# List of top-scoring protein chains for t2k-w0.5 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 1hyuA 521 1.20e-01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1f06A 320 1.75e-01 1dapA c.2.1.3 59556 d.81.1.3 59557 1dapA 320 1.75e-01 1dapA c.2.1.3 30053 d.81.1.3 39968 3dapA 320 1.75e-01 1dapA c.2.1.3 30051 d.81.1.3 39966 1d8lA 149 1.31e+00 1hjp a.60.2.1 17948 b.40.4.2 25267 1a3h 300 1.49e+00 7a3hA c.1.8.3 28819 1hjp 203 1.50e+00 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 7a3hA 303 1.50e+00 7a3hA c.1.8.3 28817 1h5vA 304 1.50e+00 1qi2A 305 1.50e+00 7a3hA c.1.8.3 28824 1cuk 203 1.52e+00 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1fl2A 310 1.68e+00 1hyuA c.3.1.5 59869 c.3.1.5 59870 1a8uA 277 2.05e+00 1brt c.69.1.12 34703 1brt 277 2.16e+00 1brt c.69.1.12 34699 1broA 277 2.26e+00 1brt c.69.1.12 34700 1jvnA 555 2.46e+00 c.1.2.1 67355 c.23.16.1 67356 1k28A 584 3.24e+00 b.40.8.1 68049 b.108.1.2 68050 d.2.1.3 68051 1ebfA 358 4.19e+00 1ebuA c.2.1.3 30033 d.81.1.2 39948 1ebuA 358 4.19e+00 1ebuA c.2.1.3 30035 d.81.1.2 39950 1khbA 625 4.45e+00 c.91.1.1 68606 c.109.1.1 68607 1gu6A 452 4.51e+00 1ccg 291 4.63e+00 1ryc a.93.1.1 18627 1ds4A 292 4.66e+00 1ryc a.93.1.1 59129 1dseA 292 4.66e+00 1ryc a.93.1.1 59130 1rbu 155 4.68e+00 2rn2 c.55.3.1 33552 1rbt 155 4.74e+00 2rn2 c.55.3.1 33555 1lf1A 308 4.83e+00 1b7gO 340 5.27e+00 1b7gO c.2.1.3 29992 d.81.1.1 39907 1rnh 155 5.30e+00 2rn2 c.55.3.1 33563 1kheA 625 5.84e+00 c.91.1.1 68609 c.109.1.1 68610 1rpxA 230 5.90e+00 1rpxA c.1.2.2 28536 1rdc 155 6.28e+00 2rn2 c.55.3.1 33568 1goa 156 6.29e+00 2rn2 c.55.3.1 33564 1dmmA 131 6.45e+00 1opy d.17.4.3 38114 1goc 156 6.64e+00 2rn2 c.55.3.1 33566 1kva 155 6.70e+00 2rn2 c.55.3.1 33559 1kvb 155 6.78e+00 2rn2 c.55.3.1 33562 2rn2 155 6.82e+00 2rn2 c.55.3.1 33551 1kvc 155 6.83e+00 2rn2 c.55.3.1 33560 1rdb 155 6.94e+00 2rn2 c.55.3.1 33561 1gob 155 7.09e+00 2rn2 c.55.3.1 33565 1cf2O 337 7.09e+00 1b7gO c.2.1.3 29994 d.81.1.1 39909 1e97A 131 7.11e+00 d.17.4.3 64803 1dmnA 131 7.14e+00 1opy d.17.4.3 38115 1jayA 212 7.17e+00 c.2.1.6 66478 1jaxA 212 7.17e+00 c.2.1.6 66476 1awqA 164 7.29e+00 2cpl b.62.1.1 27461 2cpl 165 7.38e+00 2cpl b.62.1.1 27420 1cwoA 165 7.46e+00 2cpl b.62.1.1 27445 1iaqC 166 7.47e+00 c.37.1.8 62122 1cynA 178 7.55e+00 2cpl b.62.1.1 27489 1d9xA 658 7.61e+00 1d2mA c.37.1.13 32419 c.37.1.13 32420 1d9zA 657 7.64e+00 1d2mA c.37.1.13 32421 