# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 3.09e-26 1pdr b.36.1.1 60400 1i92A 91 5.19e-26 1pdr b.36.1.1 61990 1bfeA 119 3.23e-23 1pdr b.36.1.1 24775 1be9A 119 3.46e-23 1pdr b.36.1.1 24774 1tp5A 119 3.79e-23 1pdr 99 3.19e-22 1pdr b.36.1.1 24771 2fe5A 94 6.52e-22 2fcfA 103 9.10e-22 2fneA 117 1.14e-21 1q3oA 109 4.09e-21 b.36.1.1 95700 1n99A 166 4.42e-20 b.36.1.1,b.36.1.1 85459,85460 1qavA 90 9.47e-20 1qauA b.36.1.1 24777 1wf7A 103 1.03e-19 1n7eA 97 1.85e-19 b.36.1.1 91691 1n7fA 97 1.93e-19 b.36.1.1 91692 2f5yA 91 2.66e-19 1qavB 115 2.72e-19 1qauA b.36.1.1 24780 1qauA 112 6.96e-19 1qauA b.36.1.1 24779 1ihjA 98 9.93e-19 1pdr b.36.1.1 62382 1v5lA 103 1.53e-18 b.36.1.1 108378 1mfgA 95 2.75e-18 b.36.1.1 79043 1m5zA 91 1.10e-17 b.36.1.1 78676 1b8qA 127 1.64e-17 1qauA b.36.1.1 24781 1fc6A 388 2.06e-17 1fc6A b.36.1.3,c.14.1.2 64738,64739 1nf3C 128 2.62e-17 b.36.1.1 85596 1l6oA 95 2.65e-17 b.36.1.1 84534 2f0aA 98 6.98e-17 1kwaA 88 8.24e-17 1kwaA b.36.1.1 24772 1kwaB 88 1.72e-16 1kwaA b.36.1.1 24773 1i16 130 3.82e-15 1i16 b.36.1.2 24787 1nteA 82 1.61e-14 b.36.1.1 86163 1r6jA 82 3.75e-14 b.36.1.1 97151 1lcyA 325 1.26e-13 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 1.09e-12 1ky9B 448 2.89e-11 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1y8tA 324 5.79e-11 1sotA 320 9.76e-09 b.36.1.4,b.47.1.1 105852,105853 1ky9A 448 3.61e-08 b.36.1.4,b.47.1.1 73198,73199 1db3A 372 1.05e-03 1db3A c.2.1.2 29813 1gph1 465 7.52e-03 1ecfB 1ao0A 459 8.80e-03 1ecfB c.61.1.1,d.153.1.1 34049,41816 1bx4A 345 2.51e-02 1bx4A c.72.1.1 34935 1zn8A 180 3.35e-02 1t6t1 118 1.43e-01 1skyB 502 3.09e-01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1vc3B 97 4.59e-01 1ugmA 125 4.71e-01 d.15.1.3 107827 1hvyA 288 4.84e-01 1bkpA d.117.1.1 41049 1zsyA 357 4.88e-01 1vkmA 297 5.79e-01 c.138.1.1 108670 1fxrA 64 6.13e-01 1fxd d.58.1.4 38993 1xfoA 357 6.85e-01 1y0yA 353 6.99e-01 1qb7A 236 7.38e-01 1qb7A c.61.1.1 34087 1kw4A 89 7.67e-01 a.60.1.2 73077 1fdr 248 7.71e-01 1fdr b.43.4.2,c.25.1.1 25653,31543 1wnfA 328 8.74e-01 1dekA 241 9.06e-01 1dekA c.37.1.1 31842 1opr 213 1.15e+00 1opr c.61.1.1 34091 1wlsA 328 1.19e+00 1rutX 188 1.24e+00 1lh0A 213 1.30e+00 c.61.1.1 73896 1ti6A 875 1.37e+00 b.52.2.2,c.81.1.1 106974,106975 1zm8A 259 1.40e+00 1dfd 64 1.43e+00 1fxd d.58.1.4 38995 1uc2A 481 1.51e+00 d.261.1.1 99161 1ypvA 313 1.57e+00 1se8A 301 1.57e+00 b.40.4.3 105448 1fr3A 67 1.64e+00 1fr3A b.40.6.1 25436 1befA 181 1.66e+00 1befA b.47.1.3 26419 1vheA 373 1.68e+00 b.49.3.1,c.56.5.4 100669,100670 1a8p 258 1.68e+00 1fdr b.43.4.2,c.25.1.1 25654,31544 1nepA 130 1.73e+00 b.1.18.7 80440 1ex2A 189 1.76e+00 1ex2A c.51.4.2 33225 1uheA 97 1.77e+00 1dax 64 1.86e+00 1fxd d.58.1.4 38996 1g8aA 227 1.95e+00 c.66.1.3 90506 1dioA 554 2.05e+00 1dioA c.1.19.3 29656 1r13A 148 2.06e+00 d.169.1.1,h.1.1.1 96782,96783 1ecfB 504 2.08e+00 1ecfB c.61.1.1,d.153.1.1 34054,41821 1jalA 363 2.17e+00 c.37.1.8,d.15.10.2 84138,84139 1eexA 554 2.23e+00 1dioA c.1.19.3 