# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 1tiqA 180 2.82e-25 1vhsA 175 9.44e-23 d.108.1.1 -10794 1s3zA 165 2.38e-18 1gheA 177 5.18e-18 d.108.1.1 76222 1qsmA 152 2.72e-17 1qsmA d.108.1.1 40808 1qsoA 149 1.56e-16 1qsmA d.108.1.1 40812 1i12A 160 3.75e-15 1i21A d.108.1.1 61515 1kuxA 207 8.06e-15 d.108.1.1 73021 1i21A 159 8.65e-15 1i21A d.108.1.1 61549 1i1dA 161 9.25e-15 1i21A d.108.1.1 61526 1cjwA 166 2.30e-14 1cjwA d.108.1.1 40818 1ufhA 180 4.51e-14 d.108.1.1 88485 1on0A 158 6.28e-14 d.108.1.1 87095 1p0hA 318 7.04e-14 d.108.1.1 -10802 1q2yA 140 8.15e-14 d.108.1.1 -10791 1nslA 184 2.31e-13 d.108.1.1 86137 1mk4A 157 2.42e-13 d.108.1.1 84979 1qstA 160 3.41e-13 1yghA d.108.1.1 40804 1b87A 181 8.51e-13 1b87A d.108.1.1 40797 1n71A 180 1.58e-12 d.108.1.1 85370 1bo4B 168 6.09e-12 1bo4A d.108.1.1 40799 5gcnA 166 1.44e-11 1yghA d.108.1.1 40807 1bo4A 168 2.97e-11 1bo4A d.108.1.1 40798 1sqhA 312 5.47e-09 unknown_sccs -10812 1yghA 164 5.68e-08 1yghA d.108.1.1 40802 1m4iA 181 1.65e-07 d.108.1.1 74457 1nmtA 392 6.94e-07 1nmtA d.108.1.2 40823 d.108.1.2 40824 1iicA 422 4.17e-05 1nmtA d.108.1.2 62422 d.108.1.2 62423 1bob 320 1.08e-04 1bob d.108.1.1 40816 1fy7A 278 3.60e-04 1fy7A d.108.1.1 40817 1lrzA 426 6.90e-03 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1ne9A 335 1.63e-02 d.108.1.4 -10805 d.108.1.4 -10806 1kzfA 230 4.62e-02 d.108.1.3 73354 1k4jA 230 1.05e-01 d.108.1.3 72057 1n0uA 842 1.07e-01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1j6zA 376 1.55e-01 1yagA c.55.1.1 62667 c.55.1.1 62668 1ml4A 308 1.62e-01 c.78.1.1 79255 c.78.1.1 79256 1qz5A 375 1.70e-01 c.55.1.1 -7590 c.55.1.1 -7591 1d4xA 375 2.57e-01 1yagA c.55.1.1 59107 c.55.1.1 59108 1dgaA 375 2.74e-01 1yagA 1oltA 457 3.33e-01 unknown_sccs -5688 1kblA 873 4.42e-01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1afwA 393 6.89e-01 1afwA c.95.1.1 35900 c.95.1.1 35901 1dik 874 6.93e-01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1pxtB 390 7.98e-01 1afwA c.95.1.1 35906 c.95.1.1 35907 1yagA 375 8.02e-01 1yagA c.55.1.1 33449 c.55.1.1 33450 1jmxA 494 9.12e-01 a.3.1.7 66901 a.3.1.7 66902 b.1.18.14 66903 b.1.18.14 66904 b.61.4.1 66905 1uyrA 737 1.13e+00 c.14.1.4 -6258 c.14.1.4 -6259 1n9lA 109 1.20e+00 d.110.3.6 85468 1ig8A 486 1.34e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1o20A 427 1.97e+00 c.82.1.1 86556 1l3kA 196 2.01e+00 d.58.7.1 73539 d.58.7.1 73540 2btfA 375 2.06e+00 1yagA c.55.1.1 33429 c.55.1.1 33430 1o50A 157 2.16e+00 d.37.1.1 -9604 d.37.1.1 -9605 1cg2A 393 2.22e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 1hrdA 449 2.27e+00 