# List of top-scoring protein chains for t2k-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 1gr3A 160 1.08e-15 b.22.1.1 65476 1c3hA 137 1.10e-15 1c28A 135 4.44e-15 1c28A b.22.1.1 23857 1o91A 178 1.75e-14 1pk6C 129 2.33e-12 1pk6B 132 1.23e-11 1pk6A 133 1.44e-11 1rj8A 164 1.51e-03 1iqaA 160 2.24e-03 b.22.1.1 71274 1d2qA 173 6.42e-03 1d4vB b.22.1.1 23894 1dg6A 191 1.23e-02 1d4vB b.22.1.1 23883 1d4vB 163 1.30e-02 1d4vB b.22.1.1 23884 1jh5A 144 2.81e-02 b.22.1.1 66697 1kxgA 152 4.19e-02 b.22.1.1 73145 1tnrA 144 8.60e-02 2tnfA b.22.1.1 23867 1aly 146 9.52e-02 1aly b.22.1.1 23856 2tnfA 156 1.53e-01 2tnfA b.22.1.1 23880 4tsvA 150 1.55e-01 2tnfA b.22.1.1 23860 1uxzA 131 2.09e-01 1phm 310 5.16e-01 1phm b.121.1.2 59015 b.121.1.2 59016 1sdwA 314 5.59e-01 1tnfA 158 1.01e+00 2tnfA b.22.1.1 23871 1dlc 584 1.02e+00 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1smlA 269 1.27e+00 1smlA d.157.1.1 42053 1d7qA 143 2.00e+00 1d7qA b.40.4.5 25331 1avk 638 2.06e+00 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1j05B 121 2.23e+00 1gttA 429 2.42e+00 d.177.1.1 70529 d.177.1.1 70530 1i7oA 429 2.48e+00 1i7oA d.177.1.1 61893 d.177.1.1 61894 1hdmB 193 2.51e+00 1hdmB b.1.1.2 21584 d.19.1.1 38158 1oq1A 223 2.52e+00 1iqyA 638 3.00e+00 b.30.2.1 76763 d.17.2.1 76764 d.17.2.1 76765 1f3lA 321 3.11e+00 1g6q2 c.66.1.6 59630 1kopA 223 3.17e+00 2cba b.74.1.1 27966 1ju3A 583 3.49e+00 b.18.1.13 67300 c.69.1.21 67301 1ui8A 638 3.76e+00 3seb 238 3.86e+00 3seb b.40.2.2 25184 d.15.6.1 37773 1pguA 615 3.96e+00 b.69.4.1 88069 b.69.4.1 88070 1l7lA 121 4.25e+00 b.18.1.16 77790 1vkdA 338 4.33e+00 1oj4A 283 4.41e+00 1ivwA 638 4.90e+00 b.30.2.1 71456 d.17.2.1 71457 d.17.2.1 71458 1o04A 500 4.94e+00 c.82.1.1 86508 1xgsA 295 5.28e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1cid 177 5.39e+00 1cid b.1.1.1 19740 b.1.1.3 21679 1ng2A 193 6.19e+00 b.34.2.1 85660 b.34.2.1 85661 1epwA 1290 6.34e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1ewkA 490 7.12e+00 1ewkA c.93.1.1 35712 1i05A 180 7.15e+00 1mup b.60.1.1 27130 1tuc 63 7.47e+00 1tuc b.34.2.1 24492 1j1bA 420 7.51e+00 1lslA 113 7.88e+00 g.60.1.1 78178 g.60.1.1 78179 1mvuB 121 8.45e+00 1bxsA 501 8.48e+00 1bpwA c.82.1.1 35357 1jofA 365 8.63e+00 b.69.10.1 71775 2bpa2 175 8.71e+00 2bpa2 1kl9A 182 8.86e+00 b.40.4.5 72681 1lw3A 657 9.03e+00 1mup 166 9.08e+00 1mup b.60.1.1 27133 1m2vB 926 9.80e+00 a.71.2.1 78497 b.2.8.1 78498 c.62.1.2 78499 d.109.2.1 78500 g.41.10.1 78501 1ktbA 405 9.95e+00 b.71.1.1 72960 c.1.8.1 72961 1i06A 180 1.00e+01 1mup b.60.1.1 27131 1ihmA 530 1.08e+01 1ihmA b.121.4.3 62385 1j83A 180 1.10e+01 b.18.1.12 66430 1duzB 100 1.10e+01 1agdB b.1.1.2 20671 