# List of top-scoring protein chains for t2k-100-30-alpha 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 1i12A 160 9.30e-06 1i21A d.108.1.1 61515 1i21A 159 1.20e-05 1i21A d.108.1.1 61549 1i1dA 161 1.82e-05 1i21A d.108.1.1 61526 1cjwA 166 6.38e-05 1cjwA d.108.1.1 40818 1qsmA 152 1.18e-03 1qsmA d.108.1.1 40808 1bob 320 3.56e-02 1bob d.108.1.1 40816 1qstA 160 2.46e-01 1yghA d.108.1.1 40804 1yghA 164 3.28e-01 1yghA d.108.1.1 40802 1b87A 181 8.75e-01 1b87A d.108.1.1 40797 1qg3A 195 9.13e-01 1qg3A b.1.2.1 21993 b.1.2.1 21994 1atg 231 1.01e+00 1atg c.94.1.1 35834 1fjgK 129 1.26e+00 1fjfK c.55.4.1 33733 1nar 290 1.59e+00 1nar c.1.8.5 28988 1i52A 236 1.99e+00 1i52A c.68.1.13 61767 1ndk 155 2.28e+00 1npk d.58.6.1 39118 1npk 154 2.53e+00 1npk d.58.6.1 39099 1pmaP 211 2.65e+00 1pmaP d.153.1.4 41863 1d3yA 301 2.72e+00 1d3yA e.12.1.1 43252 1bx2B 191 3.15e+00 1iakB b.1.1.2 21610 d.19.1.1 38184 1dxeA 256 3.22e+00 1dxeA c.1.12.5 29310 2dri 271 3.31e+00 2dri c.93.1.1 35637 1gefA 123 3.47e+00 1gefA c.52.1.18 60465 1agi 125 3.51e+00 7rsa d.5.1.1 37303 1f2tA 149 3.55e+00 1f2tA c.37.1.12 32373 2pleA 105 3.70e+00 1qadA d.93.1.1 40522 2pldA 105 3.79e+00 1qadA d.93.1.1 40521 1seiA 130 3.99e+00 1seiA d.140.1.1 41463 1gjwA 637 4.84e+00 b.71.1.1 60582 c.1.8.1 60583 1gjuA 637 4.89e+00 b.71.1.1 60580 c.1.8.1 60581 1i05A 180 4.93e+00 1mup b.60.1.1 27130 1g2qA 187 4.96e+00 c.61.1.1 65117 1lgyA 269 5.13e+00 3tgl c.69.1.17 34758 1ccwA 137 5.26e+00 1be1 c.23.6.1 31238 2napA 723 5.42e+00 2napA b.52.2.2 26926 c.81.1.1 35334 1jv4A 162 5.45e+00 b.60.1.1 67343 1qqqA 264 5.55e+00 1bkpA d.117.1.1 40931 1mup 166 5.56e+00 1mup b.60.1.1 27133 1aerA 205 5.64e+00 1aerA d.166.1.1 42249 1dn1A 594 5.72e+00 1dn1A e.25.1.1 43357 1g55A 343 5.77e+00 1g55A c.66.1.10 34247 1iicA 422 6.05e+00 1nmtA d.108.1.2 62422 d.108.1.2 62423 1dypA 271 6.36e+00 1dypA b.29.1.2 24185 1kafA 108 6.38e+00 d.199.1.1 68372 1art 396 6.47e+00 1ajsA c.67.1.1 34285 2matA 264 6.57e+00 1c24A d.127.1.1 41146 1ew3A 159 6.58e+00 1mup b.60.1.1 27114 1d4tA 104 6.64e+00 1d4tA d.93.1.1 40537 1agx 331 6.95e+00 4pgaA c.88.1.1 35564 1an7A 136 7.00e+00 1seiA d.140.1.1 41465 1dmaA 214 7.09e+00 1aerA d.166.1.1 42251 1hdhA 536 7.38e+00 c.76.1.2 65805 2i1b 153 7.43e+00 2i1b b.42.1.2 25538 1c24A 263 7.58e+00 1c24A d.127.1.1 41148 1i06A 180 7.65e+00 1mup b.60.1.1 27131 1fp2A 352 7.66e+00 1fpxA a.4.5.29 59941 c.66.1.12 59942 1fpxA 352 7.84e+00 1fpxA a.4.5.29 59950 c.66.1.12 59951 1spa 396 8.09e+00 1ajsA c.67.1.1 34291 2tscA 264 8.83e+00 1bkpA d.117.1.1 40952 1opc 110 8.83e+00 1opc a.4.6.1 16231 2aat 396 8.98e+00 1ajsA c.67.1.1 34348 1eudA 311 9.11e+00 2scuA c.2.1.8 30312 c.23.4.1 31140 1evfA 264 9.21e+00 1bkpA d.117.1.1 40932 1li5A 461 9.43e+00 1thjA 214 9.50e+00 1qreA b.81.1.5 28072 1ars 396 9.75e+00 1ajsA c.67.1.1 34287 1esmA 316 1.01e+01 1esmA c.37.1.6 31953 1mat 264 1.03e+01 1c24A d.127.1.1 41152 1gm6A 175 1.07e+01 1bqcA 302 1.08e+01 1bqcA c.1.8.3 28831 1qreA 247 1.09e+01 1qreA b.81.1.5 28066 1qcsA 211 1.12e+01 1qcsA b.52.2.3 26927 d.31.1.1 38461 1bo4A 168 1.14e+01 1bo4A d.108.1.1 40798 1tys 265 1.15e+01 1bkpA d.117.1.1 40937 1b72B 87 