# 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 1fo5A 85 4.25e-04 1fo5A c.47.1.1 59922 1egr 85 8.48e-04 1kte c.47.1.1 32765 1hyuA 521 5.62e-03 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1ego 85 1.82e-02 1kte c.47.1.1 32767 1ksiB 642 2.87e-02 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1ksiA 642 3.05e-02 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1qfnA 85 6.98e-02 1qfnA c.47.1.1 32768 1grx 85 8.84e-02 1kte c.47.1.1 32766 1gseA 221 1.07e-01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1k3lA 221 1.13e-01 a.45.1.1 77229 c.47.1.5 77230 1k3yA 221 1.13e-01 a.45.1.1 77245 c.47.1.5 77246 1kte 105 1.62e-01 1kte c.47.1.1 32771 1ej6A 1289 2.41e-01 i.7.1.1 45967 1f3aA 222 2.48e-01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1dp4A 435 2.74e-01 1dp4A c.93.1.1 35710 1s4nA 348 2.90e-01 unknown_sccs -8262 1j3vA 289 3.05e-01 a.100.1.1 -1303 c.2.1.6 -5947 1jhb 106 4.24e-01 1kte c.47.1.1 32772 1r5tA 142 4.53e-01 1xgsA 295 9.73e-01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1thx 115 1.02e+00 1thx c.47.1.1 32732 1f37A 110 1.30e+00 1f37A c.47.1.11 33088 1jmoA 480 1.44e+00 e.1.1.1 77138 1zfjA 491 1.61e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1hmcB 148 1.64e+00 1hmcB a.26.1.2 16868 1eu8A 409 1.90e+00 1eu8A c.94.1.1 59502 1hv8A 367 2.37e+00 1hv8A c.37.1.19 32405 c.37.1.19 32406 1o94A 729 2.93e+00 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1djnA 729 2.95e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 2tmdA 729 3.05e+00 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1r26A 125 3.15e+00 c.47.1.1 -7389 1ayl 541 3.33e+00 1ayl c.91.1.1 64718 c.109.1.1 64719 1a2vA 655 3.34e+00 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 1m2dA 110 3.47e+00 c.47.1.11 78476 1r5pA 108 3.51e+00 unknown_sccs -7487 1ytbB 180 3.66e+00 1ytbA d.129.1.1 41278 d.129.1.1 41279 1o0yA 260 3.68e+00 c.1.10.1 80756 1gumA 222 3.70e+00 1pgtA a.45.1.1 17683 c.47.1.5 32977 1qdlB 195 3.70e+00 1qdlB c.23.16.1 31437 1s6yA 450 3.71e+00 1ghsA 306 3.77e+00 1aq0A c.1.8.3 28840 1gulA 222 4.07e+00 1pgtA a.45.1.1 17675 c.47.1.5 32969 1oen 540 4.36e+00 1ayl c.91.1.1 64750 c.109.1.1 64751 1ytbA 180 4.48e+00 1ytbA d.129.1.1 41276 d.129.1.1 41277 1ecxA 384 4.51e+00 1ecxA c.67.1.3 34431 1pvyA 227 4.56e+00 d.115.1.2 -10937 1eg5A 384 4.60e+00 1ecxA c.67.1.3 34429 1j08A 226 4.86e+00 c.47.1.2 83855 c.47.1.2 83856 1b1cA 181 5.04e+00 1amoA c.23.5.2 31212 1r8sA 164 5.45e+00 c.37.1.8 -7082 1vjqA 79 5.57e+00 unknown_sccs -13478 1tbaB 180 5.65e+00 1ytbA d.129.1.1 41286 d.129.1.1 41287 1m2aA 110 5.77e+00 c.47.1.11 78472 1o0pA 104 6.10e+00 d.58.7.1 86535 1m2bA 110 6.19e+00 c.47.1.11 78474 1aq0A 306 6.33e+00 1aq0A c.1.8.3 28842 1dctA 324 6.38e+00 6mhtA c.66.1.26 34244 