1k89 c.2.1.7 30219 c.58.1.1 33867 1idk 359 2.38e+00 1qcxA b.80.1.2 28025 1rypI 222 2.43e+00 d.153.1.4 41877 1cvjB 190 2.66e+00 1cvjB d.58.7.1 39193 d.58.7.1 39194 1han 297 2.69e+00 1han d.32.1.3 38506 d.32.1.3 38507 1lkdA 297 2.92e+00 d.32.1.3 78059 d.32.1.3 78060 1bgvA 449 3.03e+00 1k89 c.2.1.7 30217 c.58.1.1 33865 1ecfA 504 3.11e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 1ecfB 504 3.16e+00 1ecfB c.61.1.1 34054 d.153.1.1 41821 1s01 283 3.41e+00 1gci c.41.1.1 32511 1cvjA 190 3.42e+00 1cvjB d.58.7.1 39191 d.58.7.1 39192 1ha1 184 3.47e+00 1ha1 d.58.7.1 39147 d.58.7.1 39148 1gci 269 3.47e+00 1gci c.41.1.1 32503 1skyE 473 3.62e+00 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1tuhA 156 3.72e+00 1ve9A 347 3.79e+00 c.4.1.2 -6056 d.16.1.3 -9214 1ofdA 1520 3.88e+00 b.80.4.1 86935 c.1.4.1 86936 d.153.1.1 86937 1mo9A 523 4.00e+00 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1i0rA 169 4.17e+00 1i0rA b.45.1.2 61489 1i0sA 169 4.17e+00 1i0rA b.45.1.2 61491 1an9A 340 4.36e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1k89 449 4.41e+00 1k89 c.2.1.7 30218 c.58.1.1 33866 1mngA 203 4.52e+00 1avmA a.2.11.1 15776 d.44.1.1 38701 1stfI 98 4.53e+00 1stfI d.17.1.2 38006 1jqgA 433 4.78e+00 c.56.5.1 71791 d.58.3.1 71792 1ci0A 228 4.81e+00 1ci0A b.45.1.1 25750 1od2A 805 4.83e+00 c.14.1.4 86821 c.14.1.4 86822 1vicA 262 4.84e+00 c.68.1.13 -8252 1gr8A 412 5.01e+00 1ockA 412 5.01e+00 c.117.1.1 86802 1f1uA 323 5.06e+00 d.32.1.3 83200 d.32.1.3 83201 1iznB 277 5.28e+00 e.43.1.2 83848 1o1zA 234 5.58e+00 c.1.18.3 86555 1hqsA 423 5.63e+00 1iso c.77.1.1 61154 1uufA 369 5.69e+00 b.35.1.2 -3706 c.2.1.1 -5730 1lgtA 297 5.81e+00 d.32.1.3 77956 d.32.1.3 77957 1gk8I 140 6.09e+00 d.73.1.1 65242 1vhmA 195 6.30e+00 d.110.2.1 -10828 1ck7A 631 6.39e+00 1ck7A a.20.1.2 58969 b.66.1.1 27538 d.92.1.11 58970 g.14.1.2 44674 g.14.1.2 44675 g.14.1.2 44676 1fxlA 167 6.39e+00 1b7fA d.58.7.1 39183 d.58.7.1 39184 1i9zA 347 6.83e+00 1i9yA d.151.1.2 62102 1rfmA 344 6.96e+00 c.122.1.1 -8032 1f1xA 322 7.08e+00 d.32.1.3 83208 d.32.1.3 83209 1jatA 155 7.12e+00 1u9aA d.20.1.1 62818 1i9yA 347 7.42e+00 1i9yA d.151.1.2 62101 1aop 497 7.52e+00 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1shdA 107 7.87e+00 1fmk d.93.1.1 40440 1rz1A 161 8.13e+00 b.45.1.2 -4088 1pbjA 125 8.15e+00 d.37.1.1 -9608 d.37.1.1 -9609 1j7xA 302 8.30e+00 c.14.1.2 66425 1cwoA 165 8.31e+00 2cpl b.62.1.1 27445 2cpl 165 8.36e+00 2cpl b.62.1.1 27420 2aop 497 8.52e+00 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 1ds1A 324 8.53e+00 1drtA b.82.2.2 28127 1p5dX 463 