# List of top-scoring protein chains for t04-100-30-str2 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 1ihrA 76 8.61e-16 1ihrA d.212.1.2 62392 1lr0A 129 7.67e-09 d.212.1.1 74213 1iow 306 2.87e-02 1iow c.30.1.2 31713 d.142.1.1 41481 1f5mA 180 8.95e-02 1f5mB d.110.2.1 40895 1h16A 759 1.05e-01 c.7.1.1 76462 1a2vA 655 1.18e-01 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 1cm5A 759 1.37e-01 1cm5A c.7.1.1 30671 1dkzA 219 1.86e-01 1dkzA unknown_sccs -445 unknown_sccs -3060 1tuhA 156 2.08e-01 1esiA 262 2.15e-01 1skf e.3.1.1 42682 1skoB 130 2.78e-01 1q48A 134 3.70e-01 unknown_sccs -9776 1n8jA 186 3.81e-01 c.47.1.10 85401 1qmvA 197 4.05e-01 1qq2A c.47.1.10 33066 5croA 66 4.72e-01 1orc a.35.1.2 17044 1sdjA 310 4.75e-01 d.21.1.2 -9420 d.21.1.2 -9421 1ospO 257 4.98e-01 1ospO b.76.1.1 27971 1b6rA 355 5.20e-01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1r26A 125 5.81e-01 c.47.1.1 -7389 1qnaA 200 5.84e-01 1ytbA d.129.1.1 41226 d.129.1.1 41227 1avmA 201 6.05e-01 1avmA a.2.11.1 15782 d.44.1.1 38745 1st9A 143 6.60e-01 c.47.1.10 -7503 1ojjA 402 6.86e-01 b.29.1.10 -3473 1dymA 402 7.06e-01 1celA b.29.1.10 24304 1quqB 121 7.49e-01 1quqB b.40.4.3 25305 1hn2A 159 7.57e-01 b.60.1.1 65890 1obpA 159 7.57e-01 1obpA b.60.1.1 27092 1gt1A 159 7.58e-01 b.60.1.1 -4436 1q47A 495 8.25e-01 1orc 71 8.65e-01 1orc a.35.1.2 17054 1kngA 156 9.54e-01 c.47.1.10 72777 1r6lA 239 1.02e+00 d.14.1.4 -9057 d.101.1.1 -10747 1j8bA 112 1.05e+00 d.222.1.1 77101 3cox 507 1.10e+00 1b8sA c.3.1.2 30332 d.16.1.1 37863 1ei5A 520 1.43e+00 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1e25A 282 1.45e+00 1e25A e.3.1.1 42731 1q98A 165 1.47e+00 c.47.1.10 -7499 1tif 78 1.47e+00 1tif d.15.8.1 37836 1qyaA 307 1.63e+00 1oyeA 1049 1.72e+00 d.58.44.1 87587 d.58.44.1 87588 d.58.44.1 87589 d.58.44.1 87590 d.225.1.1 87591 d.225.1.1 87592 f.35.1.1 87593 f.35.1.1 87594 1bsmA 201 1.88e+00 1avmA a.2.11.1 15780 d.44.1.1 38743 1jcfA 344 2.03e+00 c.55.1.1 62878 c.55.1.1 62879 1vetB 125 2.05e+00 1elqA 390 2.05e+00 1elqA c.67.1.3 34436 2trxA 108 2.17e+00 1thx c.47.1.1 32719 1fecA 490 2.21e+00 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1j6qA 136 2.26e+00 b.40.9.1 77091 1cc1L 498 2.30e+00 1h2rL e.18.1.1 43301 1iwlA 182 2.52e+00 b.125.1.1 83757 1eluA 390 2.62e+00 1elqA c.67.1.3 34434 1q18A 332 2.68e+00 1vkdA 338 2.97e+00 1k8wA 327 3.02e+00 b.122.1.1 83094 unknown_sccs -10143 