# List of top-scoring protein chains for t04-100-30-alpha 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 1dnlA 199 1.35e-17 1ci0A b.45.1.1 25753 1nrgA 261 1.96e-14 b.45.1.1 80694 1flmA 122 1.91e-06 1axj b.45.1.1 25747 1ejeA 192 2.03e-03 1ejeA b.45.1.2 25757 1pvtA 238 3.90e-02 c.74.1.1 -8444 1obpA 159 4.72e-02 1obpA b.60.1.1 27092 1j58A 385 6.26e-02 b.82.1.2 71531 1ko3A 230 2.46e-01 d.157.1.1 -11454 1vkbA 161 1.27e+00 1jykA 254 1.80e+00 c.68.1.13 67458 1ualA 274 1.90e+00 c.116.1.4 88383 1kr4A 125 2.01e+00 d.58.5.2 72889 1qyaA 307 2.23e+00 1gal 583 2.27e+00 1gpeA c.3.1.2 30386 d.16.1.1 37950 1sdjA 310 2.39e+00 d.21.1.2 -9420 d.21.1.2 -9421 1cr5A 189 2.54e+00 1cr5A b.52.2.3 26931 d.31.1.1 38465 1t5yA 190 2.70e+00 1gpeA 587 2.76e+00 1gpeA c.3.1.2 30387 d.16.1.1 37951 1efyA 350 3.35e+00 1a26 a.41.1.1 17413 d.166.1.2 42275 1od5A 492 3.68e+00 b.82.1.2 86832 b.82.1.2 86833 1qrrA 394 3.83e+00 1qrrA c.2.1.2 29824 1i24A 404 4.39e+00 c.2.1.2 83663 3seb 238 4.73e+00 3seb b.40.2.2 25184 d.15.6.1 37773 1r6lA 239 5.08e+00 d.14.1.4 -9057 d.101.1.1 -10747 1b16A 254 5.22e+00 1b16A c.2.1.2 29875 1g5cA 170 5.51e+00 1g5cA c.53.2.1 60264 1lxnA 99 5.58e+00 d.58.48.1 84737 1nar 290 5.61e+00 1nar c.1.8.5 28988 1nr4A 71 5.61e+00 d.9.1.1 -8957 1i45A 248 5.82e+00 1amk c.1.1.1 61665 1ukuA 102 6.02e+00 d.58.5.2 -9992 1viaA 175 6.06e+00 c.37.1.2 -7021 1prxA 224 6.11e+00 1prxA c.47.1.10 33076 1i9zA 347 6.21e+00 1i9yA d.151.1.2 62102 1gt1A 159 6.37e+00 b.60.1.1 -4436 1jpc 109 6.48e+00 1b2pA b.78.1.1 27986 1nf2A 268 6.74e+00 c.108.1.10 -6842 1iejA 332 6.84e+00 1nnt c.94.1.2 62328 1uirA 314 7.21e+00 c.66.1.17 -8114 1neyA 247 7.21e+00 c.1.1.1 80449 1q8iA 783 7.23e+00 c.55.3.5 -7635 e.8.1.1 -11885 1o22A 170 7.26e+00 d.238.1.1 86557 1btl 263 7.39e+00 1btl e.3.1.1 42691 1al3 324 7.39e+00 1al3 c.94.1.1 35835 1go3E 187 7.43e+00 b.40.4.5 83054 d.230.1.1 83055 1ufyA 122 7.63e+00 d.79.1.2 88489 1apmE 350 7.71e+00 1cdkA d.144.1.7 41628 1n3oA 252 7.81e+00 b.29.1.1 79967 1kv9A 668 8.23e+00 a.3.1.6 73056 b.70.1.1 73057 1uuzA 137 8.27e+00 d.233.1.1 -9478 1jenA 267 8.39e+00 1jenA 1d2nA 272 8.40e+00 1d2nA c.37.1.20 32428 1r2zA 274 8.53e+00 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1nsf 273 8.56e+00 1d2nA c.37.1.20 32429 1s72E 178 8.57e+00 1ermA 263 8.61e+00 1btl e.3.1.1 42690 1kbvA 327 8.81e+00 b.6.1.3 68395 b.6.1.3 68396 1q0bA 367 8.82e+00 c.37.1.9 -7105 1ukgA 252 9.24e+00 b.29.1.1 -3390 1ry6A 360 1.03e+01 c.37.1.9 -7111 1b8aA 438 1.06e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1eqjA 511 1.10e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1m40A 263 1.15e+01 e.3.1.1 74437 1hkeA 137 1.17e+01 1opd 