# 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 1mat 264 6.22e-45 1c24A d.127.1.1 41152 1c24A 263 6.48e-45 1c24A d.127.1.1 41148 2matA 264 6.50e-45 1c24A d.127.1.1 41146 3matA 265 6.51e-45 1c24A d.127.1.1 41149 4matA 278 6.55e-45 1c24A d.127.1.1 41150 1jaw 440 1.68e-39 1az9 c.55.2.1 33549 d.127.1.1 41166 1a16 440 1.69e-39 1az9 c.55.2.1 33548 d.127.1.1 41165 1az9 457 1.70e-39 1az9 c.55.2.1 33547 d.127.1.1 41164 1xgsA 295 1.35e-33 1bn5 a.4.5.25 16216 d.127.1.1 41153 1b59A 370 1.85e-33 1bn5 a.4.5.25 16225 d.127.1.1 41162 1b6a 478 7.83e-33 1bn5 a.4.5.25 16223 d.127.1.1 41160 1bn5 478 9.54e-33 1bn5 a.4.5.25 16224 d.127.1.1 41161 1chmB 401 5.05e-28 1chmA c.55.2.1 33546 d.127.1.1 41143 1chmA 401 5.05e-28 1chmA c.55.2.1 33545 d.127.1.1 41142 1akaA 401 2.41e-02 1ajsA c.67.1.1 34258 1ewcA 214 3.80e-01 3seb b.40.2.2 25199 d.15.6.1 37788 1qf6A 642 4.60e-01 1qf6A c.51.1.1 33210 d.66.1.1 39551 d.67.1.1 39562 d.104.1.1 40759 1f77B 217 5.96e-01 3seb b.40.2.2 25201 d.15.6.1 37790 1enfA 212 6.84e-01 3seb b.40.2.2 25198 d.15.6.1 37787 1hxyD 213 7.00e-01 b.40.2.2 61390 d.15.6.1 61391 7aatA 401 1.38e+00 1ajsA c.67.1.1 34250 1bl0A 129 2.95e+00 1d5yA a.4.1.8 16053 a.4.1.8 16054 1djuA 388 3.06e+00 1bjwA c.67.1.1 59116 1gdeA 389 3.14e+00 c.67.1.1 60456 1ka8A 100 4.47e+00 1knrA 540 4.77e+00 1eubA 171 4.87e+00 1hfc d.92.1.11 59503 1bcg 77 5.27e+00 1aho g.3.7.1 44130 1smrA 335 5.40e+00 1smrA b.50.1.2 26878 1bu8A 452 5.67e+00 1gpl b.12.1.2 23647 c.69.1.19 34795 1fnqL 281 6.01e+00 6prcL f.2.1.2 59918 830cA 168 6.12e+00 1ck7A d.92.1.11 40400 1mnc 163 6.18e+00 1hfc d.92.1.11 40353 1gkdA 163 6.23e+00 2aacB 177 6.31e+00 2arcA b.82.4.1 28151 1flsA 165 6.42e+00 1hfc d.92.1.11 59875 1f6nL 281 6.56e+00 6prcL f.2.1.2 59660 1chuA 540 6.57e+00 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 2cgrH 214 6.61e+00 1igtB b.1.1.1 19919 b.1.1.2 21013 1diiA 521 7.03e+00 1qltA d.58.32.1 39481 d.145.1.1 41744 1jh0L 281 7.05e+00 f.2.1.2 63036 1fnpL 281 7.10e+00 6prcL f.2.1.2 59914 1aijL 281 7.98e+00 6prcL f.2.1.2 43461 1d6vH 221 8.19e+00 1igtB b.1.1.1 20197 b.1.1.2 21213 1dnpA 471 8.35e+00 1qnf a.99.1.1 18775 c.28.1.1 31630 1i17A 107 8.37e+00 1i17A d.6.1.1 61519 1gkcA 163 8.38e+00 1c5dA 213 8.72e+00 8fabA b.1.1.1 20414 b.1.1.2 21386 1e3jA 352 8.97e+00 1e3jA b.35.1.2 24765 c.2.1.1 29781 2arcB 164 9.27e+00 2arcA b.82.4.1 28149 2arcA 164 9.27e+00 2arcA b.82.4.1 28148 1ystL 273 9.29e+00 6prcL