.2 21468 1dn0A 215 1.68e+00 32c2A b.1.1.1 19830 b.1.1.2 20934 1d02A 202 1.94e+00 1d02A c.52.1.8 33313 1dxy 333 2.15e+00 1dxy c.2.1.4 30094 c.23.12.1 31354 1ako 268 2.18e+00 1ako d.151.1.1 41779 1b74A 254 2.30e+00 1b74A c.78.2.1 35264 c.78.2.1 35265 1b73A 254 2.30e+00 1b74A c.78.2.1 35266 c.78.2.1 35267 1tif 78 2.63e+00 1tif d.15.8.1 37836 1j5eE 161 2.93e+00 1fjgE 162 2.94e+00 1pkp d.14.1.1 37553 d.50.1.2 38789 1gpjA 404 3.48e+00 a.151.1.1 65451 c.2.1.10 65452 d.58.39.1 65453 1fsz 372 3.48e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1ala 321 3.90e+00 1avc a.65.1.1 18153 1cc4A 394 4.37e+00 1pbe c.3.1.2 30340 d.16.1.2 37871 1fotA 318 4.81e+00 1cdkA d.144.1.1 59938 1d9sA 136 4.83e+00 1bd8 i.11.1.1 46013 1g5iD 454 5.42e+00 1g5hA c.51.1.1 60284 d.104.1.1 60285 1g5hA 454 5.47e+00 1g5hA c.51.1.1 60270 d.104.1.1 60271 1bgj 394 5.47e+00 1pbe c.3.1.2 30352 d.16.1.2 37883 1pkn 530 5.52e+00 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1cj3A 392 5.83e+00 1pbe c.3.1.2 30347 d.16.1.2 37878 1e69B 322 6.44e+00 1e69B c.37.1.12 32377 1bpyA 335 6.85e+00 1bpyA a.60.6.1 17980 e.9.1.1 43122 1c1eL 216 7.25e+00 8fabA b.1.1.1 20238 b.1.1.2 21250 7aatA 401 7.87e+00 1ajsA c.67.1.1 34250 1srrA 124 7.94e+00 1dz3A c.23.1.1 31110 1f51F 119 8.13e+00 1dz3A c.23.1.1 31115 1i0hA 205 8.25e+00 1avmA a.2.11.1 15760 d.44.1.1 38685 1en4A 205 8.30e+00 1avmA a.2.11.1 59457 d.44.1.1 59458 1en5A 205 8.43e+00 1avmA a.2.11.1 59465 d.44.1.1 59466 1i08A 205 8.44e+00 1avmA a.2.11.1 15770 d.44.1.1 38695 1d5nA 205 8.46e+00 1avmA a.2.11.1 15762 d.44.1.1 38687 1reiA 107 8.53e+00 8fabA b.1.1.1 20520 1vpe 398 8.56e+00 16pk c.86.1.1 35453 1php 394 8.89e+00 16pk c.86.1.1 35452 1cjmA 295 8.89e+00 1aquA c.37.1.5 31950 1igmL 115 8.96e+00 8fabA b.1.1.1 19826 1yrgA 385 9.05e+00 1yrgA c.10.1.2 30854 1yrgB 385 9.05e+00 1yrgA c.10.1.2 30855 1h70A 255 9.07e+00 1h70A d.126.1.3 60711 1k5dC 386 9.08e+00 c.10.1.2 68170 1iqdA 211 9.14e+00 32c2A b.1.1.1 62644 b.1.1.2 62645 1en6A 205 9.49e+00 1avmA a.2.11.1 59473 d.44.1.1 59474 1vgeL 214 9.76e+00 8fabA b.1.1.1 20094 b.1.1.2 21126 1akaA 401 1.00e+01 1ajsA c.67.1.1 34258 1bxlA 181 1.01e+01 1maz f.1.4.1 43396 1jw9B 249 1.01e+01 c.111.1.1 67377 2nadA 393 1.01e+01 2nadA c.2.1.4 30090 c.23.12.1 31350 2nacA 393 1.01e+01 2nadA c.2.1.4 30088 c.23.12.1 31348 1cc6A 394 1.02e+01 1pbe c.3.1.2 30344 d.16.1.2 37875 1jexA 94 1.04e+01 1cyo d.120.1.1 62923 