8.61e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1aa8A 347 8.64e+00 1an9A 1drtA 324 8.76e+00 1drtA b.82.2.2 28130 1d2fA 390 8.94e+00 1d2fA c.67.1.3 34411 1cqqA 180 9.00e+00 1cqqA b.47.1.4 26422 1feuA 206 9.11e+00 1feuA b.53.1.1 59801 1jflA 228 9.24e+00 c.78.2.1 71656 c.78.2.1 71657 1gv3A 248 9.41e+00 a.2.11.1 70585 d.44.1.1 70586 1awqA 164 9.46e+00 2cpl b.62.1.1 27461 1awsA 164 9.53e+00 2cpl b.62.1.1 27431 1igs 248 9.61e+00 1a53 c.1.2.4 28565 1a53 247 9.65e+00 1a53 c.1.2.4 28564 1cr1A 296 9.88e+00 1cr1A c.37.1.11 32286 1fcbA 511 9.90e+00 1gox c.1.4.1 28620 d.120.1.1 41087 1juk 248 9.91e+00 1a53 c.1.2.4 28567 1thm 279 9.91e+00 1gci c.41.1.1 32544 1nmeA 146 9.97e+00 c.17.1.1 85874 1vhoA 346 9.98e+00 unknown_sccs -4283 c.56.5.4 -7893 1dmtA 696 1.00e+01 1dmtA d.92.1.4 40296 1r31A 428 1.04e+01 d.58.20.1 -10108 d.179.1.1 -11716 1tahB 318 1.07e+01 1cvl c.69.1.18 34774 1dioA 554 1.07e+01 1dioA c.1.19.3 29656 1tahA 318 1.08e+01 1cvl c.69.1.18 34775 1eexA 554 1.09e+01 1dioA c.1.19.3 29650 1cr0A 296 1.10e+01 1cr1A c.37.1.11 32287 1n6aA 259 1.13e+01 b.76.2.1 80121 b.85.7.1 80122 1o5oA 221 1.13e+01 c.61.1.1 -7954 1pvmA 184 1.14e+01 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1isaA 192 1.16e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1j5yA 187 1.17e+01 a.4.5.1 71592 d.94.2.1 71593 1gc0A 398 1.17e+01 c.67.1.3 70168 1kllA 130 1.19e+01 d.32.1.2 72720 1iscA 192 1.20e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1h1nA 305 1.21e+01 c.1.8.3 70855 1gox 370 1.22e+01 1gox c.1.4.1 28607 1lh0A 213 1.22e+01 c.61.1.1 73896 1b34B 118 1.25e+01 1b34B b.38.1.1 24797 1fsgA 233 1.28e+01 1qk3A c.61.1.1 34029 1qaxA 428 1.29e+01 1qaxA d.58.20.1 39376 d.179.1.1 42597 1kvs 338 1.30e+01 1xel c.2.1.2 29799 1fr9A 194 1.32e+01 1fr9A c.68.1.8 34579 1eysH 259 1.34e+01 6prcH b.41.1.1 25484 f.23.10.1 43517 1fs0G 230 1.36e+01 1fs0G c.49.2.1 59999 1opr 213 1.36e+01 1opr c.61.1.1 34091 1klqA 197 1.37e+01 d.135.1.1 68689 1nrgA 261 1.39e+01 b.45.1.1 80694 1qayA 428 1.40e+01 1qaxA d.58.20.1 39378 d.179.1.1 42599 1h0pA 182 1.42e+01 b.62.1.1 76450 1h3iA 293 1.43e+01 b.76.2.1 76635 b.85.7.1 76636 1s48A 609 1.49e+01 e.8.1.4 -11955 1vheA 373 1.50e+01 unknown_sccs -4280 c.56.5.4 -7890 1cvl 319 1.51e+01 1cvl c.69.1.18 34786 1vaoA 560 1.64e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1k2yX 463 1.64e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1h75A 81 1.67e+01 1h75A c.47.1.1 60716 1eulA 994 1.68e+01 1eulA 1iu9A 111 1.69e+01 c.78.2.1 -8500 1m7yA 435 1.73e+01 c.67.1.4 78761 1dryA 324 1.77e+01 1drtA b.82.2.2 28128 1k1tA 99 1.80e+01 b.50.1.1 71995 