f.2.1.2 43509 1c8tA 167 9.70e+00 1hfc d.92.1.11 40390 1pssL 266 1.02e+01 6prcL f.2.1.2 43500 1hfs 160 1.06e+01 1hfc d.92.1.11 40370 1usn 165 1.09e+01 1hfc d.92.1.11 40372 1k4cA 219 1.09e+01 b.1.1.1 68126 b.1.1.2 68127 1b8yA 167 1.10e+01 1hfc d.92.1.11 40377 1cizA 168 1.11e+01 1hfc d.92.1.11 40371 1hy7A 173 1.12e+01 d.92.1.11 65957 1umsA 174 1.12e+01 1hfc d.92.1.11 40368 1h6kA 757 1.12e+01 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 1k3iA 656 1.14e+01 b.1.1.5 68113 b.18.1.1 68114 b.69.1.1 68115 1gof 639 1.15e+01 1gof b.1.1.5 21807 b.18.1.1 23709 b.69.1.1 27631 1goh 639 1.15e+01 1gof b.1.1.5 21809 b.18.1.1 23711 b.69.1.1 27633 1cknB 330 1.18e+01 1ckmA b.40.4.6 25361 d.142.2.3 41588 1qmuA 380 1.20e+01 1qmuA b.3.2.1 22534 c.56.5.1 33827 1cknA 330 1.25e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1ckmA 330 1.25e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1cxvA 164 1.31e+01 1ck7A d.92.1.11 40404 2mysA 843 1.48e+01 1lvk b.34.3.1 24557 c.37.1.9 32154 1ueaA 173 1.49e+01 1hfc d.92.1.11 40365 1gkuB 1054 1.55e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1frb 315 1.71e+01 1frb c.1.7.1 28665 1k4vA 289 1.72e+01 1iag 202 1.73e+01 1atlA d.92.1.9 40319 1xsm 390 1.74e+01 1xsm a.25.1.2 16804 2ora 296 1.77e+01 1rhs c.46.1.2 32707 c.46.1.2 32708 1rhs 296 1.77e+01 1rhs c.46.1.2 32703 c.46.1.2 32704 1har 216 1.77e+01 1rthA e.8.1.2 43025 1g8oA 310 1.80e+01 1g8oA c.68.1.9 60375 1dp2A 293 1.81e+01 1rhs c.46.1.2 32705 c.46.1.2 32706 1c9wA 315 1.82e+01 1frb c.1.7.1 28699 1orb 296 1.88e+01 1rhs c.46.1.2 32711 c.46.1.2 32712 1i7cA 267 1.89e+01 1jenA 3aig 202 1.89e+01 1atlA d.92.1.9 40321 4aig 201 1.90e+01 1atlA d.92.1.9 40318 3hflH 215 1.94e+01 1igtB b.1.1.1 19969 b.1.1.2 21027 1fbl 370 1.94e+01 1hfc b.66.1.1 27539 d.92.1.11 40347 1mjyA 175 1.96e+01 2prd b.40.5.1 25421 1rhd 293 2.02e+01 1rhs c.46.1.2 32715 c.46.1.2 32716 1fg5N 310 2.06e+01 1g8oA c.68.1.9 59816 1hxvA 113 2.08e+01 1axsB 221 2.10e+01 1mfa b.1.1.1 20201 b.1.1.2 21217 1f2rC 87 2.14e+01 1c9fA d.15.2.1 37640 1do0A 442 2.18e+01 1do0A c.37.1.13 32432 1c9fA 90 2.19e+01 1c9fA d.15.2.1 37639 1g4bE 443 2.19e+01 1do0A c.37.1.13 32446 1jqkA 639 2.21e+01 e.26.1.2 67101 1ht1E 449 2.22e+01 c.37.1.13 65928 1nmbH 122 2.24e+01 1mfa b.1.1.1 20063 1nmaH 122 2.25e+01 1mfa b.1.1.1 20065 1iciA 256 2.38e+01 1iciA c.31.1.5 62266 3pdzA 96 2.38e+01 1pdr b.36.1.1 24782 1d5bB 221 2.38e+01 8fabA b.1.1.1 20205 b.1.1.2 