29650 1g2qA 187 2.38e+00 c.61.1.1 65117 1ecfA 504 2.41e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1g57A 217 2.42e+00 1g57A d.115.1.2 60253 1tys 265 2.42e+00 1bkpA d.117.1.1 40937 1axwA 265 2.60e+00 1bkpA d.117.1.1 40938 2g8oA 264 2.62e+00 1aiqA 264 2.68e+00 1bkpA d.117.1.1 40967 1evfA 264 2.71e+00 1bkpA d.117.1.1 40932 1cis 66 2.71e+00 2sniI k.1.1.1 46375 1qqqA 264 2.74e+00 1bkpA d.117.1.1 40931 1h8eA 510 2.84e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1jzxK 205 2.90e+00 i.1.1.2 67885 2fa1A 160 2.92e+00 1o54A 277 3.17e+00 c.66.1.13 92482 2fvgA 340 3.28e+00 2aefA 234 3.34e+00 2f51A 118 3.38e+00 2ck3A 510 3.39e+00 1k32A 1045 3.41e+00 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1y0bA 197 3.42e+00 2g8mA 264 3.57e+00 1s72M 194 3.82e+00 d.12.1.2 105332 1e79A 510 3.83e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1vqoM 195 3.86e+00 1mn4A 282 3.99e+00 b.2.5.7 79313 1oi7A 288 4.07e+00 c.2.1.8,c.23.4.1 87049,87050 1df9A 191 4.18e+00 1befA b.47.1.3 26420 2sxl 88 4.32e+00 1b7fA d.58.7.1 39179 1cfyA 143 4.65e+00 1cof d.109.1.2 40858 1ciqA 40 4.79e+00 2sniI d.40.1.1 38576 1xebA 150 5.13e+00 1ad3A 452 5.33e+00 1ad3A c.82.1.1 35335 1reqD 637 5.46e+00 1reqB c.1.19.1,c.23.6.1 29623,31250 1bmfA 510 5.50e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1yloA 348 5.53e+00 1uzcA 71 5.55e+00 a.159.2.1 100222 1bvoA 175 5.60e+00 1a3qA b.2.5.3 22457 7reqB 637 5.63e+00 1reqB c.1.19.1,c.23.6.1 29617,31244 2bh8A 101 5.67e+00 2c9wA 169 5.69e+00 2cfxA 144 5.74e+00 1zq9A 285 5.87e+00 1mdoA 393 5.91e+00 c.67.1.4 79013 1lnh 857 6.10e+00 1yge a.119.1.1,b.12.1.1 19237,23637 1nwaA 203 6.36e+00 d.58.28.1 86295 1wspA 84 6.36e+00 1ug8A 87 6.68e+00 d.68.7.1 107825 1cof 143 6.72e+00 1cof d.109.1.2 40860 1vraB 215 7.04e+00 1iezA 217 7.12e+00 d.115.1.2 66129 1jj2L 194 7.16e+00 1ffkI d.12.1.2 63097 3sxlA 184 7.59e+00 1b7fA d.58.7.1,d.58.7.1 39173,39174 1q52A 314 7.77e+00 c.14.1.3 95846 1o50A 157 7.80e+00 d.37.1.1,d.37.1.1 92478,92479 1korA 400 7.97e+00 c.26.2.1,d.210.1.1 72824,72825 1ybhA 590 8.01e+00 1delA 241 8.17e+00 1dekA c.37.1.1 31844 1mjhA 162 8.26e+00 1mjhA c.26.2.4 31639 1tsm 316 8.46e+00 1bkpA d.117.1.1 41024 1n6aA 259 8.47e+00 b.76.2.1,b.85.7.1 80121,80122 1mo1A 87 8.67e+00 d.94.1.1 91363 1yjmA 110 8.67e+00 1vhoA 346 8.88e+00 b.49.3.1,c.56.5.4 100694,100695 1ks2A 219 9.16e+00 c.124.1.4,d.58.40.1 72908,72909 1lkzA 219 9.34e+00 c.124.1.4,d.58.40.1 73991,73992 1rypL 212 9.41e+00 d.153.1.4 41880 1g65K 211 9.42e+00 d.153.1.4 41907 1mjhB 162 9.98e+00 1mjhA c.26.2.4 31640 1mnnA 340 1.00e+01 b.2.5.7 79324 1mt6A 280 1.01e+01 b.76.2.1,b.85.7.1 79446,79447 1o8bA 219 1.01e+01 c.124.1.4,d.58.40.1 81180,81181 1oroA 213 1.03e+01 1opr c.61.1.1 34093 1ifyA 49 1.05e+01 a.5.2.1 71207 1mkmA 249 1.10e+01 a.4.5.33,d.110.2.2 79242,79243 1fsgA 233 1.12e+01 1qk3A c.61.1.1 34029 1fwkA 296 1.13e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1qhlA 227 1.16e+01 1qhlA c.37.1.12 32382 1q7rA 219 1.16e+01 c.23.16.1 