# 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 1gm6A 175 2.34e-01 b.60.1.1 70272 1d8iA 311 2.75e-01 1d8iA d.63.1.1 39541 1d8hA 311 3.33e-01 1d8iA d.63.1.1 39544 1r9cA 139 5.04e-01 1hn2A 159 7.97e-01 b.60.1.1 65890 1gt1A 159 9.63e-01 1cjxA 357 1.17e+00 1cjxA d.32.1.3 38516 d.32.1.3 38517 1rhs 296 1.43e+00 1rhs c.46.1.2 32703 c.46.1.2 32704 1ew3A 159 1.58e+00 1mup b.60.1.1 27114 1czaN 917 1.74e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1rhd 293 1.87e+00 1rhs c.46.1.2 32715 c.46.1.2 32716 1dgkN 917 1.91e+00 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1lngA 87 2.03e+00 d.201.1.1 74045 1g8lA 411 2.21e+00 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1jflA 228 2.28e+00 c.78.2.1 71656 c.78.2.1 71657 1b7yA 350 2.67e+00 1pysA d.104.1.1 40776 1l7mA 211 2.72e+00 c.108.1.4 73664 1f5sA 211 2.79e+00 1f5sA c.108.1.4 59656 1j97A 211 2.79e+00 1f5sA c.108.1.4 62753 1i4uA 181 2.94e+00 b.60.1.1 61732 1hkbA 917 3.05e+00 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1sqc 631 3.19e+00 2sqcA a.102.4.2 18858 a.102.4.2 18859 1atiA 505 3.28e+00 1atiA c.51.1.1 33196 d.104.1.1 40745 1obpA 159 3.49e+00 1obpA b.60.1.1 27092 1hkcA 917 3.69e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1kr4A 125 3.98e+00 d.58.5.2 72889 1p9vA 310 3.98e+00 d.21.1.2 88007 d.21.1.2 88008 1sdjA 310 3.98e+00 1atiB 505 4.18e+00 1atiA c.51.1.1 33197 d.104.1.1 40746 1p8kZ 254 4.42e+00 1ofv 169 4.54e+00 1rcf c.23.5.1 31184 1k3eA 156 4.55e+00 d.198.1.1 68103 1lfpA 249 4.72e+00 e.39.1.1 73885 1pysA 350 5.18e+00 1pysA d.104.1.1 40775 1iu9A 111 5.25e+00 1h91A 180 5.53e+00 b.60.1.1 60805 1a88A 275 6.74e+00 1brt c.69.1.12 34707 1rkqA 282 7.01e+00 1cr6B 554 7.14e+00 1cr6B c.108.1.2 43338 c.69.1.11 34688 2sqcA 631 7.52e+00 2sqcA a.102.4.2 18854 a.102.4.2 18855 1cznA 169 8.07e+00 1rcf c.23.5.1 31181 1aw0 72 8.18e+00 1aw0 d.58.17.1 39342 1v5sA 126 8.54e+00 1ukuA 102 8.79e+00 2if1 126 9.55e+00 2if1 d.64.1.1 39547 1yal 218 1.04e+01 1cs8A d.3.1.1 37025 1oz9A 150 1.05e+01 1ex2A 189 1.05e+01 1ex2A c.51.4.2 33225 1kk9A 221 1.08e+01 d.115.1.1 77432 1v8cA 168 1.09e+01 1ppo 216 1.09e+01 1cs8A d.3.1.1 37020 1ecxA 384 1.12e+01 1ecxA c.67.1.3 34431 1gtdA 85 1.17e+01 d.58.45.1 76344 2ay1A 394 1.23e+01 1ajsA c.67.1.1 34357 1i1dA 161 1.24e+01 1i21A d.108.1.1 61526 1sqsA 242 1.24e+01 2pflA 759 1.27e+01 1cm5A c.7.1.1 30675 1o5uA 101 1.27e+01 1eg5A 384 1.32e+01 1ecxA c.67.1.3 34429 3bamA 213 1.34e+01 1bam c.52.1.3 33288 1e2tA 284 1.38e+01 1e2tA d.3.1.5 37121 1oglA 283 1.43e+01 1cm5A 759 1.45e+01 1cm5A c.7.1.1 30671 3pflA 759 1.46e+01 1cm5A c.7.1.1 30673 1h16A 759 1.46e+01 c.7.1.1 76462 1iq4A 179 1.48e+01 1iq4A d.77.1.1 62641 1lxkA 721 1.52e+01 a.102.3.2 74331 b.24.1.1 74332 b.30.5.2 74333 1fwkA 296 1.66e+01 1fwkA d.14.1.5 37576 d.58.26.1 39398 1smrA 335 1.74e+01 1smrA b.50.1.2 26878 1esgA 213 1.74e+01 1bam c.52.1.3 33286 1qhaA 917 1.77e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1jyhA 157 1.80e+01 d.60.1.3 71956 1o4sA 389 1.81e+01 c.67.1.1 86620 1l0bA 229 1.83e+01 c.15.1.3 73391 