# 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 1dusA 194 3.98e-13 1dusA c.66.1.4 34182 1g6q2 328 7.63e-13 1g6q2 1dl5A 317 9.59e-13 1dl5A c.66.1.7 64720 d.197.1.1 64721 1xvaA 292 1.96e-12 1xvaA c.66.1.5 34183 1bhjA 292 1.96e-12 1xvaA c.66.1.5 34189 1d2gA 292 2.24e-12 1xvaA c.66.1.5 34187 1jg1A 235 2.94e-12 c.66.1.7 66661 2admA 421 3.29e-12 2admA c.66.1.10 34238 1aqjB 421 3.29e-12 2admA c.66.1.10 34243 1g38A 393 4.14e-12 2admA c.66.1.10 60235 1i9gA 280 5.74e-12 c.66.1.13 62090 1kpgA 287 1.02e-10 c.66.1.18 68735 1kphB 287 1.06e-10 c.66.1.18 68740 1kpiA 302 1.13e-10 c.66.1.18 68743 1f3lA 321 1.53e-10 1g6q2 c.66.1.6 59630 1i1nA 226 7.13e-10 1l1eA 287 9.21e-10 1yub 245 1.50e-08 2ercA c.66.1.9 34219 1im8A 244 2.93e-08 c.66.1.14 66212 1ej0A 180 5.41e-08 1ej0A c.66.1.2 34179 1inlA 296 1.22e-07 c.66.1.17 66220 1jsxA 207 1.42e-06 1fp1D 372 3.40e-06 1fpqA a.4.5.29 59939 c.66.1.12 59940 1qamA 244 3.92e-06 2ercA c.66.1.9 34220 2ercA 244 3.92e-06 2ercA c.66.1.9 34224 1vid 221 5.57e-06 1vid c.66.1.1 34178 1fbnA 230 8.54e-06 1fbnA c.66.1.3 34181 1fpqA 372 1.05e-05 1fpqA a.4.5.29 59947 c.66.1.12 59948 1khhA 198 1.16e-05 c.66.1.16 68615 1g55A 343 1.01e-03 1g55A c.66.1.10 34247 1g60A 260 2.51e-03 1bg6 359 3.52e-03 1bg6 a.100.1.5 18810 c.2.1.6 30214 1bc5A 269 3.55e-03 1af7 a.58.1.1 17929 c.66.1.8 34204 1fp2A 352 3.58e-03 1fpxA a.4.5.29 59941 c.66.1.12 59942 1af7 274 3.64e-03 1af7 a.58.1.1 17928 c.66.1.8 34203 1eg2A 319 4.23e-03 1eg2A c.66.1.11 34249 2lao 238 4.35e-03 1lst c.94.1.1 35758 1lst 239 4.39e-03 1lst c.94.1.1 35755 6mhtA 327 4.67e-03 6mhtA c.66.1.10 34226 1hmy 327 4.67e-03 6mhtA c.66.1.10 34229 3mhtA 327 4.67e-03 6mhtA c.66.1.10 34234 1fjxA 327 4.69e-03 6mhtA c.66.1.10 34228 1fpxA 352 4.86e-03 1fpxA a.4.5.29 59950 c.66.1.12 59951 1ja9A 274 2.02e-02 c.2.1.2 62817 1hslA 238 2.14e-02 1lst c.94.1.1 35804 1jbqE 435 2.26e-02 c.79.1.1 62854 1a71A 374 3.20e-02 2ohxA b.35.1.2 24673 c.2.1.1 29689 1axgA 374 3.24e-02 2ohxA b.35.1.2 24691 c.2.1.1 29707 1g0oA 283 3.94e-02 1ybvA c.2.1.2 60181 1ybvA 283 3.94e-02 1ybvA c.2.1.2 29948 1ej6A 1289 4.58e-02 i.7.1.1 45967 1cydA 244 1.16e-01 1cydA c.2.1.2 29825 1pjcA 361 1.76e-01 1sayA c.2.1.4 30101 c.23.12.2 31361 1sayA 361 1.76e-01 1sayA c.2.1.4 30102 c.23.12.2 31362 1pjbA 361 1.76e-01 1sayA c.2.1.4 30103 c.23.12.2 31363 1kevA 351 1.85e-01 1pedA b.35.1.2 24749 c.2.1.1 29765 1pedA 351 1.85e-01 1pedA b.35.1.2 24753 c.2.1.1 29769 1ju9A 374 1.87e-01 b.35.1.2 63293 c.2.1.1 63294 1dctA 324 2.71e-01 6mhtA c.66.1.10 34244 1ht0A 374 2.73e-01 2ohxA