# List of top-scoring protein chains for t2k-100-30-str2-scores 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 1g9oA 91 1.74e-24 1pdr b.36.1.1 60400 1i92A 91 1.15e-23 1pdr b.36.1.1 61990 1tp5A 119 4.03e-22 1be9A 119 4.89e-22 1pdr b.36.1.1 24774 1bfeA 119 5.47e-22 1pdr b.36.1.1 24775 2fe5A 94 5.98e-21 1pdr 99 9.87e-21 1pdr b.36.1.1 24771 2fneA 117 1.27e-20 2fcfA 103 1.27e-19 1q3oA 109 5.44e-19 b.36.1.1 95700 1n99A 166 9.23e-19 b.36.1.1,b.36.1.1 85459,85460 1n7eA 97 1.46e-18 b.36.1.1 91691 2f5yA 91 1.50e-18 1qavA 90 4.36e-18 1qauA b.36.1.1 24777 1n7fA 97 6.63e-18 b.36.1.1 91692 1wf7A 103 8.75e-18 1ihjA 98 1.05e-17 1pdr b.36.1.1 62382 1mfgA 95 5.18e-17 b.36.1.1 79043 1m5zA 91 8.44e-17 b.36.1.1 78676 1v5lA 103 1.47e-16 b.36.1.1 108378 1fc6A 388 1.04e-15 1fc6A b.36.1.3,c.14.1.2 64738,64739 1nf3C 128 1.28e-15 b.36.1.1 85596 1qavB 115 1.45e-15 1qauA b.36.1.1 24780 1b8qA 127 1.48e-15 1qauA b.36.1.1 24781 1qauA 112 1.81e-15 1qauA b.36.1.1 24779 2f0aA 98 2.10e-15 1kwaA 88 2.15e-15 1kwaA b.36.1.1 24772 1l6oA 95 2.18e-15 b.36.1.1 84534 1kwaB 88 1.00e-14 1kwaA b.36.1.1 24773 1nteA 82 3.97e-14 b.36.1.1 86163 1r6jA 82 7.98e-14 b.36.1.1 97151 1i16 130 1.23e-13 1i16 b.36.1.2 24787 1lcyA 325 4.88e-12 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 1.27e-10 1y8tA 324 2.16e-09 1ky9B 448 3.14e-09 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1ky9A 448 2.03e-06 b.36.1.4,b.47.1.1 73198,73199 1sotA 320 5.65e-06 b.36.1.4,b.47.1.1 105852,105853 1db3A 372 4.46e-03 1db3A c.2.1.2 29813 1bx4A 345 4.75e-02 1bx4A c.72.1.1 34935 1ugmA 125 4.76e-02 d.15.1.3 107827 1cof 143 5.97e-02 1cof d.109.1.2 40860 1cfyA 143 1.06e-01 1cof d.109.1.2 40858 1skyB 502 1.25e-01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1uc2A 481 1.51e-01 d.261.1.1 99161 1fr3A 67 3.23e-01 1fr3A b.40.6.1 25436 1ti6A 875 3.83e-01 b.52.2.2,c.81.1.1 106974,106975 1kw4A 89 4.75e-01 a.60.1.2 73077 1t6t1 118 5.16e-01 1e79A 510 6.69e-01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1zsyA 357 7.08e-01 1vkmA 297 7.35e-01 c.138.1.1 108670 1r13A 148 7.36e-01 d.169.1.1,h.1.1.1 96782,96783 1vc3B 97 7.74e-01 2ck3A 510 7.74e-01 1g57A 217 8.17e-01 1g57A d.115.1.2 60253 1bmfA 510 8.49e-01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1gph1 465 8.96e-01 1ecfB 1h8eA 510 9.28e-01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1yvkA 163 1.06e+00 1ao0A 459 1.17e+00 1ecfB c.61.1.1,d.153.1.1 34049,41816 1rutX 188 1.27e+00 1uheA 97 1.29e+00 1eexA 554 1.37e+00 1dioA c.1.19.3 29650 1xfoA 357 1.40e+00 1dioA 554 1.41e+00 1dioA c.1.19.3 29656 1y0yA 353 1.43e+00 1l0wA 580 1.49e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1zn8A 180 1.50e+00 1hvyA 288 1.54e+00 1bkpA d.117.1.1 41049 1oi7A 288 1.76e+00 c.2.1.8,c.23.4.1 87049,87050 2d4pA 141 1.80e+00 1se8A 301 2.13e+00 b.40.4.3 105448 1zm8A 259 2.41e+00 1dfd 64 2.47e+00 1fxd d.58.1.4 38995 1g2qA 187 2.55e+00 c.61.1.1 65117 1cq3A 233 2.92e+00 1cq3A b.27.1.1 23923 1vraB 215 3.14e+00 1dax 64 3.18e+00 