96054 1reqB 637 1.16e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1e2wA 251 1.18e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1lnqA 336 1.18e+01 c.2.1.9,f.14.1.1 74049,74050 2cw8A 537 1.19e+01 2c5qA 240 1.19e+01 1eb0A 147 1.20e+01 b.107.1.1,d.58.38.1 64890,64891 1kuuA 202 1.20e+01 d.153.2.1 73019 1koe 172 1.20e+01 1koe d.169.1.5 42448 1hkvA 453 1.21e+01 b.49.2.3,c.1.6.1 83559,83560 1b4uA 139 1.24e+01 1bouA a.88.1.1 18523 1a8vA 121 1.27e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1ojhA 65 1.30e+01 a.214.1.1 103976 1h3iA 293 1.30e+01 b.76.2.1,b.85.7.1 76635,76636 1e0gA 48 1.31e+01 1e01A d.7.1.1 37325 1l0wA 580 1.35e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1wvhA 134 1.38e+01 1uc7A 125 1.38e+01 c.47.1.1 99163 1n6eA 1071 1.38e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1dvh 79 1.39e+01 1c53 a.3.1.1 15802 1vpqA 273 1.40e+01 1v8eA 224 1.44e+01 1jihA 531 1.45e+01 d.240.1.1,e.8.1.7 90374,90375 1t3qB 788 1.45e+01 d.41.1.1,d.133.1.1 106369,106370 1cq3A 233 1.45e+01 1cq3A b.27.1.1 23923 1jdbB 1073 1.46e+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 18574,31503,31705,31706,41550,41551 1ebfA 358 1.46e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1xm7A 195 1.47e+01 1vd6A 224 1.47e+01 1xneA 113 1.47e+01 1l1qA 186 1.51e+01 c.61.1.1 77653 1jem 87 1.51e+01 1ptf d.94.1.1 40548 2tscA 264 1.57e+01 1bkpA d.117.1.1 40952 1gg6B 131 1.58e+01 5ptp 2cvdA 198 1.62e+01 1bu6O 501 1.63e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1xygD 359 1.63e+01 1ebuA 358 1.64e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1o5oA 221 1.64e+01 c.61.1.1 92509 1aw8B 91 1.64e+01 1aw8B 1earA 147 1.65e+01 b.107.1.1,d.58.38.1 64875,64876 1cs0C 1073 1.66e+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 18559,31488,31675,31676,41520,41521 1bouA 139 1.66e+01 1bouA a.88.1.1 18521 2b4aA 138 1.68e+01 1yb2A 275 1.69e+01 1keeG 1073 1.70e+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 1c3oG 1073 1.71e+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 1c3oC 1073 1.71e+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 1iyhA 198 1.72e+01 a.45.1.1,c.47.1.5 83790,83791 1x3mA 415 1.75e+01 1x92A 199 1.76e+01 1xv5A 401 1.77e+01 1rpnA 335 1.80e+01 c.2.1.2 97708 1w30A 201 1.80e+01 1dxrH 258 1.83e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 6prcH 258 1.84e+01 6prcH b.41.1.1,f.23.10.1 25457,43436 1cs0A 1073 1.84e+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 18558,31487,31673,31674,41518,41519 2cw5A 255 1.86e+01 1coaI 64 1.86e+01 2sniI d.40.1.1 38574 1keeA 1073 1.87e+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 68492,68493,68494,68495,68496,68497 1fmaE 150 1.87e+01 1fmaE d.41.5.1 38630 1qu9A 128 1.89e+01 1qu9A d.79.1.1 39755 1qu9C 128 1.89e+01 1qu9A d.79.1.1 39757 1fm0E 150 1.90e+01 1fmaE d.41.5.1 38629 1keeC 1073 1.91e+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 68500,68501,68502,68503,68504,68505 1c3oA 1073 1.91e+01 