1dxrH 258 3.24e+00 6prcH b.41.1.1 25456 f.23.10.1 43433 1aisA 182 3.43e+00 1ytbA d.129.1.1 41288 d.129.1.1 41289 1lvk 762 3.49e+00 1lvk b.34.3.1 24576 c.37.1.9 32173 1g13A 162 3.53e+00 1g13A b.95.1.1 60194 1pu5A 164 3.55e+00 1t4oA 117 3.59e+00 1qxhA 167 3.74e+00 c.47.1.10 -7496 1auvA 311 3.85e+00 1auvA c.30.1.5 31723 d.142.1.3 41558 1d0yA 761 3.91e+00 1lvk b.34.3.1 24581 c.37.1.9 32178 1iba 101 3.96e+00 1iba d.95.1.1 40567 1q0rA 298 4.16e+00 unknown_sccs -8330 1fohA 664 4.31e+00 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1oo0A 147 4.46e+00 d.232.1.1 87182 1urnA 97 4.77e+00 1urnA d.58.7.1 39153 1uolA 219 4.85e+00 b.2.5.2 -2886 1jfuA 186 5.02e+00 c.47.1.10 62940 1lkdA 297 5.45e+00 d.32.1.3 78059 d.32.1.3 78060 1ehiA 377 5.61e+00 1iow c.30.1.2 31716 d.142.1.1 41484 1cqyA 99 5.65e+00 1b9zA b.3.1.1 22527 1v04A 355 5.66e+00 unknown_sccs -4592 1han 297 5.78e+00 1han d.32.1.3 38506 d.32.1.3 38507 1gp1A 198 5.82e+00 1gp1A c.47.1.10 33059 1n4kA 381 5.86e+00 unknown_sccs 79992 b.42.6.1 79993 1mp9A 198 6.08e+00 a.74.1.2 -1127 a.74.1.2 -1128 1iloA 77 6.19e+00 c.47.1.1 66205 1uf5A 303 6.29e+00 1erzA 303 6.34e+00 1erzA d.160.1.2 59498 1p5tA 127 6.39e+00 b.55.1.2 -4368 1itg 166 6.40e+00 1b9dA c.55.3.2 33661 1fjgJ 105 6.46e+00 1fjfJ d.58.15.1 39330 1f9zA 135 6.48e+00 1qipA d.32.1.1 38484 1pn0A 665 6.75e+00 c.3.1.2 -5992 c.47.1.10 -7513 d.16.1.2 -9210 1ocvA 125 6.83e+00 d.17.4.3 86810 1dnlA 199 6.98e+00 1ci0A b.45.1.1 25753 1iazA 179 7.32e+00 1iazA b.97.1.1 62131 1p4kA 295 7.96e+00 d.153.1.5 87772 1od3A 168 8.33e+00 b.18.1.10 86825 1lvmA 229 8.57e+00 b.47.1.3 78243 1oh0A 131 8.61e+00 d.17.4.3 87004 1opy 131 8.64e+00 1opy d.17.4.3 38113 1js3A 486 8.84e+00 c.67.1.6 67215 1prxA 224 9.16e+00 1prxA c.47.1.10 33076 1k5nA 276 9.64e+00 b.1.1.2 77266 d.19.1.1 77267 1dmmA 131 1.02e+01 1opy d.17.4.3 38114 1f89A 291 1.04e+01 d.160.1.1 64988 1xgsA 295 1.04e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1jofA 365 1.04e+01 b.69.10.1 71775 1ri6A 343 1.07e+01 unknown_sccs -4621 1g8kA 825 1.08e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 1rkuA 206 1.13e+01 unknown_sccs -6823 1bh9B 89 1.18e+01 1bh9B a.22.1.3 16485 1onxA 390 1.18e+01 b.92.1.7 87176 c.1.9.13 87177 1cqqA 180 1.19e+01 1cqqA b.47.1.4 26422 1t4wA 196 1.20e+01 1avyA 74 1.23e+01 1avyB h.1.17.1 45656 1v2yA 105 1.24e+01 d.15.1.1 -9148 1dv1A 449 1.26e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1tupA 