1tmy 120 1.06e+01 1dbwA c.23.1.1 31083 1anxA 319 1.07e+01 1avc a.65.1.1 18161 1avhA 320 1.07e+01 1avc a.65.1.1 18159 1hvd 319 1.07e+01 1avc a.65.1.1 18154 1bf3 394 1.08e+01 1pbe c.3.1.2 30346 d.16.1.2 37877 1maz 221 1.09e+01 1maz f.1.4.1 43393 1e1eB 512 1.11e+01 1e70M c.1.8.4 28945 1e55A 512 1.11e+01 1e70M c.1.8.4 28934 1bwwA 109 1.12e+01 8fabA b.1.1.1 20518 1k6dA 220 1.12e+01 1sav 320 1.14e+01 1avc a.65.1.1 18158 1b2pA 119 1.14e+01 1b2pA b.78.1.1 27998 1hvg 319 1.18e+01 1avc a.65.1.1 18166 1hvf 319 1.19e+01 1avc a.65.1.1 18155 1bkwA 394 1.19e+01 1pbe c.3.1.2 30343 d.16.1.2 37874 1bc1 319 1.19e+01 1avc a.65.1.1 18173 1bc3 319 1.19e+01 1avc a.65.1.1 18175 1bgn 394 1.21e+01 1pbe c.3.1.2 30339 d.16.1.2 37870 1cj4A 392 1.22e+01 1pbe c.3.1.2 30345 d.16.1.2 37876 1pbf 394 1.23e+01 1pbe c.3.1.2 30349 d.16.1.2 37880 1pbd 394 1.23e+01 1pbe c.3.1.2 30342 d.16.1.2 37873 1bcw 319 1.24e+01 1avc a.65.1.1 18176 1fehA 574 1.26e+01 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1bcz 319 1.26e+01 1avc a.65.1.1 18177 1ce1L 211 1.27e+01 8fabA b.1.1.1 20318 b.1.1.2 21310 1cm7A 363 1.28e+01 1cnzA c.77.1.1 35063 2ran 316 1.28e+01 1avc a.65.1.1 18170 1cj2A 391 1.29e+01 1pbe c.3.1.2 30351 d.16.1.2 37882 1a8b 318 1.29e+01 1avc a.65.1.1 18171 1beyL 214 1.30e+01 8fabA b.1.1.1 20320 b.1.1.2 21312 1jf5A 585 1.31e+01 1in8A 334 1.31e+01 1hqcA a.4.5.11 62605 c.37.1.13 62606 1jf6A 585 1.31e+01 1bvzA 585 1.31e+01 1bvzA b.1.1.5 21856 b.71.1.1 27783 c.1.8.1 28770 1awcB 153 1.32e+01 1bd8 a.118.2.1 19156 1bc0 319 1.33e+01 1avc a.65.1.1 18174 1smlA 269 1.38e+01 1smlA d.157.1.1 42053 1bcy 319 1.38e+01 1avc a.65.1.1 18172 1kafA 108 1.40e+01 d.199.1.1 68372 1jl8A 585 1.44e+01 b.1.1.5 63163 b.71.1.1 63164 c.1.8.1 63165 1hyxL 216 1.49e+01 8fabA b.1.1.1 20166 b.1.1.2 21190 1ycsB 239 1.52e+01 1ycsB a.118.2.1 19155 b.34.2.1 24553 1gm5A 780 1.54e+01 a.29.4.1 65298 b.40.4.9 65299 c.37.1.13 65300 c.37.1.13 65301 2pdd 43 1.61e+01 1ebdC a.9.1.1 16358 2pde 43 1.61e+01 2pde a.9.1.1 16359 1dsfL 112 1.62e+01 8fabA b.1.1.1 20246 2fsp 124 1.63e+01 1dz3A c.23.1.1 31119 1ebdC 41 1.65e+01 1ebdC a.9.1.1 16355 1l9uA 314 1.69e+01 1ar2 109 1.69e+01 8fabA b.1.1.1 20522 1j97A 211 1.71e+01 1f5sA c.108.1.4 62753 1f5sA 211 1.71e+01 1f5sA c.108.1.4 59656 1iw7A 315 1.72e+01 1g7hA 107 1.73e+01 32c2A b.1.1.1 19948 1cnzA 363 1.75e+01 1cnzA c.77.1.1 35061 1doc 394 1.77e+01 1pbe c.3.1.2 30356 d.16.1.2 