# 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 1c3hA 137 2.47e-13 b.22.1.1 -3255 1gr3A 160 2.79e-13 b.22.1.1 65476 1c28A 135 3.52e-13 1c28A b.22.1.1 23857 1o91A 178 4.67e-12 b.22.1.1 -3282 1pk6C 129 1.45e-10 b.22.1.1 -3293 1pk6A 133 1.20e-09 b.22.1.1 -3287 1pk6B 132 1.27e-09 b.22.1.1 -3290 1rj8A 164 2.43e-03 b.22.1.1 -3263 1iqaA 160 3.86e-03 b.22.1.1 71274 1d2qA 173 5.97e-03 1d4vB b.22.1.1 23894 1dg6A 191 1.13e-02 1d4vB b.22.1.1 23883 1d4vB 163 1.36e-02 1d4vB b.22.1.1 23884 1jh5A 144 4.22e-02 b.22.1.1 66697 1kxgA 152 9.23e-02 b.22.1.1 73145 1aly 146 9.25e-02 1aly b.22.1.1 23856 6prcH 258 9.68e-02 6prcH b.41.1.1 25457 f.23.10.1 43436 1dxrH 258 1.41e-01 6prcH b.41.1.1 25456 f.23.10.1 43433 4tsvA 150 2.14e-01 2tnfA b.22.1.1 23860 2tnfA 156 2.30e-01 2tnfA b.22.1.1 23880 1tnrA 144 3.61e-01 2tnfA b.22.1.1 23867 1ng2A 193 4.80e-01 b.34.2.1 85660 b.34.2.1 85661 1gttA 429 5.64e-01 d.177.1.1 70529 d.177.1.1 70530 1tnfA 158 6.36e-01 2tnfA b.22.1.1 23871 1i7oA 429 6.62e-01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1uxzA 131 9.05e-01 b.18.1.10 -3110 1i05A 180 1.22e+00 1mup b.60.1.1 27130 1i06A 180 1.87e+00 1mup b.60.1.1 27131 1eysH 259 2.54e+00 6prcH b.41.1.1 25484 f.23.10.1 43517 1bkb 136 2.74e+00 1bkb b.34.5.2 24609 b.40.4.5 25341 3seb 238 2.77e+00 3seb b.40.2.2 25184 d.15.6.1 37773 7ahlA 293 2.99e+00 7ahlA f.6.1.1 43812 1qexA 288 3.23e+00 1qexA b.32.1.1 24425 1edhA 226 3.28e+00 1edhA b.1.6.1 22198 b.1.6.1 22199 1qovH 260 3.31e+00 6prcH b.41.1.1 25464 f.23.10.1 43457 1jv4A 162 3.31e+00 b.60.1.1 67343 1hd7A 318 3.46e+00 1bix d.151.1.1 41780 1avk 638 3.54e+00 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1kopA 223 3.62e+00 2cba b.74.1.1 27966 1ov3A 138 3.82e+00 b.34.2.1 87451 b.34.2.1 87452 1qy1A 174 3.82e+00 b.60.1.1 -4445 1ja1A 622 3.83e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1ju3A 583 3.85e+00 b.18.1.13 67300 c.69.1.21 67301 1vkdA 338 3.93e+00 1nkqA 259 4.26e+00 1rzhH 260 4.29e+00 b.41.1.1 -3979 f.23.10.1 -12092 1bix 287 4.61e+00 1bix d.151.1.1 41781 1dlc 584 4.95e+00 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1mup 166 4.99e+00 1mup b.60.1.1 27133 1ux6A 350 5.30e+00 unknown_sccs -3451 unknown_sccs -12886 1oq1A 223 5.31e+00 unknown_sccs -3455 1nt0A 286 5.36e+00 b.23.1.1 86143 b.23.1.1 86144 g.3.11.1 86145 1mv3A 213 5.54e+00 b.34.2.1 -3555 1fi2A 201 5.64e+00 