# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1euu 605 2.79e-07 1eut b.1.18.2 21892 b.18.1.1 23713 b.68.1.1 27610 1eut 605 2.49e-06 1eut b.1.18.2 21891 b.18.1.1 23712 b.68.1.1 27609 1gqpA 221 3.40e-06 b.18.1.9 70372 1jhjA 171 8.73e-04 b.18.1.9 66714 1gof 639 1.03e-03 1gof b.1.18.2 21807 b.18.1.1 23709 b.69.1.1 27631 1goh 639 1.07e-03 1gof b.1.18.2 21809 b.18.1.1 23711 b.69.1.1 27633 1k3iA 656 2.16e-03 b.1.18.2 68113 b.18.1.1 68114 b.69.1.1 68115 1ng5A 215 1.08e-02 b.100.1.1 -4541 1qwzA 235 1.30e-02 b.100.1.1 -4543 1k12A 158 1.67e-02 b.18.1.15 71978 1rz2A 254 6.06e-02 1xnaA 183 1.93e-01 1xnaA b.18.1.8 23773 1d7pM 159 2.63e-01 1cztA b.18.1.2 23718 1q8bA 105 3.17e-01 unknown_sccs -9958 1jhfA 202 4.86e-01 a.4.5.2 63057 b.87.1.1 63058 1c3hA 137 5.32e-01 b.22.1.1 -3255 1kexA 155 5.89e-01 b.18.1.2 77350 1puiA 210 7.35e-01 c.37.1.8 88292 1cztA 160 1.04e+00 1cztA b.18.1.2 23715 1aa8A 347 1.09e+00 1an9A 1czsA 160 1.19e+00 1cztA b.18.1.2 23714 1dl5A 317 1.29e+00 1dl5A c.66.1.7 64720 d.197.1.1 64721 1smvA 260 1.60e+00 1smvA b.121.4.7 23288 1ayaA 101 1.69e+00 1qadA d.93.1.1 40460 1k8kF 168 1.82e+00 d.198.2.1 68312 1f2tA 149 1.83e+00 1f2tA c.37.1.12 32373 1ve9A 347 1.91e+00 c.4.1.2 -6056 d.16.1.3 -9214 1ofhA 310 1.94e+00 c.37.1.20 86948 1rhoC 145 2.10e+00 1rhoA b.1.18.8 21901 1prtD 110 2.15e+00 1bcpD b.40.2.1 25128 1pqzA 238 2.50e+00 1pn0A 665 2.69e+00 c.3.1.2 -5992 c.47.1.10 -7513 d.16.1.2 -9210 1qniA 581 2.70e+00 1qniA b.6.1.4 23042 b.69.3.1 27642 1ry9A 145 2.80e+00 d.198.1.1 -9020 1gr3A 160 2.81e+00 b.22.1.1 65476 1jwwA 80 2.89e+00 d.58.17.1 71919 1bcpD 110 3.00e+00 1bcpD b.40.2.1 25132 1l4iA 206 3.21e+00 b.1.11.1 73564 b.7.2.1 73565 1rhoA 145 3.27e+00 1rhoA b.1.18.8 21899 1kmtA 141 3.58e+00 b.1.18.8 77442 1fohA 664 3.59e+00 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1erxA 184 3.80e+00 1np1A b.60.1.1 27164 1hh2P 344 3.89e+00 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1a78A 134 3.90e+00 1c1lA b.29.1.3 24212 1ju5A 109 4.15e+00 d.93.1.1 77173 1j27A 102 4.16e+00 unknown_sccs -10116 1qpxA 218 4.29e+00 1qpxA b.1.11.1 22318 b.7.2.1 23200 1c28A 135 4.62e+00 1c28A b.22.1.1 23857 1im2A 444 5.27e+00 1do0A c.37.1.20 62564 1larA 575 5.60e+00 1larA c.45.1.2 32693 c.45.1.2 32694 1i3zA 103 5.70e+00 d.93.1.1 83667 1dujA 187 5.82e+00 1dujA d.135.1.1 41449 1vjuA 309 6.19e+00 unknown_sccs -9594 1mnd 762 