c.15.1.3 73392 3bamB 213 1.85e+01 1bam c.52.1.3 33289 1tdj 514 1.85e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1i21A 159 1.87e+01 1i21A d.108.1.1 61549 1i12A 160 1.89e+01 1i21A d.108.1.1 61515 1imuA 107 1.93e+01 d.204.1.1 66218 1ii7A 333 2.06e+01 1ii7A d.159.1.4 62415 1kyqA 274 2.06e+01 c.2.1.11 73281 e.37.1.1 73282 1oboA 169 2.09e+01 c.23.5.1 86776 1p3wA 404 2.09e+01 c.67.1.3 87752 1k7jA 206 2.21e+01 d.115.1.1 72103 1iv3A 152 2.22e+01 d.79.5.1 76828 1thg 544 2.23e+01 1thg c.69.1.17 34763 1ytbA 180 2.24e+01 1ytbA d.129.1.1 41276 d.129.1.1 41277 1h72C 296 2.29e+01 d.14.1.5 60712 d.58.26.1 60713 1e8cA 498 2.33e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1hl6A 165 2.43e+01 d.58.7.1 83609 1s7jA 262 2.44e+01 1qwdA 177 2.44e+01 1nddD 76 2.46e+01 1ubi d.15.1.1 37602 2hdhA 293 2.47e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1nddA 76 2.49e+01 1ubi d.15.1.1 37599 1tbaB 180 2.60e+01 1ytbA d.129.1.1 41286 d.129.1.1 41287 1irxA 523 2.60e+01 a.97.1.2 71378 c.26.1.1 71379 1uyrA 737 2.63e+01 1n7oA 721 2.64e+01 a.102.3.2 80259 b.24.1.1 80260 b.30.5.2 80261 2rslA 140 2.65e+01 2rslA c.53.1.1 33345 1rcf 169 2.71e+01 1rcf c.23.5.1 31170 1c0aA 585 2.72e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1na6A 404 2.73e+01 3chy 128 2.74e+01 3chy c.23.1.1 31038 1jwyB 315 2.85e+01 c.37.1.8 67401 1akz 223 2.86e+01 3eugA c.18.1.1 31007 1iznA 286 2.89e+01 e.43.1.1 83847 1opd 85 2.90e+01 1ptf d.94.1.1 40560 1eguA 731 2.98e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.5.2 24423 1aipE 405 2.99e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1uteA 313 3.01e+01 1uteA d.159.1.1 42078 1sspE 223 3.04e+01 3eugA c.18.1.1 31009 1nd4A 264 3.06e+01 1mmiA 366 3.10e+01 1qtoA 122 3.12e+01 1bylA d.32.1.2 38494 1e6mA 128 3.14e+01 3chy c.23.1.1 31039 1k4fA 248 3.16e+01 e.3.1.1 68138 1be3A 446 3.18e+01 1be3A d.185.1.1 58950 d.185.1.1 58951 1qqsA 174 3.23e+01 1nglA b.60.1.1 27143 1exmA 405 3.26e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1h75A 81 3.36e+01 1h75A c.47.1.1 60716 1l6rA 227 3.37e+01 c.108.1.10 77768 1bdo 80 3.38e+01 1bdo b.84.1.1 28214 1gr8A 412 3.40e+01 1ockA 412 3.40e+01 c.117.1.1 86802 1b04A 318 3.49e+01 1b04A d.142.2.2 41579 1jbeA 128 3.49e+01 3chy c.23.1.1 62845 1f1xA 322 3.49e+01 d.32.1.3 83208 d.32.1.3 83209 1su8A 636 3.58e+01 1mjoA 104 3.60e+01 1cmbA a.43.1.2 17466 1oghA 204 3.62e+01 b.85.4.1 86994 1ytbB 180 3.63e+01 1ytbA d.129.1.1 41278 d.129.1.1 41279 1d2eA 397 3.70e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1f0yA 302 3.72e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1cmbA 104 3.74e+01 1cmbA a.43.1.2 17460 1jjyA 636 3.78e+01 1jjyA e.26.1.2 63141 1bncB 449 3.80e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1bncA 449 3.81e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 2polA 366 3.85e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1nnmA 652 3.93e+01 1pg4A 652 3.93e+01 e.23.1.1 88067 1ha3A 405 3.96e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1f1uA 323 3.99e+01 d.32.1.3 83200 d.32.1.3 83201