37887 1pxb 394 1.77e+01 1pbe c.3.1.2 30367 d.16.1.2 37898 1k0iA 394 1.77e+01 c.3.1.2 67942 d.16.1.2 67943 1pxc 394 1.77e+01 1pbe c.3.1.2 30361 d.16.1.2 37892 1dob 394 1.77e+01 1pbe c.3.1.2 30362 d.16.1.2 37893 1pxa 394 1.77e+01 1pbe c.3.1.2 30366 d.16.1.2 37897 1f3xA 530 1.78e+01 b.58.1.1 64958 c.1.12.1 64959 c.49.1.1 64960 1qsrA 162 1.79e+01 1yghA d.108.1.1 40805 1a49A 530 1.79e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1f3wA 530 1.79e+01 b.58.1.1 64934 c.1.12.1 64935 c.49.1.1 64936 1huoA 335 1.81e+01 1bpyA a.60.6.1 61273 e.9.1.1 61274 1nqbA 256 1.83e+01 1mfa b.1.1.1 20042 b.1.1.1 20043 1pbe 394 1.83e+01 1pbe c.3.1.2 30338 d.16.1.2 37869 2phh 394 1.83e+01 1pbe c.3.1.2 30353 d.16.1.2 37884 1do5A 154 1.83e+01 1mfmA b.1.8.1 22303 1gn0A 108 1.84e+01 c.46.1.3 65358 1qstA 160 1.85e+01 1yghA d.108.1.1 40804 1i6vB 314 1.85e+01 d.74.3.1 61854 d.181.1.1 61855 5gcnA 166 1.86e+01 1yghA d.108.1.1 40807 1bpe 335 1.87e+01 1bpyA a.60.6.1 18076 e.9.1.1 43228 1hqmB 313 1.92e+01 i.8.1.1 45973 1b0wA 108 1.95e+01 8fabA b.1.1.1 20532 1qp1A 107 1.97e+01 8fabA b.1.1.1 20535 1hy3A 294 2.02e+01 1gmxA 108 2.06e+01 c.46.1.3 65355 1qqcA 773 2.08e+01 1tgoA c.55.3.5 33724 e.8.1.1 43013 1igfL 219 2.09e+01 8fabA b.1.1.1 19812 b.1.1.2 20922 1b8aA 438 2.17e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1dlfL 113 2.18e+01 8fabA b.1.1.1 20382 1fgvL 109 2.20e+01 8fabA b.1.1.1 19852 1vbe1 300 2.22e+01 1pov1 1bqcA 302 2.23e+01 1bqcA c.1.8.3 28831 1rpl 251 2.25e+01 1bpyA e.9.1.1 43212 1vbb1 300 2.28e+01 1pov1 1pvc1 301 2.29e+01 1pov1 1g1yA 585 2.30e+01 1bvzA b.1.1.5 60210 b.71.1.1 60211 c.1.8.1 60212 1nom 248 2.31e+01 1bpyA e.9.1.1 43220 1bpb 248 2.31e+01 1bpyA e.9.1.1 43215 1clzL 219 2.34e+01 8fabA b.1.1.1 20104 b.1.1.2 21136 1in5A 334 2.35e+01 1hqcA a.4.5.11 62599 c.37.1.13 62600 1pkp 150 2.42e+01 1pkp d.14.1.1 37551 d.50.1.2 38787 1do9A 94 2.44e+01 1cyo d.120.1.1 41084 1dv4E 145 2.46e+01 i.1.1.3 45875 1clyL 219 2.46e+01 8fabA b.1.1.1 20102 b.1.1.2 21134 1jr1A 514 2.47e+01 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1dxsA 80 2.48e+01 1cokA a.60.1.2 17944 1eg0B 148 2.50e+01 1pkp i.1.1.1 45808 1jn3A 251 2.62e+01 1bpyA e.9.1.1 63183 1jl9B 51 2.69e+01 g.3.11.1 66832 1b2wL 214 2.71e+01 8fabA b.1.1.1 20306 b.1.1.2 21298 1a8q 274 2.72e+01 1brt c.69.1.12 34702 1ktrL 116 2.75e+01 1mnuL 219 2.75e+01 8fabA b.1.1.1 20358 b.1.1.2 21350 1vkxA 273 2.80e+01 