b.35.1.2 24709 c.2.1.1 29725 1axeA 374 2.84e-01 2ohxA b.35.1.2 24681 c.2.1.1 29697 1hetA 374 2.89e-01 2ohxA b.35.1.2 60975 c.2.1.1 60976 1heuA 374 2.89e-01 2ohxA b.35.1.2 60979 c.2.1.1 60980 2ohxA 374 2.89e-01 2ohxA b.35.1.2 24669 c.2.1.1 29685 8adh 374 2.89e-01 2ohxA b.35.1.2 24690 c.2.1.1 29706 1ee2B 373 3.09e-01 2ohxA b.35.1.2 24664 c.2.1.1 29680 1ee2A 373 3.09e-01 2ohxA b.35.1.2 24663 c.2.1.1 29679 1k0sA 151 3.25e-01 b.40.7.1 67969 1dehA 374 3.85e-01 2ohxA b.35.1.2 24713 c.2.1.1 29729 1qlhA 374 3.85e-01 2ohxA b.35.1.2 24685 c.2.1.1 29701 1hdyA 374 3.87e-01 2ohxA b.35.1.2 24723 c.2.1.1 29739 1htbA 374 3.90e-01 2ohxA b.35.1.2 24715 c.2.1.1 29731 1a1s 314 3.96e-01 1othA c.78.1.1 35258 c.78.1.1 35259 1hdzA 374 3.96e-01 2ohxA b.35.1.2 24725 c.2.1.1 29741 1fmcA 255 4.27e-01 1cydA c.2.1.2 29856 1tehA 373 4.38e-01 2ohxA b.35.1.2 24733 c.2.1.1 29749 7adh 374 4.39e-01 b.35.1.2 24708 c.2.1.1 29724 1lssA 140 4.54e-01 1hsoA 374 4.94e-01 2ohxA b.35.1.2 24731 c.2.1.1 29747 2fcr 173 7.18e-01 1rcf c.23.5.1 31151 1gzhB 249 7.26e-01 1kzyC 259 7.67e-01 1dkgA 197 8.67e-01 1dkgA b.73.1.1 27812 h.1.9.1 45626 1dkgB 197 8.67e-01 1dkgA b.73.1.1 27813 h.1.9.1 45627 1ionA 243 8.83e-01 c.37.1.10 62633 1g3qA 237 9.73e-01 1hyqA c.37.1.10 60237 1bdb 277 1.07e+00 1bdb c.2.1.2 29874 1e3jA 352 1.07e+00 1e3jA b.35.1.2 24765 c.2.1.1 29781 1ab6A 125 1.15e+00 3chy c.23.1.1 31054 1kepA 348 1.26e+00 c.2.1.2 68536 1ae1B 273 1.33e+00 1bdb c.2.1.2 29944 1ab5A 125 1.38e+00 3chy c.23.1.1 31056 1dj2A 443 1.38e+00 1adeA c.37.1.10 32237 1i4wA 353 1.50e+00 c.66.1.9 66028 1d1tA 373 1.60e+00 2ohxA b.35.1.2 24719 c.2.1.1 29735 1agnA 373 1.62e+00 2ohxA b.35.1.2 24737 c.2.1.1 29753 1hqmC 1119 1.80e+00 i.8.1.1 45974 1i6vC 1118 1.80e+00 e.29.1.1 61856 1l9uC 1118 1.83e+00 1dzfA 215 2.05e+00 1dzfA c.52.3.1 33344 d.78.1.1 39753 1booA 323 2.09e+00 1booA c.66.1.11 34248 1kj8A 391 2.16e+00 1ez1A 392 2.16e+00 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1eyzA 392 2.16e+00 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1hnnA 282 2.91e+00 c.66.1.15 65895 1iw7C 1119 3.00e+00 1fjhA 257 3.07e+00 1fjhB c.2.1.2 29870 1fjhB 257 3.07e+00 1fjhB c.2.1.2 29871 2ayqB 366 3.07e+00 1cnzA c.77.1.1 35058 1eokA 290 3.27e+00 1eokA c.1.8.5 28991 1lsuA 147 3.35e+00 1gegA 256 3.39e+00 1ybvA c.2.1.2 29888 2che 128 3.49e+00 3chy c.23.1.1 31080 1i01E 244 3.84e+00 1ybvA c.2.1.2 29901 2chy 128 4.09e+00 3chy c.23.1.1 31081 1fyhA 258 4.15e+00 1d9cA a.26.1.3 16907 a.26.1.3 16908 1hu4A 288 4.67e+00 1hu4A c.2.1.2 61268 1eif 135 4.81e+00 1bkb