1k9tA 540 1.11e+01 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1g4uS 383 1.11e+01 1g4uS a.24.11.1 16643 c.45.1.2 32691 1jtdB 273 1.11e+01 b.69.5.2 67265 1i4fB 100 1.12e+01 1agdB b.1.1.2 61689 1edqA 540 1.15e+01 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 1jv4A 162 1.17e+01 b.60.1.1 67343 1uebA 184 1.20e+01 1agdB 99 1.24e+01 1agdB b.1.1.2 20742 1hsbB 99 1.24e+01 1agdB b.1.1.2 20737 1bkb 136 1.24e+01 1bkb b.34.5.2 24609 b.40.4.5 25341 1oxcA 114 1.25e+01 1suuA 312 1.25e+01 2fcbA 173 1.27e+01 2fcbA b.1.1.4 21781 b.1.1.4 21782 1ygs 234 1.29e+01 1ygs b.26.1.1 23907 1im3D 95 1.33e+01 1im3D b.1.18.5 62568 1f00I 282 1.33e+01 1f00I b.1.14.1 22368 b.1.14.1 22369 d.169.1.3 42439 1qy1A 174 1.42e+01 1fnlA 175 1.43e+01 2fcbA b.1.1.4 21783 b.1.1.4 21784 1ycsB 239 1.43e+01 1ycsB b.34.2.1 24553 d.211.1.1 19155 1a8p 258 1.49e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 1ctn 540 1.49e+01 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1khiA 176 1.51e+01 b.34.5.2 77408 b.40.4.5 77409 1n7vA 555 1.53e+01 b.126.1.1 85377 1p2zA 968 1.53e+01 1gztA 115 1.58e+01 b.115.1.1 76428 1dazC 99 1.59e+01 1hvc b.50.1.1 26501 1yer 228 1.60e+01 1yer d.122.1.1 41101 1ekgA 127 1.63e+01 1dlxA d.82.2.1 40021 1pcxA 810 1.64e+01 1k5nB 100 1.64e+01 b.1.1.2 77268 1koqA 253 1.66e+01 2cba b.74.1.1 27964 1ok8A 394 1.82e+01 1difA 99 1.85e+01 1fmb b.50.1.1 26503 3hhrB 203 1.85e+01 1axiB b.1.2.1 22005 b.1.2.1 22006 1g4wR 383 1.85e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 2bbkH 355 1.86e+01 2bbkH b.69.2.1 27634 1dyoA 160 1.90e+01 1dyoA b.18.1.7 23771 1ncwH 222 1.90e+01 b.1.1.1 85555 b.1.1.2 85556 2rmcA 182 1.91e+01 2cpl b.62.1.1 27491 1gc1H 229 1.92e+01 1gc1H b.1.1.1 20265 b.1.1.2 21265 1kzkA 99 1.98e+01 b.50.1.1 73371 1vpsA 289 1.98e+01 1vpsA b.121.6.1 23336 1rewA 114 1.98e+01 1cx1A 153 1.99e+01 1ulo b.18.1.14 23770 1et9A 204 2.00e+01 1an8 b.40.2.2 25204 d.15.6.1 37793 1axiB 236 2.09e+01 1axiB b.1.2.1 21997 b.1.2.1 21998 1mv3A 213 2.10e+01 35c8H 217 2.10e+01 8fabA b.1.1.1 20297 b.1.1.2 21289 1ew3A 159 2.10e+01 1mup b.60.1.1 27114 1jguH 217 2.12e+01 b.1.1.1 66688 b.1.1.2 66689 1kb5B 117 2.19e+01 1kb5B b.1.1.1 20632 1nh0A 99 2.22e+01 1h54B 754 2.23e+01 a.102.1.4 60636 b.30.5.3 60637 1p9rA 418 2.23e+01 1k1tA 99 2.24e+01 b.50.1.1 71995 1mtpA 323 2.25e+01 e.1.1.1 85107 1gm6A 175 2.25e+01 b.60.1.1 70272 1ootA 60 2.26e+01 1h54A 754 2.27e+01 a.102.1.4 60634 b.30.5.3 60635 1dfx 125 2.33e+01 1dfx b.1.13.1 22367 g.41.5.2 45255 1cauB 184 2.35e+01 1caxB b.82.1.2 28103 1uqxA 113 2.35e+01 1bmfA 510 2.36e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1dzkA 157 2.44e+01 1obpA b.60.1.1 27096 6prcH 258 2.44e+01 6prcH