1gdgA 293 1.83e+01 1k8qA 377 1.83e+01 c.69.1.6 72177 1bywA 110 1.83e+01 1bywA d.110.3.6 40912 1bdg 451 1.84e+01 1qhaA c.55.1.3 33461 c.55.1.3 33462 1g6oA 330 1.85e+01 1g6oA c.37.1.11 32430 1udb 338 1.85e+01 1xel c.2.1.2 29787 1gsa 316 1.87e+01 1gsa c.30.1.3 31718 d.142.1.1 41477 1bzyA 217 1.87e+01 1qk3A c.61.1.1 34071 1j0hA 588 1.87e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1a8vA 121 1.88e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1xel 338 1.89e+01 1xel c.2.1.2 29786 1qysA 106 1.91e+01 unknown_sccs -13432 1iv0A 98 1.91e+01 unknown_sccs -7667 1udc 338 1.93e+01 1xel c.2.1.2 29785 2hsdA 253 1.93e+01 1e6wA c.2.1.2 29866 1try 224 1.96e+01 5ptp b.47.1.2 26017 2udpA 338 1.96e+01 1xel c.2.1.2 29791 1oalA 151 1.96e+01 b.1.8.1 86739 1w1kA 560 1.98e+01 1hdcA 253 1.99e+01 1e6wA c.2.1.2 29862 1zfjA 491 2.03e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1hvbA 349 2.04e+01 3pte e.3.1.1 42686 1su4A 994 2.07e+01 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1qoiA 177 2.08e+01 2cpl b.62.1.1 27490 1j2rA 199 2.08e+01 unknown_sccs -6799 1q7lA 198 2.11e+01 c.56.5.4 -7886 1ihgA 370 2.13e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1ri6A 343 2.15e+01 unknown_sccs -4621 1a58 177 2.16e+01 2cpl b.62.1.1 27495 1ne6A 283 2.17e+01 b.82.3.2 -4918 b.82.3.2 -4919 1pq7A 224 2.21e+01 b.47.1.2 -4190 1fn8A 224 2.22e+01 5ptp b.47.1.2 26012 1o0wA 252 2.23e+01 a.149.1.1 80751 d.50.1.1 80752 2wsyB 396 2.26e+01 2tysB c.79.1.1 35288 1ao0A 459 2.27e+01 1ecfB c.61.1.1 34049 d.153.1.1 41816 2bbkH 355 2.30e+01 2bbkH b.69.2.1 27634 1cp3A 277 2.32e+01 1pauA c.17.1.1 30992 1dazC 99 2.36e+01 1hvc b.50.1.1 26501 1q16A 1247 2.36e+01 b.52.2.2 -4337 c.81.1.1 -8547 1j5eK 129 2.38e+01 c.55.4.1 71554 1sjwA 144 2.44e+01 unknown_sccs -9296 1yaiA 151 2.46e+01 1yaiA b.1.8.1 22289 1b0pA 1231 2.48e+01 c.36.1.8 31831 c.36.1.12 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1qq4A 198 2.50e+01 1qq4A b.47.1.1 25768 1mt6A 280 2.53e+01 b.76.2.1 79446 b.85.7.1 79447 2alp 198 2.54e+01 1qq4A b.47.1.1 25772 1rpl 251 2.54e+01 1bpyA a.60.12.1 75933 d.218.1.2 75934 1p04A 198 2.55e+01 1qq4A b.47.1.1 25805 1ssxA 198 2.56e+01 b.47.1.1 -4112 1h3nA 878 2.60e+01 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1bqyA 234 2.64e+01 5ptp b.47.1.2 26332 1dar 691 2.65e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1kekA 1231 2.66e+01 c.36.1.8 68524 c.36.1.12 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1gtmA 419 2.67e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1pauA 147 2.68e+01 1pauA c.17.1.1 30994 1rypH 205 2.69e+01 d.153.1.4 