1fxd d.58.1.4 38996 1g8aA 227 3.28e+00 c.66.1.3 90506 1vheA 373 3.52e+00 b.49.3.1,c.56.5.4 100669,100670 1yjmA 110 3.72e+00 1ypvA 313 3.83e+00 1vybA 238 3.92e+00 d.151.1.1 108897 1wmiA 90 4.10e+00 1c3oA 1073 4.12e+00 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 1cs0A 1073 4.14e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1o8bA 219 4.19e+00 c.124.1.4,d.58.40.1 81180,81181 1a9xA 1058 4.22e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1yloA 348 4.31e+00 1a62 130 4.37e+00 1a62 a.140.3.1,b.40.4.5 64708,64709 1keeA 1073 4.44e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68492,68493,68494,68495,68496,68497 1jdbB 1073 4.46e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1lh0A 213 4.53e+00 c.61.1.1 73896 1gutA 68 4.62e+00 b.40.6.1 65576 1cs0C 1073 4.63e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1fxrA 64 4.63e+00 1fxd d.58.1.4 38993 1lkzA 219 4.78e+00 c.124.1.4,d.58.40.1 73991,73992 1mo1A 87 4.94e+00 d.94.1.1 91363 1keeC 1073 4.97e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 1t3qB 788 5.20e+00 d.41.1.1,d.133.1.1 106369,106370 2c5qA 240 5.20e+00 1o6aA 96 5.23e+00 b.139.1.1 92562 1cis 66 5.44e+00 2sniI k.1.1.1 46375 1ks2A 219 5.46e+00 c.124.1.4,d.58.40.1 72908,72909 1xebA 150 5.76e+00 1dzfA 215 5.94e+00 1dzfA c.52.3.1,d.78.1.1 33344,39753 2fa1A 160 6.22e+00 1opr 213 6.25e+00 1opr c.61.1.1 34091 1tys 265 6.33e+00 1bkpA d.117.1.1 40937 1jzxK 205 6.37e+00 i.1.1.2 67885 2g8oA 264 6.46e+00 1aiqA 264 6.46e+00 1bkpA d.117.1.1 40967 1axwA 265 6.46e+00 1bkpA d.117.1.1 40938 1ebfA 358 6.56e+00 1ebuA c.2.1.3,d.81.1.2 30033,39948 1ggxA 223 6.62e+00 1ggxA d.22.1.1 38367 1zgoA 223 6.71e+00 1lnh 857 7.12e+00 1yge a.119.1.1,b.12.1.1 19237,23637 1kobA 387 7.16e+00 1tkiA d.144.1.7 41640 1y9kA 157 7.16e+00 1reqD 637 7.27e+00 1reqB c.1.19.1,c.23.6.1 29623,31250 7reqB 637 7.31e+00 1reqB c.1.19.1,c.23.6.1 29617,31244 1fdr 248 7.50e+00 1fdr b.43.4.2,c.25.1.1 25653,31543 1c7nA 399 7.87e+00 1d2fA c.67.1.3 34413 2cvdA 198 7.94e+00 1iyhA 198 7.99e+00 a.45.1.1,c.47.1.5 83790,83791 1vpqA 273 8.16e+00 2aefA 234 8.37e+00 2g8mA 264 8.58e+00 1wmhB 86 8.75e+00 1ybhA 590 8.94e+00 1qqqA 264 8.98e+00 1bkpA d.117.1.1 40931 1evfA 264 9.01e+00 1bkpA d.117.1.1 40932 1iezA 217 9.16e+00 d.115.1.2 66129 2brfA 110 9.35e+00 1hi9A 274 9.39e+00 1hi9A c.99.1.1 61063 1x47A 98 9.50e+00 2bh8A 101 9.52e+00 1mdoA 393 9.58e+00 c.67.1.4 79013 1ebuA 358 9.76e+00 1ebuA c.2.1.3,d.81.1.2 30035,39950 1uh5A 329 1.00e+01 c.2.1.2 107840 1uc7A 125 1.01e+01 c.47.1.1 99163 1uzcA 71 1.03e+01 a.159.2.1 100222 1q52A 314 1.04e+01 c.14.1.3 95846 1c3oC 1073 1.05e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18563,31492,31683,31684,41528,41529 1mzhA 225 1.05e+01 c.1.10.1 79698 2fe7A 166 1.06e+01 1reqB 637 1.07e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1mtpB 43 1.08e+01 1ciqA 40 1.09e+01 2sniI d.40.1.1 38576 1wnfA 328 1.11e+01 1keeE 1073 1.13e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 2fokA 