b.34.5.2 24608 b.40.4.5 25340 2eifA 136 4.85e+00 1bkb b.34.5.2 24607 b.40.4.5 25339 1eqjA 511 5.03e+00 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ejjA 511 5.03e+00 1ejjA c.105.1.1 59422 c.76.1.3 59423 1culC 380 5.26e+00 1cipA a.66.1.1 18204 c.37.1.8 32087 1bg3A 919 5.41e+00 1qhaA c.55.1.3 33491 c.55.1.3 33492 c.55.1.3 33493 c.55.1.3 33494 1aztB 388 5.45e+00 1cipA a.66.1.1 18202 c.37.1.8 32085 1ehc 128 5.48e+00 3chy c.23.1.1 31053 1b2pA 119 5.99e+00 1b2pA b.78.1.1 27998 1d1rA 116 6.70e+00 1d1rA d.64.1.1 39548 1qe0A 420 6.72e+00 1adjA c.51.1.1 33186 d.104.1.1 40735 1fcdA 401 7.50e+00 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1ak5 503 7.81e+00 1ak5 c.1.5.1 28639 1iqqA 200 8.14e+00 d.124.1.1 66274 1djmA 129 8.24e+00 3chy c.23.1.1 31078 1e6lA 127 8.57e+00 3chy c.23.1.1 59307 2ts1 419 8.86e+00 2ts1 c.26.1.1 31564 1e4iA 447 9.03e+00 1e70M c.1.8.4 59225 1jxlA 352 9.20e+00 e.8.1.5 67419 1lwhA 441 9.32e+00 1udrA 129 9.60e+00 3chy c.23.1.1 31041 1tr1A 447 9.76e+00 1e70M c.1.8.4 28957 1a8q 274 1.00e+01 1brt c.69.1.12 34702 5chy 128 1.03e+01 3chy c.23.1.1 31050 1i7iA 292 1.03e+01 1kfvA 271 1.05e+01 1qg6A 261 1.05e+01 1eny c.2.1.2 29919 1c14A 262 1.05e+01 1eny c.2.1.2 29927 1qsgA 265 1.06e+01 1eny c.2.1.2 29935 3chy 128 1.06e+01 3chy c.23.1.1 31038 1dj3A 442 1.08e+01 1adeA c.37.1.10 32239 1qfxA 460 1.08e+01 1qfxA c.60.1.3 33994 6chyB 128 1.08e+01 3chy c.23.1.1 31063 1bgaA 447 1.10e+01 1e70M c.1.8.4 28961 1bggA 448 1.10e+01 1e70M c.1.8.4 28953 1vlzA 128 1.10e+01 3chy c.23.1.1 31048 1e3lA 376 1.12e+01 2ohxA b.35.1.2 24745 c.2.1.1 29761 1eqfA 280 1.12e+01 1eqfA a.29.2.1 16972 a.29.2.1 16973 1cye 129 1.12e+01 3chy c.23.1.1 31077 1cey 128 1.13e+01 3chy c.23.1.1 31082 1d4zA 128 1.14e+01 3chy c.23.1.1 31047 1e3iA 376 1.15e+01 2ohxA b.35.1.2 24741 c.2.1.1 29757 1jbeA 128 1.19e+01 3chy c.23.1.1 62845 1prgA 270 1.23e+01 2prgA a.123.1.1 19314 1h5qA 265 1.26e+01 1cydA c.2.1.2 60643 1gn2A 207 1.27e+01 a.2.11.1 65359 d.44.1.1 65360 2prgA 271 1.27e+01 2prgA a.123.1.1 19311 1fm9D 272 1.27e+01 2prgA a.123.1.1 19313 3prgA 278 1.27e+01 2prgA a.123.1.1 19318 1k74D 283 1.28e+01 a.123.1.1 68252 1kkqA 269 1.30e+01 a.123.1.1 68679 1i9cA 137 1.30e+01 1i7gA 287 1.30e+01 1ekuB 265 1.30e+01 1d9cA a.26.1.3 16913 a.26.1.3 16914 1k7lA 288 1.31e+01 a.123.1.1 68268 1kgsA 225 1.37e+01 a.4.6.1 68596 c.23.1.1 68597 1rfbA 119 1.37e+01 1d9cA a.26.1.3 16905 1gl9B 1054 1.38e+01 c.37.1.16 65291 c.37.1.16 65292 e.10.1.1 65293 1gkuB 1054 1.38e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1d9cA 