219 1.27e+01 1tupA b.2.5.2 22434 1alo 907 1.30e+01 1alo 1gsoA 431 1.32e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 3ladA 476 1.34e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1hlrA 907 1.34e+01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1vlbA 907 1.35e+01 1bfg 146 1.35e+01 1bfg b.42.1.1 25485 1bl3A 160 1.36e+01 1b9dA c.55.3.2 33655 1pj5A 830 1.38e+01 unknown_sccs -4066 c.3.1.2 -6031 d.16.1.5 -9251 unknown_sccs -10171 1h0pA 182 1.40e+01 b.62.1.1 76450 1h12A 405 1.40e+01 a.102.1.2 83447 1fxlA 167 1.41e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1b7yA 350 1.42e+01 1pysA d.104.1.1 40776 1omiA 248 1.45e+01 a.4.5.4 87079 b.82.3.3 87080 1uc2A 481 1.47e+01 unknown_sccs -11725 1iuhA 198 1.48e+01 d.61.1.2 83711 1j5yA 187 1.51e+01 a.4.5.1 71592 d.94.2.1 71593 1swuA 127 1.53e+01 1swuA b.61.1.1 27230 1gtdA 85 1.55e+01 d.58.45.1 76344 1uy4A 145 1.56e+01 1lvwA 295 1.57e+01 c.68.1.6 84723 1itwA 741 1.61e+01 c.77.1.2 76793 1l3lA 234 1.62e+01 a.4.6.2 73541 d.110.5.1 73542 1pysA 350 1.62e+01 1pysA d.104.1.1 40775 9gafA 295 1.62e+01 1apyA d.153.1.5 42008 1nwzA 125 1.65e+01 d.110.3.1 86370 3pyp 125 1.65e+01 3pyp d.110.3.1 40897 1vk8A 106 1.65e+01 1svpA 161 1.67e+01 1svpA b.47.1.3 26384 1fa8A 135 1.71e+01 1qipA d.32.1.1 38486 1oiaA 95 1.73e+01 d.58.7.1 87051 1g6gA 127 1.75e+01 1g6gA b.26.1.2 23916 1lmiA 131 1.75e+01 b.1.19.1 78098 1aa6 715 1.78e+01 2napA b.52.2.2 26916 c.81.1.1 35324 1s8fA 177 1.79e+01 1ubkL 534 1.79e+01 e.18.1.1 88422 1k1xA 659 1.80e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1pvmA 184 1.88e+01 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1kt6A 183 1.88e+01 b.60.1.1 84466 1m1hA 248 1.90e+01 b.114.1.1 78415 d.58.42.1 78416 1j8rA 196 1.94e+01 1j8rA b.2.3.3 62745 1ogoX 574 1.94e+01 unknown_sccs -3237 unknown_sccs -4783 4fgf 146 1.94e+01 1bfg b.42.1.1 25486 1bdyA 123 1.99e+01 1bdyA b.7.1.1 23190 1rypF 233 2.03e+01 1rypF d.153.1.4 41937 1kllA 130 2.07e+01 d.32.1.2 72720 1mrg 263 2.08e+01 1mrj d.165.1.1 42183 2pii 112 2.09e+01 2pii d.58.5.1 39071 1lwjA 441 2.09e+01 b.71.1.1 74303 c.1.8.1 74304 1aq0A 306 2.12e+01 1aq0A c.1.8.3 28842 1luqA 127 2.20e+01 b.61.1.1 -4500 1rsy 152 2.24e+01 1rsy b.7.1.2 23192 1hbq 183 2.24e+01 1aqb b.60.1.1 27078 1l3kA 196 2.25e+01 d.58.7.1 73539 d.58.7.1 73540 1es5A 262 2.26e+01 1skf e.3.1.1 42679 1bw3 125 2.29e+01 1bw4 b.52.1.2 26899 1crzA 