85 1.21e+01 1ptf d.94.1.1 40560 1rz1A 161 1.21e+01 b.45.1.2 -4088 1hn2A 159 1.23e+01 b.60.1.1 65890 1d2eA 397 1.23e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1jj2E 177 1.23e+01 1ffk1 d.141.1.1 63089 d.141.1.1 63090 1n9lA 109 1.24e+01 d.110.3.6 85468 1o98A 511 1.25e+01 c.105.1.1 86684 c.76.1.3 86685 1jmtA 104 1.26e+01 d.58.7.3 63180 1s2wA 295 1.27e+01 c.1.12.7 -5577 1vjjA 692 1.28e+01 b.1.18.9 -2758 b.1.5.1 -2786 b.1.5.1 -2787 d.3.1.4 -8893 1a8y 367 1.28e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1me4A 215 1.29e+01 d.3.1.1 79023 1f2aA 215 1.32e+01 1cs8A d.3.1.1 37040 1k8kD 300 1.34e+01 d.198.2.1 68309 d.198.2.1 68310 1l1zA 274 1.36e+01 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1v4xA 144 1.37e+01 1b25A 619 1.42e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1cdzA 96 1.43e+01 1cdzA c.15.1.1 30925 1gr3A 160 1.44e+01 b.22.1.1 65476 1iwmA 186 1.47e+01 b.125.1.2 83758 1plzA 189 1.47e+01 b.82.1.7 88160 1kafA 108 1.51e+01 d.199.1.1 68372 1k32A 1045 1.53e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1vk8A 106 1.54e+01 1fo1A 271 1.56e+01 1fo1A c.10.2.3 30869 d.58.7.2 39213 1bo4A 168 1.58e+01 1bo4A d.108.1.1 40798 3fivA 116 1.58e+01 1fmb b.50.1.1 26768 1rlkA 117 1.64e+01 unknown_sccs -7526 1js3A 486 1.65e+01 c.67.1.6 67215 1oaoC 729 1.68e+01 e.26.1.3 86746 3pmgA 561 1.77e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1rcqA 357 1.77e+01 1jx4A 352 1.78e+01 unknown_sccs -10188 unknown_sccs -11898 1ha3A 405 1.79e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1pne 140 1.81e+01 1pne d.110.1.1 40866 1m4vA 204 1.82e+01 b.40.2.2 74459 d.15.6.1 74460 1qxrA 189 1.84e+01 b.82.1.7 -4834 1v0wA 506 1.91e+01 1ru3A 732 1.93e+01 e.26.1.3 -12021 1ihgA 370 1.98e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1ogpA 393 2.00e+01 b.1.18.6 -2744 d.176.1.1 -11708 1p42A 270 2.01e+01 d.14.1.7 87754 d.14.1.7 87755 1agqA 135 2.05e+01 1agqA g.17.1.2 44789 1mjhA 162 2.08e+01 1mjhA c.26.2.4 31639 1e0tA 470 2.08e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1u9aA 160 2.10e+01 1u9aA d.20.1.1 38333 1plq 258 2.13e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1jb0F 164 2.13e+01 1jb0F f.23.16.1 62825 1h7zA 194 2.18e+01 1qhvA b.21.1.1 60733 1f0iA 504 2.21e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 2prd 174 2.21e+01 2prd b.40.5.1 25435 1nnvA 110 2.22e+01 unknown_sccs -9309 1j71A 334 2.23e+01 1eagA b.50.1.2 62669 1p4kA 295 2.23e+01 d.153.1.5 87772 1aqcA 172 2.25e+01 1x11A b.55.1.2 26983 2dpmA 284 2.27e+01 2dpmA c.66.1.28 34246 1pjjA 271 2.27e+01 1aa6 715 2.30e+01 2napA b.52.2.2 26916 c.81.1.1 35324 1g6hA 257 2.30e+01 1gajA c.37.1.12 60318 1nszA 347 