c.37.1.13 32422 1rbr 155 7.83e+00 2rn2 c.55.3.1 33556 1law 155 8.22e+00 2rn2 c.55.3.1 33557 1j4aA 333 8.34e+00 1j49A 333 8.35e+00 1smeA 329 8.57e+00 1smrA b.50.1.2 26885 1rbs 155 8.64e+00 2rn2 c.55.3.1 33558 1be1 137 8.66e+00 1be1 c.23.6.1 31237 1rbv 155 8.73e+00 2rn2 c.55.3.1 33553 1qj5A 429 8.76e+00 1dtyA c.67.1.4 34493 1lav 155 9.09e+00 2rn2 c.55.3.1 33554 1pfzA 380 9.10e+00 1smrA b.50.1.2 26881 1gcuA 295 9.23e+00 1gcuA c.2.1.3 30063 d.81.1.4 39978 1dtyA 429 9.54e+00 1dtyA c.67.1.4 34495 1awsA 164 9.58e+00 2cpl b.62.1.1 27431 1ctqA 166 9.60e+00 1ctqA c.37.1.8 31965 5p21 166 9.60e+00 1ctqA c.37.1.8 31966 6q21A 171 1.01e+01 1ctqA c.37.1.8 31979 4tsuA 130 1.02e+01 1opy d.17.4.3 38118 1opy 131 1.02e+01 1opy d.17.4.3 38113 1ea2A 131 1.03e+01 d.17.4.3 64860 1e3rA 131 1.03e+01 1opy d.17.4.3 59199 1apxA 249 1.05e+01 1ryc a.93.1.1 18669 1lfdB 167 1.06e+01 1ctqA c.37.1.8 31976 2dldA 337 1.08e+01 1dxy c.2.1.4 30099 c.23.12.1 31359 1bvuA 418 1.10e+01 1hwyA c.2.1.7 30226 c.58.1.1 33874 4q21 189 1.11e+01 1ctqA c.37.1.8 31978 1dmqA 131 1.13e+01 1opy d.17.4.3 38116 221p 166 1.13e+01 1ctqA c.37.1.8 31987 721p 166 1.13e+01 1ctqA c.37.1.8 31975 1heiA 451 1.20e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 2tmgA 415 1.20e+01 1hwyA c.2.1.7 30238 c.58.1.1 33886 1dusA 194 1.21e+01 1dusA c.66.1.4 34182 1b26A 416 1.23e+01 1hwyA c.2.1.7 30232 c.58.1.1 33880 621p 166 1.25e+01 1ctqA c.37.1.8 31988 1qp8A 303 1.26e+01 1qp8A c.2.1.4 30092 c.23.12.1 31352 1a1vA 476 1.32e+01 1heiA c.37.1.14 32467 c.37.1.14 32468 1gtmA 419 1.35e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1b3bA 415 1.36e+01 1hwyA c.2.1.7 30244 c.58.1.1 33892 1bg6 359 1.41e+01 1bg6 a.100.1.5 18810 c.2.1.6 30214 6ldh 330 1.41e+01 3ldh c.2.1.5 30161 d.162.1.1 42128 1ldm 329 1.42e+01 3ldh c.2.1.5 30160 d.162.1.1 42127 1c7hA 131 1.57e+01 1opy d.17.4.3 38117 1ll1 590 1.69e+01 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.1.5 21864 1d2kA 392 1.69e+01 1d2kA c.1.8.5 29008 d.26.3.1 38442 1hdoA 206 1.71e+01 1he2A c.2.1.2 60965 1he2A 206 1.71e+01 1he2A c.2.1.2 60966 1orb 296 1.76e+01 1rhs c.46.1.2 32711 c.46.1.2 32712 1kao 167 1.78e+01 1ctqA c.37.1.8 32014 2rmcA 182 1.80e+01 2cpl b.62.1.1 27491 1dp2A 293 1.81e+01 1rhs c.46.1.2 32705 c.46.1.2 32706 1rhs 296 1.82e+01 1rhs c.46.1.2 32703 c.46.1.2 32704 2ora 296 1.82e+01 1rhs c.46.1.2 32707 c.46.1.2 32708 1rypF 233 1.85e+01 1rypF d.153.1.4 41937 