121 1.40e+01 1d9cA a.26.1.3 16901 1lk5A 229 1.42e+01 1hdr 244 1.47e+01 1dhr c.2.1.2 29837 4dcg 307 1.47e+01 3mag c.66.1.9 34208 1a98B 152 1.47e+01 1nulA c.61.1.1 34022 1nulA 152 1.48e+01 1nulA c.61.1.1 34011 1ldnA 316 1.49e+01 1hyhA c.2.1.5 30166 d.162.1.1 42133 2ldb 317 1.50e+01 1hyhA c.2.1.5 30175 d.162.1.1 42142 1a97B 148 1.51e+01 1nulA c.61.1.1 34024 1ik6A 369 1.51e+01 c.36.1.3 66174 c.48.1.2 66175 1qj5A 429 1.53e+01 1dtyA c.67.1.4 34493 1thg 544 1.53e+01 1thg c.69.1.17 34763 1dtyA 429 1.55e+01 1dtyA c.67.1.4 34495 1h7wD 1025 1.56e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1h7wB 1025 1.56e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1h7wA 1025 1.56e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1gteA 1025 1.56e+01 1h7xB 1025 1.56e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1h7xC 1025 1.56e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1h7xD 1025 1.56e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1h7xA 1025 1.56e+01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1eny 268 1.62e+01 1eny c.2.1.2 29910 1zid 268 1.62e+01 1eny c.2.1.2 29911 1bvrA 268 1.62e+01 1eny c.2.1.2 29913 1bg7 176 1.65e+01 2fha a.25.1.1 16686 1g43A 160 1.68e+01 1nbcA b.2.2.2 22392 2mysB 166 1.70e+01 1wdcB a.39.1.5 17308 1f4lA 551 1.72e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1scmB 145 1.72e+01 1wdcB a.39.1.5 17304 1e3tA 203 1.73e+01 1d4oA c.31.1.4 31749 1v39 322 1.74e+01 3mag c.66.1.9 34206 1vp9 322 1.74e+01 3mag c.66.1.9 34210 1qqtA 551 1.75e+01 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1vp3 348 1.75e+01 3mag c.66.1.9 34209 1fo5A 85 1.79e+01 1fo5A c.47.1.1 59922 1ibxB 145 1.85e+01 1c9fA d.15.2.1 62232 1wdcB 156 1.86e+01 1wdcB a.39.1.5 17302 1qrqA 325 1.88e+01 1qrqA c.1.7.1 28667 1jx4A 352 1.92e+01 e.8.1.5 67405 1gveB 327 1.93e+01 1exbA 332 1.93e+01 1qrqA c.1.7.1 28666 1gveA 327 1.97e+01 1dgkN 917 2.06e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1ykfA 352 2.09e+01 1pedA b.35.1.2 24757 c.2.1.1 29773 1b1a 137 2.11e+01 1be1 c.23.6.1 31242 1cdoA 374 2.11e+01 2ohxA b.35.1.2 24747 c.2.1.1 29763 1czaN 917 2.13e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1brwA 433 2.13e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1vpt 348 2.33e+01 3mag c.66.1.9 34207 1qhaA 917 2.34e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1hkcA 917 2.34e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1hkbA 917 2.35e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1xjo 284 2.36e+01 1xjo c.56.5.4 33843 1qq9A 284 2.42e+01 