21221 1fpwA 190 2.67e+01 1rec a.39.1.5 17329 1gl9B 1054 2.71e+01 c.37.1.16 65291 c.37.1.16 65292 e.10.1.1 65293 1a85A 158 2.79e+01 1hfc d.92.1.11 40355 1dzoA 123 2.84e+01 1dzoA d.24.1.1 38378 1huvA 380 2.90e+01 c.1.4.1 61277 1i76A 163 2.91e+01 1hfc d.92.1.11 61877 1kbcA 164 2.93e+01 1hfc d.92.1.11 40350 1plgH 215 2.93e+01 1igtB b.1.1.1 20081 b.1.1.2 21113 1bzsA 165 2.97e+01 1hfc d.92.1.11 40348 1auoA 218 3.00e+01 1auoA c.69.1.14 34716 1aurA 218 3.00e+01 1auoA c.69.1.14 34718 1a0k 131 3.01e+01 3nul d.110.1.1 40892 1lmkA 238 3.02e+01 1mfa b.1.1.1 20034 b.1.1.1 20035 1a3gA 308 3.04e+01 1daaA e.17.1.1 43286 1i1kA 309 3.05e+01 1daaA e.17.1.1 61533 1gmzB 122 3.06e+01 a.133.1.2 65357 1e6vA 553 3.10e+01 1mroA a.89.1.1 18527 d.58.31.2 39445 1epwA 1290 3.12e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1bncA 449 3.21e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1dv1A 449 3.21e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1bncB 449 3.21e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1gm1A 94 3.24e+01 1lt3A 240 3.26e+01 1lt3A d.166.1.1 42230 1a43 87 3.27e+01 1a8o a.28.3.1 16955 2ara 149 3.28e+01 2arcA b.82.4.1 28152 1dv2A 452 3.28e+01 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1f83A 425 3.29e+01 1f82A d.92.1.7 40306 1f82A 424 3.32e+01 1f82A d.92.1.7 40307 1slm 255 3.37e+01 1hfc a.20.1.2 59042 d.92.1.11 59043 1baj 101 3.39e+01 1a8o a.28.3.1 16954 1tho 109 3.45e+01 1thx c.47.1.1 32722 1b57A 358 3.51e+01 1dosA c.1.10.2 29177 1d5vA 94 3.52e+01 2hfh a.4.5.14 16144 1dcfA 136 3.55e+01 1dcfA c.23.1.2 31124 1nmf 67 3.65e+01 1mjc b.40.4.5 25323 1vpe 398 3.66e+01 16pk c.86.1.1 35453 1g5uA 131 3.68e+01 3nul d.110.1.1 40893 1smg 90 3.68e+01 1ncx a.39.1.5 17234 1hv2A 99 3.69e+01 d.42.1.1 61287 1bc8C 93 3.70e+01 1awcA a.4.5.21 16168 1c4xA 285 3.71e+01 1c4xA c.69.1.10 34684 1csp 67 3.71e+01 1mjc b.40.4.5 25321 3nul 130 3.72e+01 3nul d.110.1.1 40891 1ie9A 259 3.72e+01 1db1A a.123.1.1 62318 1db1A 259 3.72e+01 1db1A a.123.1.1 19329 1gzgA 337 3.75e+01 1k4wA 252 3.76e+01 1qoiA 177 3.80e+01 2cpl b.62.1.1 27490 1dosA 358 3.80e+01 1dosA c.1.10.2 29175 1mjhB 162 3.82e+01 1mjhA c.29.1.2 31640 1mjhA 162 3.82e+01 1mjhA c.29.1.2 31639 6prcL 273 3.85e+01 6prcL f.2.1.2 43434 1i7mA 267 3.86e+01 1jenA 1cicB 217 3.90e+01 1igtB b.1.1.1 19965 b.1.1.2 21025 1lqh 65 3.92e+01 1aho g.3.7.1 44142 1jpaA 312 3.92e+01 d.144.1.2 67011 1b4kA 337 3.97e+01 1b4kA c.1.10.3 29184