1fi2A b.82.1.2 59845 1ygs 234 5.71e+00 1ygs b.26.1.1 23907 1phm 310 5.90e+00 1phm b.121.1.2 59015 b.121.1.2 59016 1dyoA 160 6.06e+00 1dyoA b.18.1.7 23771 1sr4B 261 6.09e+00 1jtdB 273 6.18e+00 b.69.5.2 67265 1bcpC 199 6.27e+00 1bcpB b.40.2.1 25121 d.169.1.2 42430 1o6sB 105 6.38e+00 b.1.6.1 81096 1suuA 312 6.44e+00 unknown_sccs -4610 1hdmB 193 6.50e+00 1hdmB b.1.1.2 21584 d.19.1.1 38158 1iqyA 638 6.51e+00 b.30.2.1 76763 d.17.2.1 76764 d.17.2.1 76765 1koqA 253 6.69e+00 2cba b.74.1.1 27964 1amoA 615 6.79e+00 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1ewkA 490 6.81e+00 1ewkA c.93.1.1 35712 1sdwA 314 6.93e+00 b.121.1.2 -3024 b.121.1.2 -3025 1lslA 113 6.95e+00 g.60.1.1 78178 g.60.1.1 78179 1a8p 258 7.01e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 1ystH 260 7.26e+00 6prcH b.41.1.1 25482 f.23.10.1 43511 1sv6A 269 7.27e+00 1smlA 269 7.35e+00 1smlA d.157.1.1 42053 1ncg 110 7.90e+00 1edhA b.1.6.1 22193 1l7lA 121 7.92e+00 b.18.1.16 77790 1g4uS 383 8.09e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1b35C 282 8.16e+00 1b35C 1bxsA 501 8.21e+00 1bpwA c.82.1.1 35357 1nciA 110 9.17e+00 1edhA b.1.6.1 22191 1o04A 500 9.52e+00 c.82.1.1 86508 1h6yA 170 9.56e+00 b.18.1.7 70904 1m4uA 206 9.66e+00 g.17.1.7 78625 1ekgA 127 9.72e+00 1dlxA d.82.2.1 40021 1vpsA 289 1.00e+01 1vpsA b.121.6.1 23336 1p9rA 418 1.01e+01 c.37.1.11 -7142 2bpa2 175 1.02e+01 2bpa2 1n7vA 555 1.03e+01 b.126.1.1 85377 1lw3A 657 1.06e+01 unknown_sccs -4378 unknown_sccs -7358 1epwA 1290 1.09e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1ui8A 638 1.11e+01 b.30.2.1 -3525 d.17.2.1 -9272 d.17.2.1 -9273 1mkfA 382 1.12e+01 b.116.1.1 79232 1ujxA 119 1.14e+01 b.26.1.2 -3325 1k3bA 119 1.15e+01 b.61.5.1 72016 1aym3 238 1.19e+01 1aym3 1k5dB 201 1.20e+01 b.55.1.3 68169 1khiA 176 1.21e+01 b.34.5.2 77408 b.40.4.5 77409 1kb5B 117 1.27e+01 1kb5B b.1.1.1 20632 1itbB 315 1.27e+01 1itbB b.1.1.4 21720 b.1.1.4 21721 b.1.1.4 21722 1fo0B 112 1.29e+01 1kb5B b.1.1.1 20631 1ok8A 394 1.29e+01 b.1.18.4 -2737 f.10.1.1 -12384 1ui7A 638 1.31e+01 b.30.2.1 -3523 d.17.2.1 -9268 d.17.2.1 -9269 1c9oA 66 1.31e+01 1mjc b.40.4.5 25325 1rhoC 145 1.32e+01 1rhoA b.1.18.8 21901 1caxB 184 1.36e+01 1caxB b.82.1.2 28105 2fcbA 173 1.37e+01 2fcbA b.1.1.4 21781 b.1.1.4 21782 1csp 67 1.38e+01 1mjc b.40.4.5 25321 1p2zA 968 1.40e+01 b.121.2.2 -3020 b.121.2.2 -3021 