1xjo c.56.5.4 33841 1enz 268 2.46e+01 1eny c.2.1.2 29912 1ccwA 137 2.59e+01 1be1 c.23.6.1 31238 1eamA 307 2.61e+01 3mag c.66.1.9 34212 1aup 449 2.63e+01 1k89 c.2.1.7 30222 c.58.1.1 33870 1e0jB 289 2.64e+01 1cr1A c.37.1.11 32291 2prd 174 2.67e+01 2prd b.40.5.1 25435 1ax4A 467 2.70e+01 1ax4A c.67.1.2 34391 1coo 98 2.72e+01 1coo a.60.3.1 17967 1llc 325 2.74e+01 1hyhA c.2.1.5 30176 d.162.1.1 42143 1eqa 297 2.80e+01 3mag c.66.1.9 34216 3mct 297 2.84e+01 3mag c.66.1.9 34215 1bky 307 2.85e+01 3mag c.66.1.9 34214 1b1yA 500 2.87e+01 1byb c.1.8.2 28796 1c4wA 128 2.88e+01 3chy c.23.1.1 31046 1cr1A 296 2.90e+01 1cr1A c.37.1.11 32286 1cr0A 296 2.90e+01 1cr1A c.37.1.11 32287 1hyhA 309 2.96e+01 1hyhA c.2.1.5 30150 d.162.1.1 42117 1bnlA 178 3.02e+01 1koe d.169.1.5 42444 1jztA 246 3.06e+01 c.104.1.1 63319 1e19A 314 3.08e+01 1b7bA c.73.1.1 34967 1svy 114 3.13e+01 1svy d.109.1.1 40831 1av6A 289 3.15e+01 3mag c.66.1.9 34218 1jsdB 176 3.17e+01 h.3.1.1 63259 1fjgI 128 3.28e+01 1fjfI d.14.1.1 37559 1gk1A 153 3.29e+01 d.153.1.2 65227 1qe5A 266 3.29e+01 1b8oA c.56.2.1 33784 1ffyA 917 3.33e+01 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 3.33e+01 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1ggvA 232 3.37e+01 1din c.69.1.9 34683 1a8h 500 3.42e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1fm2A 169 3.45e+01 1fm2A d.153.1.2 59877 1gk0A 153 3.45e+01 d.153.1.2 65225 2dpmA 284 3.45e+01 2dpmA c.66.1.10 34246 1nhp 447 3.48e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1ahr 146 3.50e+01 1cll a.39.1.5 17287 1f8wA 447 3.54e+01 1nhp c.3.1.5 30561 c.3.1.5 30562 d.87.1.1 40202 1lab 80 3.61e+01 1ghj b.84.1.1 28226 1bc9 200 3.61e+01 1pbv a.118.3.1 19180 1joa 447 3.62e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1av1A 201 3.63e+01 1av1A h.5.1.1 45796 1nhr 447 3.69e+01 1nhp c.3.1.5 30553 c.3.1.5 30554 d.87.1.1 40198 1nhq 447 3.69e+01 1nhp c.3.1.5 30551 c.3.1.5 30552 d.87.1.1 40197 1nhs 447 3.75e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 3mag 307 3.78e+01 3mag c.66.1.9 34205 1j9eA 147 3.80e+01 c.23.5.1 62756 1ganA 134 3.82e+01 1c1lA b.29.1.3 24214 1npx 447 3.83e+01 1nhp c.3.1.5 30557 c.3.1.5 30558 d.87.1.1 40200 1a9xA 1058 3.87e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1colA 204 3.88e+01 1a87 f.1.1.1 43378 1hzzB 384 3.89e+01 c.2.1.4 61472 c.23.12.2 61473 1au1A 166 3.92e+01 1ifa a.26.1.3 16889 1hdcA 253 3.93e+01 1e6wA c.2.1.2 29862 2hsdA 253 3.93e+01 1e6wA c.2.1.2 29866 1dabA 539 3.93e+01 1dabA b.80.1.7 28049 1f08A 148 3.99e+01 1f08A d.89.1.2 59564