b.41.1.1 25457 f.23.10.1 43436 1dxrH 258 2.44e+01 6prcH b.41.1.1 25456 f.23.10.1 43433 1h7sA 365 2.49e+01 d.14.1.3 65705 d.122.1.2 65706 1h6yA 170 2.54e+01 b.18.1.7 70904 1c9oA 66 2.55e+01 1mjc b.40.4.5 25325 2vsgA 358 2.61e+01 2vsgA h.4.1.1 45780 1evhA 112 2.62e+01 1evhA b.55.1.4 26997 1q5xA 161 2.63e+01 1viwB 198 2.63e+01 1led b.29.1.1 24170 1fyhB 229 2.63e+01 1jrhI b.1.2.1 22055 b.1.2.1 22056 1of5B 184 2.64e+01 d.17.4.2 86934 1nfdA 203 2.65e+01 1tcrA b.1.1.1 20612 b.1.1.2 21550 1ux6A 350 2.66e+01 2trxA 108 2.68e+01 1thx c.47.1.1 32719 1ocnA 362 2.69e+01 c.6.1.1 86808 1jv1A 505 2.72e+01 c.68.1.5 71892 1byqA 228 2.72e+01 1yer d.122.1.1 41100 1ab9C 97 2.73e+01 5ptp 1ppfE 218 2.78e+01 1a7s b.47.1.2 26234 1vpsB 289 2.80e+01 1vpsA b.121.6.1 23337 1pea 385 2.88e+01 1pea c.93.1.1 35662 1b3qA 379 2.90e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1g99A 408 2.92e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1pft 50 2.97e+01 1pft g.41.3.1 45206 1hvc 203 2.97e+01 1hvc b.50.1.1 26614 1obpA 159 3.00e+01 1obpA b.60.1.1 27092 1pfo 500 3.02e+01 1pfo f.9.1.1 43826 1e79A 510 3.03e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1ciy 590 3.04e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1elt 236 3.06e+01 5ptp b.47.1.2 26281 1ejfA 125 3.08e+01 1ejfA b.15.1.2 23683 1qfxA 460 3.11e+01 1qfxA c.60.1.3 33994 1ja1A 622 3.15e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1q16A 1247 3.15e+01 1bpwA 503 3.19e+01 1bpwA c.82.1.1 35365 1lf6A 684 3.21e+01 a.102.1.5 77918 b.30.5.5 77919 1opy 131 3.22e+01 1opy d.17.4.3 38113 5hvpA 99 3.23e+01 1fmb b.50.1.1 26605 1hn2A 159 3.27e+01 b.60.1.1 65890 1ov3A 138 3.27e+01 b.34.2.1 87451 b.34.2.1 87452 1gt1A 159 3.28e+01 1d2sA 170 3.29e+01 1d2sA b.29.1.4 24221 1dvfD 120 3.33e+01 1mfa b.1.1.1 20107 1cawB 184 3.35e+01 1caxB b.82.1.2 28113 1amoA 615 3.36e+01 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1gg6C 97 3.36e+01 5ptp 1dmmA 131 3.41e+01 1opy d.17.4.3 38114 1h30A 422 3.42e+01 b.29.1.4 76604 b.29.1.4 76605 1ea2A 131 3.43e+01 d.17.4.3 64860 1fo0B 112 3.46e+01 1kb5B b.1.1.1 20631 1kriA 186 3.52e+01 b.29.1.14 72897 1qwyA 291 3.57e+01 1a3yA 149 3.57e+01 1obpA b.60.1.1 27110 1csp 67 3.60e+01 1mjc b.40.4.5 25321 1b77A 228 3.66e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1qwoA 442 3.68e+01 1ruxA 951 3.69e+01 1dhx b.121.2.2 59040 b.121.2.2 59041 1qlyA 58 3.70e+01 1bbzA b.34.2.1 24530 1d5mC 239 3.72e+01 3seb b.40.2.2 25185 d.15.6.1 37774 1j1xH 114 3.74e+01 b.1.1.1 77063 1e4fT 419 3.74e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1kjvB 100 3.77e+01 b.1.1.2 77423 1caxB 184 3.82e+01 1caxB b.82.1.2 28105 1ld4A 264 3.99e+01 i.6.1.1 77886