6.23e+00 1lvk b.34.3.1 24591 c.37.1.9 32188 1an9A 340 6.25e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1o91A 178 6.27e+00 b.22.1.1 -3282 1shdA 107 6.34e+00 1fmk d.93.1.1 40440 1koiA 184 6.44e+00 b.60.1.1 68725 1hq0A 295 6.61e+00 1hzgA d.194.1.1 61122 1dkgD 383 6.63e+00 1ba1 c.55.1.1 33427 c.55.1.1 33428 1c5cH 215 6.67e+00 1igtB b.1.1.1 20475 b.1.1.2 21439 1qy1A 174 7.35e+00 b.60.1.1 -4445 1ek8A 185 7.54e+00 1ek8A d.67.3.1 59444 1h6yA 170 7.58e+00 b.18.1.7 70904 2ptd 298 7.73e+00 2plc c.1.18.2 29605 1h10A 125 7.99e+00 b.55.1.1 83446 1a87 321 7.99e+00 1a87 f.1.1.1 43380 1hzgA 295 7.99e+00 1hzgA d.194.1.1 61436 1sltA 134 8.25e+00 1c1lA b.29.1.3 24186 1m5q1 130 8.30e+00 1g86A 142 8.37e+00 b.29.1.3 70161 1scjB 71 8.63e+00 1scjB d.58.3.2 39069 1pm1X 180 8.76e+00 1iznA 286 8.76e+00 e.43.1.1 83847 1cauB 184 8.78e+00 1caxB b.82.1.2 28103 1euoA 180 8.95e+00 1np1A b.60.1.1 27163 1k92A 455 9.01e+00 c.26.2.1 68325 d.210.1.1 68326 1viwB 198 9.01e+00 1led b.29.1.1 24170 1fjgB 256 9.04e+00 1fjfB c.23.15.1 31400 1peeA 180 9.06e+00 1hdkA 141 9.16e+00 b.29.1.3 65807 2pviA 157 9.22e+00 3pviA c.52.1.6 33302 1lxjA 104 9.25e+00 d.58.48.1 84736 1ku8A 133 9.61e+00 1lcl 142 9.69e+00 1lcl b.29.1.3 24216 1o12A 376 1.00e+01 b.92.1.5 80758 c.1.9.10 80759 1i50K 120 1.01e+01 d.74.3.2 61765 1gtfA 74 1.02e+01 b.82.5.1 70460 1d0yA 761 1.02e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1gh8A 89 1.03e+01 1gh8A d.58.12.1 39309 1c3mA 147 1.08e+01 1jotA b.77.3.1 27983 1q9rB 222 1.10e+01 b.1.1.1 -2221 b.1.1.2 -2512 2nef 136 1.10e+01 1efnB d.102.1.1 40704 1smd 496 1.10e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1a73A 163 1.11e+01 1a73A d.4.1.3 37145 1o59A 355 1.11e+01 unknown_sccs -3132 unknown_sccs -3133 1nciA 110 1.11e+01 1edhA b.1.6.1 22191 1jv4A 162 1.12e+01 b.60.1.1 67343 1m26A 133 1.14e+01 1g6eA 87 1.15e+01 1g6eA b.11.1.6 60317 1e6oH 219 1.18e+01 1igtB b.1.1.1 20495 b.1.1.2 21453 1poiB 260 1.21e+01 1poiB unknown_sccs 34155 1ajw 145 1.22e+01 1rhoA b.1.18.8 21905 1ktjA 129 1.25e+01 b.1.18.7 72974 1omzA 293 1.26e+01 c.68.1.15 87093 3pviA 157 1.27e+01 3pviA c.52.1.6 33300 1rg9A 383 1.27e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1np4A 184 1.29e+01 1np1A b.60.1.1 27166 1id2A 106 1.30e+01 1aac b.6.1.1 62288 2yhx 457 1.31e+01 2yhx i.12.1.1 46024 1hlcA 129 1.33e+01 1c1lA b.29.1.3 24208 1sy3A 184 1.33e+01 1m15A 357 