579 1.13e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1ojqA 212 1.15e+01 d.166.1.1 93146 1c3oE 1073 1.15e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1koe 172 1.17e+01 1koe d.169.1.5 42448 1sw5A 275 1.22e+01 c.94.1.1 106069 1vj0A 380 1.23e+01 b.35.1.2,c.2.1.1 100786,100787 1c3oG 1073 1.24e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 1wl4A 397 1.26e+01 1befA 181 1.26e+01 1befA b.47.1.3 26419 1ifyA 49 1.26e+01 a.5.2.1 71207 1dgsA 667 1.29e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1wspA 84 1.32e+01 1f5nA 592 1.33e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1wlsA 328 1.34e+01 1fwkA 296 1.36e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1bvoA 175 1.36e+01 1a3qA b.2.5.3 22457 1eu1A 780 1.38e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1m0uA 249 1.38e+01 a.45.1.1,c.47.1.5 78359,78360 1x67A 146 1.44e+01 1fokA 568 1.46e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16137,16138,16139,33325 1l2tA 235 1.47e+01 c.37.1.12 73514 2cc0A 195 1.48e+01 1scuA 288 1.49e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1bxrA 1073 1.51e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18570,31499,31697,31698,41542,41543 1rrmA 386 1.53e+01 e.22.1.2 105081 1s72M 194 1.53e+01 d.12.1.2 105332 2d00A 109 1.55e+01 2prd 174 1.63e+01 2prd b.40.5.1 25435 2b8wA 328 1.65e+01 1jjiA 311 1.65e+01 c.69.1.2 66766 1vqoM 195 1.66e+01 1o54A 277 1.68e+01 c.66.1.13 92482 1whi 122 1.70e+01 1whi b.39.1.1 24810 1u4nA 310 1.71e+01 1hzdA 272 1.75e+01 c.14.1.3 65969 1xbsA 149 1.77e+01 1lnqA 336 1.78e+01 c.2.1.9,f.14.1.1 74049,74050 1df9A 191 1.78e+01 1befA b.47.1.3 26420 2scuA 288 1.78e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1s3zA 165 1.78e+01 d.108.1.1 105250 1ia8A 289 1.82e+01 1ia8A d.144.1.7 62112 1xa0A 328 1.86e+01 2f51A 118 1.87e+01 1e0gA 48 1.88e+01 1e01A d.7.1.1 37325 1oroA 213 1.89e+01 1opr c.61.1.1 34093 1ug8A 87 1.90e+01 d.68.7.1 107825 2c31A 568 1.91e+01 2i1b 153 1.92e+01 2i1b b.42.1.2 25538 1keeG 1073 1.93e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68516,68517,68518,68519,68520,68521 1h72C 296 1.94e+01 d.14.1.5,d.58.26.1 60712,60713 1j24A 143 1.95e+01 c.52.1.20 84008 1cozA 129 1.95e+01 1cozA c.26.1.2 31598 1coaI 64 1.97e+01 2sniI d.40.1.1 38574 1mjhA 162 2.00e+01 1mjhA c.26.2.4 31639 1cmkE 350 2.00e+01 1cdkA d.144.1.7 41623 1qb7A 236 2.02e+01 1qb7A c.61.1.1 34087 1jihA 531 2.04e+01 d.240.1.1,e.8.1.7 90374,90375 1ptf 88 2.06e+01 1ptf d.94.1.1 40549 1widA 130 2.07e+01 1a8p 258 2.07e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1ro5A 201 2.08e+01 d.108.1.3 105023 2ffjA 300 2.09e+01 1a63 130 2.09e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 3sxlA 184 2.10e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1y0bA 197 2.12e+01 1xh9A 350 2.15e+01 1qfrA 89 2.19e+01 1ptf d.94.1.1 40552 1yphC 131 2.19e+01 1ojhA 65 2.20e+01 a.214.1.1 103976 1zuoA 186 2.21e+01 1zoyA 622 2.21e+01 2bfxA 284 2.21e+01 1rdqE 350 2.22e+01 d.144.1.7 97314 1h2bA 