2.34e+01 b.30.5.4 80724 1sqgA 429 2.34e+01 1pc3A 350 2.36e+01 1ojrA 274 2.39e+01 c.74.1.1 -8441 1ny1A 240 2.52e+01 c.6.2.3 86395 1kutA 230 2.53e+01 d.143.1.1 73017 1v84A 253 2.54e+01 1lbvA 252 2.55e+01 e.7.1.1 73813 1uzbA 516 2.57e+01 c.82.1.1 -8552 1m4lA 307 2.60e+01 c.56.5.1 78604 1rl6A 177 2.65e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1r0wA 286 2.69e+01 c.37.1.12 -7158 2plc 274 2.70e+01 2plc c.1.18.2 29614 1h3gA 601 2.71e+01 b.1.18.2 -2725 b.71.1.1 -4653 c.1.8.1 -5277 1ct9A 553 2.73e+01 1ct9A c.26.2.1 31616 d.153.1.1 41834 1lci 550 2.75e+01 1lci e.23.1.1 43349 1q9jA 422 2.76e+01 1qg3A 195 2.76e+01 1qg3A b.1.2.1 21993 b.1.2.1 21994 1bj7 156 2.76e+01 1bj7 b.60.1.1 27113 1qfhA 212 2.76e+01 1qfhA b.1.18.10 21893 b.1.18.10 21894 1nif 340 2.77e+01 1nif b.6.1.3 23048 b.6.1.3 23049 1cqkA 101 2.80e+01 1cqkA b.1.1.2 21547 1q6hA 224 2.82e+01 d.26.1.1 -9487 1vhsA 175 2.83e+01 d.108.1.1 -10794 1csn 298 2.84e+01 1csn d.144.1.7 41664 1o59A 355 2.85e+01 unknown_sccs -3132 unknown_sccs -3133 1n67A 359 2.86e+01 b.2.3.4 85354 b.2.3.4 85355 1przA 252 2.98e+01 unknown_sccs -10158 1hi2A 135 3.01e+01 7rsa d.5.1.1 61057 1jx6A 342 3.02e+01 c.93.1.1 67406 1vkdA 338 3.02e+01 1kktA 511 3.05e+01 a.102.2.1 68687 1qfjA 232 3.05e+01 1qfjA b.43.4.2 25655 c.25.1.1 31545 1ow1A 195 3.06e+01 unknown_sccs -4422 1e9gA 286 3.09e+01 1wgjA b.40.5.1 59393 1skoA 143 3.09e+01 1lfwA 470 3.12e+01 c.56.5.4 77942 d.58.19.1 77943 1rocA 155 3.13e+01 unknown_sccs -2866 1q40B 219 3.14e+01 d.17.4.2 -9287 1mc0A 368 3.14e+01 d.110.2.1 78937 d.110.2.1 78938 1azwA 313 3.16e+01 1qtrA c.69.1.7 34658 1pamA 686 3.16e+01 1cxlA b.1.18.2 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 2kinA 238 3.18e+01 1bg2 c.37.1.9 32190 1v9fA 325 3.19e+01 1ipaA 274 3.22e+01 c.116.1.1 71254 d.79.3.3 71255 1tib 269 3.29e+01 3tgl c.69.1.17 34738 1gntA 553 3.29e+01 e.26.1.1 70290 4fiv 113 3.35e+01 1fmb b.50.1.1 26762 1hl9A 449 3.36e+01 unknown_sccs -4694 unknown_sccs -5365 1b2pA 119 3.47e+01 1b2pA b.78.1.1 27998 1inlA 296 3.49e+01 c.66.1.17 66220 1itg 166 3.50e+01 1b9dA c.55.3.2 33661 2ctc 307 3.51e+01 1aye c.56.5.1 33802 1n08A 163 3.59e+01 b.43.5.1 79730 1vqb 87 3.61e+01 1gvp b.40.4.7 25370 1led 243 3.69e+01 1led b.29.1.1 24039 1zfjA 491 3.73e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1qfmA 710 3.73e+01 1qfmA b.69.7.1 27673 c.69.1.4 34641 1nnjA 271 3.81e+01 a.156.1.2 80669 b.113.1.1 80670 g.39.1.8 80671 1mkmA 249 3.87e+01 a.4.5.33 79242 d.110.2.2 79243 1o58A 303 3.88e+01 c.79.1.1 -8503 1b35C 282 3.90e+01 1b35C 1naqA 112 3.91e+01 d.58.5.2 -9984 1ue1A 164 3.91e+01 b.40.4.3 -3905 1fnuA 221 3.94e+01 3seb b.40.2.2 25212 d.15.6.1 37801