1.34e+01 a.83.1.1 78368 d.128.1.2 78369 1ncg 110 1.34e+01 1edhA b.1.6.1 22193 1h6lA 353 1.36e+01 b.68.3.1 60687 1ul7A 102 1.37e+01 unknown_sccs -11020 1nlbH 218 1.37e+01 b.1.1.1 80621 b.1.1.2 80622 1l1jA 239 1.37e+01 b.47.1.1 84516 1evxA 162 1.39e+01 1a73A d.4.1.3 37149 1p90A 145 1.39e+01 unknown_sccs -7684 1h9dA 134 1.39e+01 1cmoA b.2.5.6 60821 1ugxA 133 1.40e+01 1hfeL 421 1.42e+01 1fehA c.96.1.1 36018 d.58.1.5 39001 1c8zA 265 1.43e+01 1c8zA d.23.1.1 38375 1jj2B 337 1.46e+01 1ffkB b.43.3.2 63086 1sltB 134 1.47e+01 1c1lA b.29.1.3 24187 1wapA 75 1.50e+01 1wapA b.82.5.1 28153 1qawF 74 1.52e+01 1wapA b.82.5.1 28202 1s72B 338 1.53e+01 1caxB 184 1.59e+01 1caxB b.82.1.2 28105 1vie 62 1.61e+01 1vie b.34.4.1 24592 1cx1A 153 1.61e+01 1ulo b.18.1.14 23770 1acc 735 1.62e+01 1acc f.11.1.1 43828 1gya 105 1.65e+01 1qa9A b.1.1.1 19745 8fabB 224 1.66e+01 1igtB b.1.1.1 19773 b.1.1.2 20883 1shbA 104 1.67e+01 1fmk d.93.1.1 40425 1qhlA 227 1.68e+01 1qhlA c.37.1.12 32382 1g41A 444 1.68e+01 1do0A c.37.1.20 32450 1jmsA 381 1.70e+01 a.60.6.1 66889 a.60.12.1 75862 d.218.1.2 75863 1go4A 205 1.72e+01 d.135.1.1 70292 1f15B 218 1.72e+01 1f15B b.121.4.5 23321 1al0G 175 1.72e+01 2bpa2 b.121.5.1 23275 1bpoA 494 1.73e+01 1bpoA a.118.1.4 19143 b.69.6.1 27670 1cur 155 1.73e+01 1rcy b.6.1.1 23021 1vif 62 1.73e+01 1vie b.34.4.1 24593 1xvaA 292 1.74e+01 1xvaA c.66.1.5 34183 1a3z 155 1.74e+01 1rcy b.6.1.1 23019 1kzhA 555 1.74e+01 c.89.1.1 73361 1hxmA 229 1.75e+01 1hxmA b.1.1.1 61367 b.1.1.2 61368 1slvA 142 1.77e+01 1sluA b.16.1.1 23688 1qoiA 177 1.77e+01 2cpl b.62.1.1 27490 1ngzB 220 1.81e+01 b.1.1.1 80502 b.1.1.2 80503 1khiA 176 1.85e+01 b.34.5.2 77408 b.40.4.5 77409 1bxaA 105 1.87e+01 1aac b.6.1.1 22839 1eo1A 124 1.88e+01 1eo1A c.55.5.1 33739 1np1A 184 1.88e+01 1np1A b.60.1.1 27155 1trb 320 1.89e+01 1trb c.3.1.5 30529 c.3.1.5 30530 1lnsA 763 1.89e+01 a.40.2.1 78101 b.18.1.13 78102 c.69.1.21 78103 1n0lA 224 1.90e+01 b.1.11.1 79744 b.7.2.1 79745 1ux6A 350 1.93e+01 unknown_sccs -3451 unknown_sccs -12886 1spbP 78 1.94e+01 1scjB d.58.3.2 39068 1ibcA 194 1.94e+01 1pauA c.17.1.1 30997 1fftB 315 1.94e+01 1cyx b.6.1.2 23025 f.17.2.1 43628 1pk6C 129 1.95e+01 b.22.1.1 -3293 1f2fA 104 1.95e+01 1fmk d.93.1.1 40455 1aqb 183 1.96e+01 1aqb b.60.1.1 27084 1fna 93 1.96e+01 1fnf b.1.2.1 21971 1ng0A 253 1.97e+01 b.121.4.7 80475 1ig8A 486 1.97e+01 2yhx c.55.1.3 