359 2.23e+01 b.35.1.2,c.2.1.1 90543,90544 1dxrH 258 2.24e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1obwA 175 2.24e+01 2prd b.40.5.1 25416 1vqqA 646 2.24e+01 6prcH 258 2.24e+01 6prcH b.41.1.1,f.23.10.1 25457,43436 1ex2A 189 2.24e+01 1ex2A c.51.4.2 33225 1q8uA 350 2.31e+01 d.144.1.7 96230 2b4aA 138 2.33e+01 1tzfA 259 2.36e+01 c.68.1.13 107476 1howA 373 2.37e+01 1hcl d.144.1.7 41679 1q8yA 373 2.38e+01 d.144.1.7 96234 1tsm 316 2.39e+01 1bkpA d.117.1.1 41024 2fvgA 340 2.42e+01 1o6lA 337 2.48e+01 d.144.1.7 81092 2ahqA 76 2.49e+01 1mn4A 282 2.49e+01 b.2.5.7 79313 2tscA 264 2.51e+01 1bkpA d.117.1.1 40952 1jalA 363 2.52e+01 c.37.1.8,d.15.10.2 84138,84139 1b4uA 139 2.58e+01 1bouA a.88.1.1 18523 2bw3A 534 2.60e+01 1sphA 88 2.62e+01 1ptf d.94.1.1 40544 1tw9A 206 2.65e+01 a.45.1.1,c.47.1.5 107381,107382 21bi 153 2.66e+01 2i1b b.42.1.2 25542 1wvhA 134 2.67e+01 1g7rA 594 2.67e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 2fl4A 149 2.69e+01 2sniI 83 2.73e+01 2sniI d.40.1.1 38573 1apmE 350 2.74e+01 1cdkA d.144.1.7 41628 1mvwB 145 2.75e+01 i.15.1.1 79524 1qhlA 227 2.79e+01 1qhlA c.37.1.12 32382 1mjhB 162 2.82e+01 1mjhA c.26.2.4 31640 1fxlA 167 2.82e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1rpnA 335 2.83e+01 c.2.1.2 97708 1xm7A 195 2.86e+01 1qw2A 102 2.92e+01 d.249.1.1 96456 1xwsA 313 2.98e+01 1k32A 1045 3.00e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1vkcA 158 3.00e+01 1qk8A 146 3.01e+01 1ewxA c.47.1.10 33061 1lw6I 64 3.02e+01 d.40.1.1 74294 2sodB 152 3.02e+01 1mfmA b.1.8.1 22242 1dx4A 586 3.02e+01 2bce c.69.1.1 34622 2fnbA 95 3.05e+01 2fnbA b.1.2.1 21979 1wvcA 259 3.06e+01 1xdyA 298 3.11e+01 1cdkA 350 3.13e+01 1cdkA d.144.1.7 41620 1q7rA 219 3.14e+01 c.23.16.1 96054 1bouA 139 3.15e+01 1bouA a.88.1.1 18521 3cbh 365 3.17e+01 1bvwA c.6.1.1 30665 1zp4A 304 3.23e+01 1n26A 325 3.23e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1a8vA 121 3.25e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 2b7aA 293 3.26e+01 2sxl 88 3.26e+01 1b7fA d.58.7.1 39179 1to2I 64 3.29e+01 1mkmA 249 3.36e+01 a.4.5.33,d.110.2.2 79242,79243 1iyu 79 3.38e+01 1iyu b.84.1.1 28227 1ydgA 211 3.38e+01 31bi 153 3.44e+01 2i1b b.42.1.2 25541 1nepA 130 3.45e+01 b.1.18.7 80440 1ad3A 452 3.45e+01 1ad3A c.82.1.1 35335 2atrA 138 3.49e+01 1s29A 92 3.57e+01 a.4.5.46 98373 1s1iG 119 3.63e+01 i.1.1.1 105181 1ao7D 204 3.67e+01 1tcrA b.1.1.1 20623 1o5hA 214 3.79e+01 a.191.1.1 92497 1dvh 79 3.80e+01 1c53 a.3.1.1 15802 1ngzB 220 3.84e+01 b.1.1.1,b.1.1.2 80502,80503 1oapA 109 3.90e+01 d.79.7.1 92706 1jem 87 3.92e+01 1ptf d.94.1.1 40548 1eudA 311 3.94e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 1tygB 87 3.95e+01 d.15.3.2 107455 1vjuA 309 3.96e+01 d.248.1.1 100835 1eg7A 557 4.02e+01 1eg7A c.37.1.10 32241 1k2i1 245 4.06e+01 1gctA 245 4.07e+01 5ptp b.47.1.2 26021 1sbzA 197 4.07e+01 1i1b 153 4.11e+01 2i1b b.42.1.2 25537 1y96A 86 4.12e+01 1b7fA 168 4.13e+01 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