1cx1A 153 1.43e+01 1ulo b.18.1.14 23770 1ihmA 530 1.44e+01 1ihmA b.121.4.3 62385 3dni 260 1.50e+01 3dni d.151.1.1 41791 1ivwA 638 1.51e+01 b.30.2.1 71456 d.17.2.1 71457 d.17.2.1 71458 1b6fA 159 1.51e+01 1bv1 d.129.3.1 41316 1rhoA 145 1.55e+01 1rhoA b.1.18.8 21899 1j1xH 114 1.55e+01 b.1.1.1 77063 1oxcA 114 1.56e+01 b.115.1.1 -3224 1v7wA 807 1.59e+01 1vpsB 289 1.60e+01 1vpsA b.121.6.1 23337 1eo9B 241 1.67e+01 3pchM b.3.6.1 22826 1el6B 219 1.67e+01 1el6B d.182.1.1 42607 1cauB 184 1.75e+01 1caxB b.82.1.2 28103 1ycsB 239 1.77e+01 1ycsB b.34.2.1 24553 d.211.1.1 19155 1el6A 219 1.78e+01 1el6B d.182.1.1 42606 1o6uA 403 1.82e+01 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1ffkN 95 1.82e+01 1ffkN b.34.5.1 24606 1j05B 121 1.82e+01 b.1.1.1 -2251 1q8iA 783 1.83e+01 c.55.3.5 -7635 e.8.1.1 -11885 1od3A 168 1.87e+01 b.18.1.10 86825 1sgoA 139 1.89e+01 unknown_sccs -10487 1ruxA 951 1.91e+01 1dhx 1ekbB 235 1.91e+01 5ptp b.47.1.2 26282 1fnlA 175 1.96e+01 2fcbA b.1.1.4 21783 b.1.1.4 21784 1mpxA 615 1.99e+01 b.18.1.13 85041 c.69.1.21 85042 1df3A 162 1.99e+01 1mup b.60.1.1 27134 1a12A 413 2.04e+01 1a12A b.69.5.1 27663 1mrzA 293 2.05e+01 b.43.5.1 -4048 c.26.1.3 -6616 1j1bA 420 2.09e+01 d.144.1.7 -11312 1n08A 163 2.09e+01 b.43.5.1 79730 1d2sA 170 2.14e+01 1d2sA b.29.1.4 24221 1gztA 115 2.16e+01 b.115.1.1 76428 1d5mC 239 2.16e+01 3seb b.40.2.2 25185 d.15.6.1 37774 1hh2P 344 2.17e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1dfx 125 2.19e+01 1dfx b.1.13.1 22367 g.41.5.2 45255 1gm6A 175 2.21e+01 b.60.1.1 70272 1lizA 136 2.21e+01 1cawB 184 2.26e+01 1caxB b.82.1.2 28113 1smd 496 2.29e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1f15B 218 2.31e+01 1f15B b.121.4.5 23321 1pwt 61 2.34e+01 1tud b.34.2.1 24490 1gc1G 321 2.37e+01 1gc1G d.172.1.1 42493 1o4yA 288 2.40e+01 b.29.1.2 -3404 1mvfA 135 2.43e+01 b.1.1.1 85141 1kl9A 182 2.47e+01 b.40.4.5 72681 1ycsA 199 2.48e+01 1tupA b.2.5.2 22433 1uolA 219 2.49e+01 b.2.5.2 -2886 2dnjA 260 2.49e+01 3dni d.151.1.1 41790 1nnxA 109 2.50e+01 unknown_sccs -3899 1a3qA 285 2.52e+01 1a3qA b.1.18.1 21932 b.2.5.3 22447 1b4rA 80 2.57e+01 1b4rA b.1.3.1 22072 1im3D 95 2.64e+01 1im3D b.1.18.5 62568 1f42A 306 2.67e+01 1f42A b.1.1.4 59636 b.1.2.1 59637 b.1.2.1 59638 1f13A 731 2.69e+01 1f13A b.1.18.9 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1gmiA 136 2.70e+01 b.7.1.1 