64746 c.55.1.3 64747 1lvk 762 1.98e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 1rw7A 243 1.99e+01 c.23.16.2 -6530 1shaA 104 2.02e+01 1fmk d.93.1.1 40424 1aaj 105 2.08e+01 1aac b.6.1.1 22841 1bg0 356 2.13e+01 1qh4A a.83.1.1 18476 d.128.1.2 41211 1rcy 151 2.14e+01 1rcy b.6.1.1 23018 1c3kA 147 2.16e+01 1jotA b.77.3.1 27984 1tl2A 236 2.16e+01 1tl2A b.67.1.1 27541 1cjcA 460 2.17e+01 1cjcA c.3.1.1 30319 c.4.1.1 30604 1pnsB 234 2.17e+01 i.1.1.1 88169 1j5eB 256 2.17e+01 c.23.15.1 71543 1i06A 180 2.19e+01 1mup b.60.1.1 27131 1bmbA 123 2.19e+01 1griA d.93.1.1 40466 1lqtA 456 2.19e+01 c.3.1.1 74198 c.4.1.1 74199 1o8bA 219 2.19e+01 unknown_sccs 81180 d.58.40.1 81181 1fmaE 150 2.21e+01 1fmaE d.41.5.1 38630 1d4bA 122 2.25e+01 1d4bA d.15.2.1 37638 1mlcB 218 2.25e+01 1igtB b.1.1.1 20053 b.1.1.2 21095 1swuA 127 2.26e+01 1swuA b.61.1.1 27230 1mi1A 414 2.29e+01 a.169.1.1 79137 b.55.1.6 79138 1lnqA 336 2.32e+01 c.2.1.9 74049 f.14.1.1 74050 1hf2A 210 2.36e+01 1hf2A b.80.3.1 60992 c.102.1.1 60993 1cdb 105 2.37e+01 1qa9A b.1.1.1 19744 1fc4A 401 2.37e+01 1bs0A c.67.1.4 59760 1mxa 383 2.38e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1ah2 269 2.38e+01 1gci c.41.1.1 32542 1yveJ 524 2.39e+01 1qmgA a.100.1.2 18790 c.2.1.6 30187 1hyxH 224 2.40e+01 1igtB b.1.1.1 20167 b.1.1.2 21191 1oy1A 228 2.41e+01 c.23.16.2 87548 1paz 123 2.45e+01 1bqk b.6.1.1 22878 1lq9A 112 2.46e+01 d.58.4.3 78129 1jg1A 235 2.48e+01 c.66.1.7 66661 1phk 298 2.48e+01 1cdkA d.144.1.7 41635 1d2gA 292 2.49e+01 1xvaA c.66.1.5 34187 1f9yA 158 2.50e+01 d.58.30.1 83249 1r4kA 169 2.51e+01 unknown_sccs -3625 1aac 105 2.52e+01 1aac b.6.1.1 22838 1sfp 114 2.52e+01 1sfp b.23.1.1 23895 1kpf 126 2.53e+01 1kpf d.13.1.1 37507 1upiA 225 2.53e+01 b.82.1.1 -4823 1gmeA 151 2.53e+01 b.15.1.1 65305 1pvuA 154 2.56e+01 3pviA c.52.1.6 33306 1ks2A 219 2.56e+01 unknown_sccs 72908 d.58.40.1 72909 1i05A 180 2.57e+01 1mup b.60.1.1 27130 1dyoA 160 2.58e+01 1dyoA b.18.1.7 23771 1jjgA 102 2.61e+01 b.40.4.5 71696 1l7aA 318 2.61e+01 c.69.1.25 77772 1um8A 376 2.62e+01 c.37.1.20 -7251 1a8y 367 2.62e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1e4fT 419 2.62e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1ms9A 648 2.63e+01 b.29.1.15 85088 b.68.1.1 85089 1fx3A 169 2.67e+01 1fx3B d.33.1.1 38524 2pldA 105 2.68e+01 1qadA d.93.1.1 40521 1kpeA 126 2.68e+01 1kpf d.13.1.1 