1fntF 234 1.85e+01 1l6sA 323 1.97e+01 1ji6A 589 1.98e+01 b.18.1.3 63066 b.77.2.1 63067 f.1.3.1 63068 1jw9B 249 1.99e+01 c.111.1.1 67377 1rhd 293 2.02e+01 1rhs c.46.1.2 32715 c.46.1.2 32716 1i8jA 323 2.02e+01 1b4kA c.1.10.3 61968 1b4eA 323 2.03e+01 1b4kA c.1.10.3 29186 1cqjA 286 2.04e+01 2scuA c.2.1.8 30305 c.23.4.1 31133 1scuA 288 2.04e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1jxbA 155 2.04e+01 2scuA 288 2.05e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1g0uE 234 2.06e+01 d.153.1.4 41950 1llqA 605 2.07e+01 1jew4 68 2.10e+01 1hx8B 299 2.11e+01 1hg5A a.118.10.1 19223 1lnqA 336 2.17e+01 1kkcA 221 2.19e+01 a.2.11.1 68660 d.44.1.1 68661 1g15A 155 2.28e+01 2rn2 c.55.3.1 60197 1c8bA 371 2.30e+01 1c8bA c.56.1.2 59082 1h5yA 253 2.33e+01 c.1.2.1 65638 1b5fA 239 2.37e+01 1smrA b.50.1.2 26836 1fohA 664 2.43e+01 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1f21A 155 2.45e+01 2rn2 c.55.3.1 33550 1rda 155 2.71e+01 2rn2 c.55.3.1 33567 1hdsB 145 3.00e+01 1abwA a.1.1.2 15557 1hw7A 255 3.09e+01 1i7fA d.193.1.1 61297 1ccl 291 3.10e+01 1ryc a.93.1.1 18608 1g59A 468 3.14e+01 a.97.1.1 60257 c.26.1.1 60258 1gln 468 3.14e+01 1gln a.97.1.1 18752 c.26.1.1 31588 2ldx 331 3.15e+01 3ldh c.2.1.5 30159 d.162.1.1 42126 1geqA 248 3.20e+01 2tysA c.1.2.4 28589 1jciA 294 3.37e+01 1i8tA 367 3.38e+01 c.4.1.3 66094 d.16.1.7 66095 1hyhA 309 3.40e+01 1hyhA c.2.1.5 30150 d.162.1.1 42117 1bkhB 361 3.42e+01 1mucA c.1.11.2 29239 d.54.1.1 38883 3ccp 296 3.44e+01 1ryc a.93.1.1 18616 1f9cB 372 3.45e+01 1mucA c.1.11.2 59730 d.54.1.1 59731 2reb 352 3.49e+01 2reb c.37.1.11 32282 d.48.1.1 38767 2recA 353 3.50e+01 2reb i.2.1.1 45879 1krjA 294 3.53e+01 a.93.1.1 68852 1ccj 294 3.58e+01 1ryc a.93.1.1 18644 1gsoA 431 3.60e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 2mucB 373 3.61e+01 c.1.11.2 29242 d.54.1.1 38886 1mucA 373 3.62e+01 1mucA c.1.11.2 29236 d.54.1.1 38880 1bkhC 359 3.63e+01 1mucA c.1.11.2 29240 d.54.1.1 38884 1bkhA 358 3.64e+01 1mucA c.1.11.2 29238 d.54.1.1 38882 1vasA 137 3.65e+01 2end a.18.1.1 16404 1enj 138 3.68e+01 2end a.18.1.1 16401 1enk 138 3.70e+01 2end a.18.1.1 16402 1h6vE 499 3.72e+01 c.3.1.5 60705 c.3.1.5 60706 d.87.1.1 60707 3mucA 369 3.81e+01 1mucA c.1.11.2 29243 d.54.1.1 38887 1tmy 120 3.83e+01 1dbwA c.23.1.1 31083 1b6fA 159 3.85e+01 1bv1 d.129.3.1 41316 1hrhA 136 3.87e+01 1rthA c.55.3.1 33577 1e69B 322 3.88e+01 1e69B c.37.1.12 32377