1a3qA b.1.1.5 21941 b.2.5.1 22454 2ramA 273 2.80e+01 1a3qA b.1.1.5 21937 b.2.5.1 22450 1be1 137 2.82e+01 1be1 c.23.6.1 31237 1iknA 286 2.88e+01 1a3qA b.1.1.5 21936 b.2.5.1 22449 1fl5A 217 2.88e+01 b.1.1.1 65015 b.1.1.2 65016 1in4A 334 2.94e+01 1hqcA a.4.5.11 62597 c.37.1.13 62598 1f8rA 498 2.95e+01 1f8rA c.3.1.2 30410 d.16.1.5 37974 2liv 344 2.96e+01 2liv c.93.1.1 35708 1j7kA 334 2.97e+01 1hqcA a.4.5.11 62695 c.37.1.13 62696 1in6A 334 2.98e+01 1hqcA a.4.5.11 62601 c.37.1.13 62602 1cokA 68 3.06e+01 1cokA a.60.1.2 17945 1in7A 334 3.06e+01 1hqcA a.4.5.11 62603 c.37.1.13 62604 1i9jL 219 3.07e+01 1h6vE 499 3.09e+01 c.3.1.5 60705 c.3.1.5 60706 d.87.1.1 60707 1nfiC 301 3.17e+01 b.1.1.5 21943 b.2.5.1 22456 1nfiA 301 3.17e+01 1a3qA b.1.1.5 21942 b.2.5.1 22455 1mrfL 219 3.19e+01 8fabA b.1.1.1 20020 b.1.1.2 21074 1eah1 301 3.22e+01 1pov1 1j8yF 297 3.25e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1j8mF 297 3.27e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1k1eA 180 3.32e+01 c.108.1.5 67995 1nbvL 219 3.40e+01 8fabA b.1.1.1 19898 b.1.1.2 20992 1ctaA 36 3.44e+01 1ctdA a.39.1.5 17232 1ctdA 36 3.44e+01 1ctdA a.39.1.5 17230 1ponA 36 3.44e+01 1ponA a.39.1.5 17239 1cfvL 113 3.46e+01 8fabA b.1.1.1 20160 1qfuL 217 3.47e+01 8fabA b.1.1.1 20292 b.1.1.2 21284 1jsrA 327 3.48e+01 c.88.1.1 67237 1egf 53 3.51e+01 1egf g.3.11.1 44290 3egf 53 3.51e+01 1egf g.3.11.1 44285 1dq3A 454 3.52e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1eueA 86 3.53e+01 1cyo d.120.1.1 59504 1a4jA 217 3.53e+01 8fabA b.1.1.1 20232 b.1.1.2 21244 1d3bA 75 3.53e+01 1d3bA b.38.1.1 24798 2h1pL 219 3.58e+01 8fabA b.1.1.1 20190 b.1.1.2 21206 1b3oB 514 3.59e+01 1ak5 c.1.5.1 28641 d.37.1.1 38538 d.37.1.1 38539 1eqjA 511 3.62e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ejjA 511 3.62e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1lpfA 477 3.64e+01 1lvl c.3.1.5 30569 c.3.1.5 30570 d.87.1.1 40206 1jguL 220 3.66e+01 b.1.1.1 66690 b.1.1.2 66691 1awpA 92 3.67e+01 1cyo d.120.1.1 41071 1a7oL 106 3.68e+01 8fabA b.1.1.1 19942 1fn4A 211 3.70e+01 b.1.1.1 59884 b.1.1.2 59885 1lnrD 180 3.73e+01 1a4kA 217 3.76e+01 8fabA b.1.1.1 20236 b.1.1.2 21248 1e0rB 159 3.83e+01 1a6dA c.8.5.2 30824 1dioB 224 3.94e+01 1dioB c.51.3.1 33219 1eexB 224 3.94e+01 1dioB c.51.3.1 33213 1ehlL 217 3.98e+01 32c2A b.1.1.1 20502 b.1.1.2 21458 2cgrL 219 3.99e+01 8fabA b.1.1.1 19918 b.1.1.2 21012