1adoA 363 6.42e+00 1fbaA c.1.10.1 29124 1qg0A 308 6.53e+00 1fnc b.43.4.2 25639 c.25.1.1 31529 1aba 87 6.56e+00 1aba c.47.1.1 32760 1ip9A 85 6.61e+00 1ip9A d.15.2.2 62638 1fw1A 216 6.61e+00 a.45.1.1 60051 c.47.1.5 60052 1gajA 257 6.76e+00 1gajA c.37.1.12 60416 1qpsA 261 7.00e+00 1ckqA c.52.1.1 33234 1dcfA 136 7.06e+00 1dcfA c.23.1.2 31124 1e9iA 431 7.10e+00 c.1.11.1 64818 d.54.1.1 64819 1igwA 434 7.44e+00 c.1.12.7 62370 1cl8A 276 7.47e+00 1ckqA c.52.1.1 33230 1bykA 255 7.48e+00 1bykA c.93.1.1 35706 1fnb 314 7.50e+00 1fnc b.43.4.2 25628 c.25.1.1 31518 1r9dA 787 7.54e+00 1ckqA 276 7.63e+00 1ckqA c.52.1.1 33229 1ddeA 338 7.76e+00 1dd9A e.13.1.1 43255 1nmoA 247 7.83e+00 unknown_sccs -8746 1jkgA 140 8.03e+00 d.17.4.2 66795 1ghr 306 8.26e+00 1aq0A c.1.8.3 28844 1cdwA 179 8.66e+00 1ytbA d.129.1.1 41212 d.129.1.1 41213 1j2iA 166 8.71e+00 1o3yA 166 8.71e+00 c.37.1.8 86618 1jx4A 352 8.78e+00 unknown_sccs -10188 unknown_sccs -11898 1qrqA 325 8.96e+00 1qrqA c.1.7.1 28667 1iloA 77 9.03e+00 c.47.1.1 66205 1exbA 332 9.06e+00 1qrqA c.1.7.1 28666 2tpsA 227 9.06e+00 2tpsA c.1.3.1 28591 1im4A 221 9.16e+00 unknown_sccs 62581 1r4aA 165 9.44e+00 c.37.1.8 -7089 1h75A 81 9.50e+00 1h75A c.47.1.1 60716 1m4jA 142 9.60e+00 d.109.1.2 78602 1f89A 291 9.64e+00 d.160.1.1 64988 1ovaA 386 9.81e+00 1ovaA e.1.1.1 42619 1fx2A 235 9.83e+00 1fx2A d.58.29.1 39430 1qc9A 276 9.89e+00 1ckqA c.52.1.1 33235 1mumA 295 1.01e+01 c.1.12.7 85108 1cnv 299 1.02e+01 1cnv c.1.8.5 28989 1cne 270 1.03e+01 1ndh b.43.4.2 25661 c.25.1.1 31551 1a8l 226 1.04e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1g7eA 122 1.06e+01 1g7eA c.47.1.7 33055 1jb9A 316 1.06e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1gqoH 143 1.07e+01 c.23.13.1 76302 1daaA 282 1.10e+01 1daaA e.17.1.1 43270 1jalA 363 1.10e+01 c.37.1.8 84138 d.15.10.2 84139 1s48A 609 1.10e+01 e.8.1.4 -11955 2dabA 282 1.10e+01 1daaA e.17.1.1 43274 1eriA 276 1.11e+01 1ckqA c.52.1.1 33231 1us5A 314 1.11e+01 c.94.1.1 -8686 1jtdB 273 1.11e+01 b.69.5.2 67265 1ne6A 283 1.12e+01 b.82.3.2 -4918 b.82.3.2 -4919 1uhgA 385 1.13e+01 e.1.1.1 88491 1hn0A 1021 1.13e+01 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 1b6rA 355 1.14e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1awe 130 1.17e+01 1awe b.55.1.1 26968 1g6hA 257 1.17e+01 1gajA c.37.1.12 60318 1sviA 195 1.17e+01 1hmcA 148 1.20e+01 1hmcB a.26.1.2 16867 1iyxA 432 1.20e+01 c.1.11.1 83815 d.54.1.1 83816 1sb8A 352 1.23e+01 1qk3A 233 1.25e+01 1qk3A c.61.1.1 34031 1jdpA 441 1.25e+01 c.93.1.1 62906 1sxrA 183 1.26e+01 3daaA 277 1.26e+01 1daaA e.17.1.1 43272 1ipd 345 1.29e+01 1cnzA c.77.1.1 35038 1idm 343 1.30e+01 1cnzA c.77.1.1 35035 1pms 136 1.33e+01 1awe b.55.1.1 26966 1hph 37 1.38e+01 1hph j.15.1.1 46159 1ffkI 194 1.40e+01 