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 1vj0A 380 1.92e+01 b.35.1.2,c.2.1.1 100786,100787 1lnzA 342 1.97e+01 b.117.1.1,c.37.1.8 78112,78113 2ahqA 76 1.97e+01 1a62 130 2.00e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1rxdA 159 2.06e+01 1mvwB 145 2.08e+01 i.15.1.1 79524 1keeE 1073 2.09e+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 1y96A 86 2.12e+01 1fcjA 322 2.12e+01 1oasA c.79.1.1 35289 1bxrA 1073 2.13e+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 18570,31499,31697,31698,41542,41543 1gv3A 248 2.14e+01 a.2.11.1,d.44.1.1 70585,70586 1xx6A 191 2.18e+01 1fxlA 167 2.19e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1vdmA 153 2.21e+01 1b0aA 288 2.24e+01 1a4iA c.2.1.7,c.58.1.2 30286,33934 2f69A 261 2.27e+01 2ckiA 262 2.28e+01 1jhfA 202 2.33e+01 a.4.5.2,b.87.1.1 63057,63058 1h3gA 601 2.41e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1a9xA 1058 2.42e+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 18550,31479,31657,31658,41502,41503 2aamA 309 2.42e+01 1yphC 131 2.44e+01 1fe0A 68 2.48e+01 1cc8A d.58.17.1 39345 1pqhA 143 2.52e+01 b.52.2.1 95017 1o5hA 214 2.58e+01 a.191.1.1 92497 2dvh 79 2.61e+01 1c53 a.3.1.1 15803 1m65A 245 2.63e+01 c.6.3.1 84847 2d00A 109 2.67e+01 1ar1B 298 2.68e+01 2occB b.6.1.2,f.17.2.1 23037,43619 1mzhA 225 2.68e+01 c.1.10.1 79698 1cydA 244 2.68e+01 1cydA c.2.1.2 29825 1l2tA 235 2.71e+01 c.37.1.12 73514 1hi9A 274 2.72e+01 1hi9A c.99.1.1 61063 1mtpB 43 2.72e+01 1oasA 322 2.73e+01 1oasA c.79.1.1 35293 1h9oA 112 2.73e+01 1qadA d.93.1.1 60837 1c3oE 1073 2.79e+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 1r2jA 366 2.86e+01 a.29.3.1,e.6.1.1 96869,96870 1dzfA 215 2.88e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 2fxqA 264 2.88e+01 1b7fA 168 2.89e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1k2i1 245 2.90e+01 2bw3A 534 2.91e+01 2f6uA 234 2.96e+01 1rrmA 386 2.96e+01 e.22.1.2 105081 1t3iA 420 2.98e+01 c.67.1.3 106354 1jnyA 435 3.01e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1iq8A 582 3.02e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1n2eA 300 3.02e+01 c.26.1.4 85268 1mopA 300 3.02e+01 c.26.1.4 85035 1iieA 75 3.04e+01 1iieA a.109.1.1 19039 2c3zA 222 3.04e+01 1scuA 288 3.06e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1l0bA 229 3.06e+01 c.15.1.3,c.15.1.3 73391,73392 1vchA 175 3.09e+01 1aw8E 91 3.13e+01 1aw8B 1a4yA 460 3.13e+01 1a4yA c.10.1.1 30852 1m1hA 248 3.16e+01 b.114.1.1,d.58.42.1 78415,78416 1h72C 296 3.19e+01 d.14.1.5,d.58.26.1 60712,60713 1vybA 238 3.20e+01 d.151.1.1 108897 1c53 79 3.31e+01 1c53 a.3.1.1 15801 1a53 247 3.31e+01 1a53 c.1.2.4 28564 1pt1A 143 3.31e+01 b.52.2.1 95084 1qvzA 237 3.32e+01 c.23.16.2 96453 1zh5A 195 3.33e+01 1zuoA 186 3.35e+01 2ampA 304 3.39e+01 1xdnA 277 3.41e+01 1lvoA 302 3.42e+01 b.47.1.4 74284 1s29A 92 3.43e+01 a.4.5.46 98373 2scuA 288 3.43e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1wlfA 179 3.46e+01 b.52.2.3,d.31.1.1 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