41876 1l8qA 324 2.69e+01 a.4.12.2 77809 c.37.1.20 77810 1vjqA 79 2.75e+01 unknown_sccs -13478 1go4A 205 2.81e+01 d.135.1.1 70292 1bia 321 2.82e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1ndk 155 2.86e+01 1npk d.58.6.1 39118 1llwA 1520 2.88e+01 b.80.4.1 74017 c.1.4.1 74018 d.153.1.1 74019 1t82A 155 2.90e+01 1vh5A 148 2.97e+01 d.38.1.5 -9677 1rg9A 383 2.98e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 3pfk 319 3.00e+01 3pfk c.89.1.1 35581 1hfoA 113 3.07e+01 d.80.1.3 61006 1e5kA 201 3.08e+01 1fr9A c.68.1.8 34578 1eq2A 310 3.10e+01 1eq2A c.2.1.2 29814 1o13A 136 3.11e+01 c.55.5.1 80762 1jyeA 349 3.11e+01 c.93.1.1 67455 1jmuB 666 3.12e+01 4pfk 319 3.12e+01 3pfk c.89.1.1 35582 1gt7A 274 3.17e+01 c.74.1.1 70398 1e79D 482 3.18e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 2madH 373 3.21e+01 2bbkH b.69.2.1 27639 1jp3A 253 3.22e+01 1f75A c.101.1.1 63221 1npk 154 3.23e+01 1npk d.58.6.1 39099 1eu3A 210 3.27e+01 1an8 b.40.2.2 25206 d.15.6.1 37795 1qq9A 284 3.30e+01 1xjo c.56.5.4 33841 1h7zA 194 3.31e+01 1qhvA b.21.1.1 60733 1nh2B 53 3.33e+01 a.32.1.1 -777 1f3fA 155 3.35e+01 1npk d.58.6.1 39101 1v93A 296 3.37e+01 c.1.23.1 -5654 1jqiA 388 3.40e+01 a.29.3.1 67087 e.6.1.1 67088 1mxb 383 3.41e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1r0rE 274 3.42e+01 c.41.1.1 -7293 1ltdA 506 3.42e+01 1gox c.1.4.1 28618 d.120.1.1 41086 1my6A 199 3.43e+01 a.2.11.1 85232 d.44.1.1 85233 1uurA 473 3.45e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1xjo 284 3.46e+01 1xjo c.56.5.4 33843 6pfkA 319 3.47e+01 3pfk c.89.1.1 35583 1khiA 176 3.50e+01 b.34.5.2 77408 b.40.4.5 77409 3pte 349 3.50e+01 3pte e.3.1.1 42687 1dbxA 158 3.50e+01 1dbuA d.116.1.1 40928 1crzA 403 3.57e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1kw3B 292 3.60e+01 d.32.1.3 77549 d.32.1.3 77550 1fp2A 352 3.61e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 1ei5A 520 3.70e+01 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1hvc 203 3.72e+01 1hvc b.50.1.1 26614 1p4kA 295 3.75e+01 d.153.1.5 87772 1c5kA 439 3.76e+01 1crzA b.68.4.1 27630 c.51.2.1 33212 1b5tA 275 3.77e+01 1b5tA c.1.23.1 29676 1adt 356 3.81e+01 1anv a.54.1.1 17887 g.51.1.1 45362 g.51.1.1 45368 1cqxA 403 3.87e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1mxa 383 3.87e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1bo1A 416 3.89e+01 1bo1A d.143.1.2 41591 1oniA 137 3.91e+01 d.79.1.1 87144 2minB 522 3.93e+01 1qguB c.92.2.3 35610 1hzmA 154 3.96e+01 c.46.1.1 65975 1nd4A 264 3.96e+01 d.144.1.6 -11381 1d3bA 75 3.97e+01 1d3bA b.38.1.1 24798 1j7lA 264 3.99e+01 d.144.1.6 62697