37508 1n6zA 105 2.71e+01 unknown_sccs 85369 2trxA 108 2.72e+01 1thx c.47.1.1 32719 1slaA 134 2.78e+01 1c1lA b.29.1.3 24196 1fsoA 139 2.82e+01 1rhoA b.1.18.8 60007 1n3oA 252 2.83e+01 b.29.1.1 79967 1e30A 155 2.83e+01 1rcy b.6.1.1 23016 1pfsA 78 2.83e+01 1pfsA b.40.4.7 25391 1ha1 184 2.90e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1kigI 60 2.91e+01 1kigI g.8.1.2 44567 1eqoA 158 2.95e+01 1hka 1o22A 170 2.96e+01 d.238.1.1 86557 1gadO 330 2.98e+01 1dssG c.2.1.3 29950 d.81.1.1 39865 1btkB 169 3.06e+01 1btkA b.55.1.1 26960 1fdlH 218 3.06e+01 1igtB b.1.1.1 19961 b.1.1.2 21021 1tvdA 116 3.14e+01 1tvdA b.1.1.1 20650 1qs1A 462 3.15e+01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1bvoA 175 3.15e+01 1a3qA b.2.5.3 22457 1g8aA 227 3.16e+01 c.66.1.3 -8049 1e2tA 284 3.21e+01 1e2tA d.3.1.5 37121 1h7wB 1025 3.23e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1h7wD 1025 3.39e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1g0sA 209 3.42e+01 1g0sA d.113.1.1 60187 1p9eA 331 3.45e+01 1n9pA 207 3.47e+01 b.1.18.16 80343 1quzA 34 3.48e+01 2pta k.23.1.1 46453 1qa9A 102 3.50e+01 1qa9A b.1.1.1 19742 1jytA 163 3.51e+01 b.94.1.1 67489 1griA 217 3.51e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 1g99A 408 3.51e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1rzfH 235 3.53e+01 b.1.1.1 -2188 b.1.1.2 -2453 1kebA 108 3.55e+01 c.47.1.1 77341 1i69A 219 3.56e+01 c.94.1.1 61825 2izhB 123 3.58e+01 1swuA b.61.1.1 27234 1dgwA 178 3.58e+01 1dgwA b.82.1.2 28090 1qmgA 524 3.58e+01 1qmgA a.100.1.2 18785 c.2.1.6 30182 1pmy 123 3.59e+01 1bqk b.6.1.1 22888 1wejH 223 3.60e+01 1igtB b.1.1.1 20361 b.1.1.2 21353 1nw2A 105 3.63e+01 c.47.1.1 -7380 1jp3A 253 3.64e+01 1f75A c.101.1.1 63221 1i1qA 520 3.67e+01 1qdlA d.161.1.1 61543 1liiA 363 3.69e+01 c.72.1.1 73921 1h7xC 1025 3.74e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1aqzB 149 3.80e+01 1aqzA d.1.1.3 36239 1tikA 213 3.86e+01 1yveI 524 3.86e+01 1qmgA a.100.1.2 18789 c.2.1.6 30186 1mtx 39 3.86e+01 1sco g.3.7.2 44149 1op3H 225 3.87e+01 b.1.1.1 87208 b.1.1.2 87209 1qwiA 143 3.88e+01 d.227.1.1 -11183 1g0xA 197 3.91e+01 1nkr b.1.1.4 21805 b.1.1.4 21806 1nukA 183 3.91e+01 1nukA b.18.1.4 23721 1h7xB 1025 3.95e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1gteA 1025 3.96e+01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1n91A 108 3.98e+01 d.206.1.1 80326