1.16e+01 1akhA a.4.1.1 16001 2pgi 445 1.16e+01 2pgi c.80.1.2 35308 1im2A 444 1.16e+01 1do0A c.37.1.13 62564 1bg4 302 1.17e+01 1taxA c.1.8.3 28806 1oatA 439 1.20e+01 2dkb c.67.1.4 34461 1jbgA 109 1.22e+01 a.6.1.3 66480 1qisA 396 1.24e+01 1ajsA c.67.1.1 34284 4pgaA 337 1.24e+01 4pgaA c.88.1.1 35565 1i1b 153 1.28e+01 2i1b b.42.1.2 25537 1gen 218 1.31e+01 1gen b.66.1.1 27536 1cqmA 101 1.31e+01 1ris d.58.14.1 39321 1ris 101 1.32e+01 1ris d.58.14.1 39314 1ikpA 613 1.33e+01 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1ecsA 126 1.35e+01 1ecsA d.32.1.2 59407 1an9A 340 1.39e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1ahxA 396 1.40e+01 1ajsA c.67.1.1 34293 1ewjA 126 1.43e+01 1ecsA d.32.1.2 59526 1xypA 190 1.46e+01 1axkA b.29.1.11 24327 1aa8A 347 1.46e+01 1an9A c.4.1.2 30619 d.16.1.3 37906 1c8uA 285 1.47e+01 1c8uA d.38.1.3 38547 d.38.1.3 38548 1fbnA 230 1.49e+01 1fbnA c.66.1.3 34181 1dq3A 454 1.54e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 2admA 421 1.55e+01 2admA c.66.1.10 34238 1jjiA 311 1.55e+01 c.69.1.2 66766 1bo1A 416 1.62e+01 1bo1A d.143.1.2 41591 1nmtA 392 1.63e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 2oatA 439 1.63e+01 2dkb c.67.1.4 34452 1pea 385 1.63e+01 1pea c.93.1.1 35662 1gpjA 404 1.64e+01 a.151.1.1 65451 c.2.1.10 65452 d.58.39.1 65453 1d5mB 192 1.70e+01 1iakB b.1.1.2 21618 d.19.1.1 38192 1louA 101 1.71e+01 1ris d.58.14.1 39323 1bo4B 168 1.78e+01 1bo4A d.108.1.1 40799 2dubE 261 1.79e+01 1nzyA c.14.1.3 30916 1g38A 393 1.86e+01 2admA c.66.1.10 60235 2tbs 222 1.93e+01 5ptp b.47.1.2 26009 1jetA 517 1.95e+01 1jevA c.94.1.1 35718 1g2lA 235 1.96e+01 b.47.1.2 65112 1gsmA 210 1.97e+01 b.1.1.4 65535 b.1.1.4 65536 1g57A 217 1.98e+01 1g57A d.115.1.2 60253 1hlgA 371 1.99e+01 1hlgA c.69.1.6 34656 1rtfB 252 2.00e+01 5ptp 21bi 153 2.07e+01 2i1b b.42.1.2 25542 2scuA 288 2.08e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 2mcm 112 2.08e+01 2mcm b.1.7.1 22207 1moq 368 2.09e+01 1moq c.80.1.1 35302 1fcdA 401 2.10e+01 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1fjsA 234 2.11e+01 1ucyE b.47.1.2 26336 1gl4B 98 2.17e+01 b.1.1.4 65288 1dmgA 225 2.21e+01 1dmgA c.22.1.1 31036 1oaa 259 2.21e+01 1oaa c.2.1.2 29829 1c7qA 445 2.26e+01 2pgi c.80.1.2 35307 1nal3 297 2.27e+01 1nal3 2scuB 388 2.28e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1hzdA 272 2.28e+01 c.14.1.3 65969 1nal1 297 2.29e+01 1nal3 1pne 140 2.29e+01 1pne d.110.1.1 40866 1fdyA 297 2.35e+01 1nal3 c.1.10.1 29071 1e9rA 437 2.35e+01 c.37.1.11 64827 1bx4A 345 2.38e+01 1bx4A c.72.1.1 34935 1zac 90 2.42e+01 1ncx a.39.1.5 17236 1aw0 72 2.44e+01 1aw0 d.58.17.1 39342 1hymA 45 2.47e+01 1hymA d.40.1.1 38581 1l1lA 739 2.47e+01 1scuA 288 2.52e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1cor 82 2.53e+01 451c a.3.1.1 15903 1bmlC 362 2.54e+01 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1kvkA 395 2.56e+01 1ddzA 496 2.57e+01 1ddzA c.53.2.1 33372 c.53.2.1 33373 1hnnA 282 2.57e+01 c.66.1.15 65895 1jsrA 327 2.64e+01 c.88.1.1 67237 3chbD 104 2.66e+01 3chbD b.40.2.1 24970 2xat 212 2.71e+01 2xat b.81.1.3 28058 2olbA 517 2.72e+01 1jevA c.94.1.1 35721 1hj8A 222 