403 2.30e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1hyvA 166 2.37e+01 1b9dA c.55.3.2 61424 3hhrB 203 2.38e+01 1axiB b.1.2.1 22005 b.1.2.1 22006 1lt5D 103 2.39e+01 3chbD b.40.2.1 24875 1h7sA 365 2.40e+01 d.14.1.3 65705 d.122.1.2 65706 1htyA 1015 2.43e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1icxA 155 2.53e+01 d.129.3.1 71191 1jrrA 382 2.57e+01 e.1.1.1 63256 1urrA 102 2.58e+01 1dceB 331 2.59e+01 1dceB a.102.4.3 18872 1vom 762 2.61e+01 1lvk b.34.3.1 24577 c.37.1.9 32174 1ecsA 126 2.63e+01 1ecsA d.32.1.2 59407 1fjgK 129 2.65e+01 1fjfK c.55.4.1 33733 1n9lA 109 2.69e+01 d.110.3.6 85468 1o1zA 234 2.76e+01 c.1.18.3 86555 1f2dA 341 2.81e+01 1f2dA c.79.1.1 35298 1r4xA 275 2.84e+01 unknown_sccs -2846 unknown_sccs -10776 1e3dB 542 2.94e+01 1h2rL e.18.1.1 59189 1p6oA 161 2.95e+01 c.97.1.2 -8774 1lktA 104 2.98e+01 1lktA b.90.1.1 28398 1rypE 242 2.99e+01 1rypE d.153.1.4 41936 1h1yA 228 2.99e+01 c.1.2.2 76506 1huxA 270 2.99e+01 1huxA c.55.1.5 61278 1o22A 170 3.12e+01 d.238.1.1 86557 1pmmA 466 3.14e+01 c.67.1.6 -8159 1fzoA 274 3.16e+01 1agdA b.1.1.2 60155 d.19.1.1 60156 1mk0A 97 3.16e+01 d.226.1.1 79216 1a0i 348 3.17e+01 1a0i b.40.4.6 25363 d.142.2.1 41577 1kbvA 327 3.19e+01 b.6.1.3 68395 b.6.1.3 68396 1o7eA 276 3.19e+01 e.3.1.1 -11766 1ha1 184 3.20e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1ktaA 365 3.22e+01 e.17.1.1 77533 1m93C 41 3.25e+01 1lk2A 274 3.35e+01 b.1.1.2 -2610 d.19.1.1 -9365 1dfnA 30 3.39e+01 g.9.1.1 44570 1k07A 263 3.47e+01 d.157.1.1 77218 1mo9A 523 3.48e+01 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1jmtA 104 3.48e+01 d.58.7.3 63180 1s3zA 165 3.50e+01 1thx 115 3.50e+01 1thx c.47.1.1 32732 1ugxA 133 3.51e+01 1nxiA 132 3.58e+01 d.58.47.1 86381 1kit 757 3.60e+01 1kit b.29.1.8 24272 b.29.1.8 24273 b.68.1.1 27616 1odfA 290 3.64e+01 c.37.1.6 -7045 1rh6A 55 3.64e+01 1aqb 183 3.68e+01 1aqb b.60.1.1 27084 1qb5D 99 3.70e+01 b.40.2.1 88357 1tiiD 99 3.70e+01 1tiiD b.40.2.1 24965 1pk6A 133 3.73e+01 b.22.1.1 -3287 1ejeA 192 3.74e+01 1ejeA b.45.1.2 25757 1m7vA 363 3.75e+01 d.174.1.1 78748 1n9eA 787 3.77e+01 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 1ss4A 153 3.81e+01 1oe1A 336 3.81e+01 b.6.1.3 86891 b.6.1.3 86892 1l6rA 227 3.88e+01 c.108.1.10 77768 1sdoA 203 3.88e+01 unknown_sccs -7558 1b25A 619 3.89e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1a58 177 3.91e+01 2cpl b.62.1.1 27495