65309 1et9A 204 2.70e+01 1an8 b.40.2.2 25204 d.15.6.1 37793 1pqhA 143 2.71e+01 b.52.2.1 -4318 1oh0A 131 2.80e+01 d.17.4.3 87004 1mkaA 171 2.81e+01 1mkaA d.38.1.2 38543 1rl2A 137 2.83e+01 1rl2A b.34.5.3 24610 b.40.4.5 25342 1theB 260 2.84e+01 1theB d.3.1.1 37057 1shg 62 2.85e+01 1ckaA b.34.2.1 24493 1ab9C 97 2.86e+01 5ptp 1at0 145 2.89e+01 1at0 b.86.1.1 28374 1bbt3 220 2.92e+01 1qqp3 1umhA 184 2.92e+01 unknown_sccs -3127 1dlfH 124 2.96e+01 1igtB b.1.1.1 20383 1uylA 236 2.98e+01 1rlw 126 2.98e+01 1rlw b.7.1.1 23177 1opy 131 2.99e+01 1opy d.17.4.3 38113 1kmtA 141 3.01e+01 b.1.18.8 77442 1uqxA 113 3.02e+01 b.115.1.1 -3230 1t9fA 187 3.03e+01 1theA 260 3.03e+01 1theB d.3.1.1 37056 1uwzA 136 3.04e+01 1jtkA 136 3.05e+01 c.97.1.1 71862 1qqp3 220 3.07e+01 1qqp3 1q42A 201 3.09e+01 d.17.4.2 -9292 1ft9A 222 3.10e+01 1ft9A a.4.5.4 16107 b.82.3.1 28131 1aipE 405 3.16e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1tuc 63 3.16e+01 1tuc b.34.2.1 24492 1dmmA 131 3.18e+01 1opy d.17.4.3 38114 1ppfE 218 3.25e+01 1a7s b.47.1.2 26234 1a34A 159 3.27e+01 1a34A b.121.7.1 23286 1mvuB 121 3.29e+01 b.1.1.1 -2250 1f3lA 321 3.31e+01 1g6q2 c.66.1.6 59630 1f8vA 355 3.31e+01 2bbvA b.121.4.4 23329 1keoA 154 3.32e+01 b.64.1.1 68534 1ea2A 131 3.35e+01 d.17.4.3 64860 1ggtB 731 3.37e+01 1f13A b.1.18.9 21882 b.1.5.1 22173 b.1.5.1 22174 d.3.1.4 37112 1g9mC 185 3.38e+01 1cdy b.1.1.1 19721 b.1.1.3 21660 1suh 146 3.40e+01 1edhA b.1.6.1 22206 1duzB 100 3.50e+01 1agdB b.1.1.2 20671 1kzlA 208 3.59e+01 b.43.4.3 77635 b.43.4.3 77636 1pguA 615 3.63e+01 b.69.4.1 88069 b.69.4.1 88070 1lf7A 182 3.65e+01 b.60.1.1 73878 1i4fB 100 3.65e+01 1agdB b.1.1.2 61689 1tsrA 219 3.74e+01 1tupA b.2.5.2 22437 1ootA 60 3.75e+01 b.34.2.1 -3576 8prn 289 3.75e+01 3prn f.4.3.1 43767 1jnyA 435 3.77e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1bcpB 199 3.78e+01 1bcpB b.40.2.1 25120 d.169.1.2 42429 1tupA 219 3.79e+01 1tupA b.2.5.2 22434 1rhi3 236 3.81e+01 1aym3 1elvA 333 3.81e+01 5ptp b.47.1.2 59454 g.18.1.1 59455 1agdB 99 3.85e+01 1agdB b.1.1.2 20742 1xgsA 295 3.85e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1qlyA 58 3.88e+01 1bbzA b.34.2.1 24530 1ic7H 114 3.90e+01 1f3rB b.1.1.1 62258 1hsbB 99 3.90e+01 1agdB b.1.1.2 20737 1uacH 114 3.92e+01 b.1.1.1 -2285 1ew3A 159 3.94e+01 1mup b.60.1.1 27114 3hhrB 203 3.97e+01 1axiB b.1.2.1 22005 b.1.2.1 22006