2.73e+01 b.47.1.2 65844 1l7mA 211 2.75e+01 1xat 212 2.76e+01 2xat b.81.1.3 28059 1ckmA 330 2.77e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1pba 81 2.78e+01 1pytA d.58.3.1 39067 1rcf 169 2.78e+01 1rcf c.23.5.1 31170 1ofv 169 2.79e+01 1rcf c.23.5.1 31184 1be3D 241 2.80e+01 1be3D a.3.1.3 15955 f.2.1.8 43666 1jc4A 148 2.80e+01 1jc4A d.32.1.4 62863 1eudB 396 2.82e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1hnoA 280 2.82e+01 1hnoA c.14.1.3 61095 1tdj 514 2.83e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 2fha 183 2.89e+01 2fha a.25.1.1 16674 1j97A 211 2.91e+01 1f5sA c.108.1.4 62753 1dfoA 417 2.91e+01 1bj4A c.67.1.4 34480 1f5sA 211 2.92e+01 1f5sA c.108.1.4 59656 1ejrC 567 2.93e+01 1ubpC b.92.1.1 28420 c.1.9.2 29042 1xel 338 3.00e+01 1xel c.2.1.2 29786 1cknA 330 3.03e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1fha 183 3.05e+01 2fha a.25.1.1 16675 1h75A 81 3.05e+01 1h75A c.47.1.1 60716 1fwcC 567 3.14e+01 1ubpC b.92.1.1 28410 c.1.9.2 29032 1hnuA 280 3.16e+01 1hnoA c.14.1.3 61096 1tin 69 3.21e+01 2sniI d.40.1.1 38580 1chmA 401 3.23e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 1jg5A 83 3.27e+01 d.205.1.1 66666 1ejjA 511 3.30e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1booA 323 3.34e+01 1booA c.66.1.11 34248 1a9xA 1058 3.35e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1lddA 74 3.38e+01 1gqwA 283 3.39e+01 1g4wR 383 3.46e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1t7pA 698 3.47e+01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1b77A 228 3.51e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1dpe 507 3.52e+01 1dpe c.94.1.1 35799 1who 96 3.52e+01 1who b.7.3.1 23215 1g4uS 383 3.57e+01 1g4uS a.24.11.1 16643 c.45.1.2 32691 1ezvD 245 3.57e+01 1be3D a.3.1.3 59546 f.2.1.8 59547 1bkb 136 3.58e+01 1bkb b.34.5.2 24609 b.40.4.5 25341 1eqjA 511 3.58e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1jdbB 1073 3.59e+01 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1fmtB 314 3.62e+01 1fmtA b.46.1.1 25759 c.65.1.1 34175 1bglA 1023 3.62e+01 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.1.1 24358 c.1.8.3 28857 1iqpA 327 3.63e+01 a.80.1.1 62649 c.37.1.13 62650 1h2rL 534 3.65e+01 1h2rL e.18.1.1 43298 1jbeA 128 3.66e+01 3chy c.23.1.1 62845 1bqsA 209 3.67e+01 1bqsA b.1.1.4 21704 b.1.1.4 21705 1dlhB 188 3.67e+01 1iakB b.1.1.2 21598 d.19.1.1 38172 1c3oA 1073 3.75e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1c3oE 1073 3.76e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1c3oC 1073 3.78e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 2ptd 298 3.79e+01 2plc c.1.18.2 29605 1dmmA 131 3.81e+01 1opy d.17.4.3 38114 3pga1 337 3.82e+01 4pgaA 1cznA 169 3.85e+01 1rcf c.23.5.1 31181 1e1aA 314 3.86e+01 1e1aA b.68.6.1 59155 2udpA 338 3.88e+01 1xel c.2.1.2 29791 1dppA 507 3.88e+01 1dpe c.94.1.1 35800 1hynP 379 3.91e+01 1hynP d.112.1.2 61408 1di1A 300 3.92e+01 1di1A a.128.1.4 19446 1c3cA 429 3.92e+01 1c3cA a.127.1.1 19425 1fqtA 112 3.92e+01 1fqtA b.33.1.1 24441 1ctt 294 3.93e+01 1ctt c.97.1.1 36022 c.97.1.1 36023 1c3oG 1073 4.00e+01 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533