1ffkI d.12.1.2 37494 1co4A 42 1.41e+01 1co4A g.47.1.1 45347 1nycA 111 1.44e+01 unknown_sccs -4522 1r5jA 337 1.48e+01 unknown_sccs -8471 3grx 82 1.50e+01 1aba c.47.1.1 32769 1hizA 379 1.50e+01 c.1.8.3 65841 1rch 155 1.51e+01 2rn2 c.55.3.1 33570 1qdlA 422 1.53e+01 1qdlA d.161.1.1 42088 1edg 380 1.55e+01 1edg c.1.8.3 28807 1fnc 314 1.61e+01 1fnc b.43.4.2 25627 c.25.1.1 31517 1bu8A 452 1.62e+01 1gpl b.12.1.2 23647 c.69.1.19 34795 1gqoX 143 1.63e+01 c.23.13.1 76317 1ja1A 622 1.66e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1f61A 429 1.69e+01 1dquA c.1.12.7 29319 1rgs 288 1.70e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1rjdA 334 1.70e+01 unknown_sccs -8079 1erv 105 1.71e+01 1erv c.47.1.1 32743 1fgyA 127 1.71e+01 1faoA b.55.1.1 26976 1gcb 454 1.72e+01 3gcb d.3.1.1 37034 1j79A 347 1.74e+01 1j79A c.1.9.4 62675 1o0wA 252 1.79e+01 a.149.1.1 80751 d.50.1.1 80752 1h7eA 245 1.82e+01 c.68.1.13 60717 1whsA 255 1.83e+01 1ivyA c.69.1.5 34649 1rf6A 427 1.85e+01 d.68.2.2 -10314 1mvoA 136 1.87e+01 c.23.1.1 79513 1qlpA 394 1.87e+01 1ovaA e.1.1.1 42628 1fx4A 231 1.87e+01 1fx2A d.58.29.1 39431 1f2dA 341 1.88e+01 1f2dA c.79.1.1 35298 1s0uA 408 1.93e+01 b.43.3.1 -4053 b.44.1.1 -4061 c.37.1.8 -7096 1bwx 39 1.93e+01 1bwx j.15.1.1 46155 1jn5A 140 1.94e+01 d.17.4.2 66921 1jqeA 292 1.95e+01 c.66.1.19 71789 1ek4A 418 1.95e+01 1dd8A c.95.1.1 59436 c.95.1.1 59437 1gqoF 143 1.98e+01 c.23.13.1 76300 1oeqA 418 1.99e+01 1gqoR 143 1.99e+01 c.23.13.1 76312 1p68A 102 2.00e+01 k.8.1.1 -13460 2scuB 388 2.02e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1n57A 291 2.03e+01 c.23.16.2 85328 3lynA 136 2.04e+01 1lis a.19.1.1 16413 1fnd 314 2.05e+01 1fnc b.43.4.2 25626 c.25.1.1 31516 3gcb 470 2.06e+01 3gcb d.3.1.1 37032 1fv5A 36 2.06e+01 1fv5A g.37.1.2 45075 1s1hM 132 2.07e+01 1toaA 313 2.07e+01 1toaA c.92.2.2 35598 1b6sA 355 2.13e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1orvA 728 2.15e+01 b.70.3.1 87354 c.69.1.24 87355 1nrfA 262 2.16e+01 e.3.1.1 -11780 1a6r 471 2.17e+01 3gcb d.3.1.1 37033 1fn9A 365 2.19e+01 1fn9A d.196.1.1 59894 1hk9A 74 2.24e+01 b.38.1.2 83541 1jvwA 167 2.26e+01 d.26.1.1 71907 1dr8B 344 2.29e+01 1cnzA c.77.1.1 35052 1hurA 180 2.30e+01 1hurA c.37.1.8 32052 1thfD 253 2.30e+01 1thfD c.1.2.1 28535 1gqoY 143 2.34e+01 c.23.13.1 76318 1vapA 123 2.36e+01 1poa a.133.1.2 19548 1imdA 277 2.38e+01 1imbA e.7.1.1 42968 1dd8A 406 2.42e+01 1dd8A c.95.1.1 35932 c.95.1.1 35933 1gqoK 143 2.43e+01 c.23.13.1 76305 1ovnA 248 2.46e+01 a.71.1.1 -1096 c.47.1.7 -7477 1fc6A 388 2.53e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1kkoA 413 2.54e+01 c.1.11.2 68675 d.54.1.1 68676 1gskA 513 2.55e+01 b.6.1.3 83314 b.6.1.3 83315 b.6.1.3 83316 1dd9A 338 2.55e+01 1dd9A e.13.1.1 43254 1clxA 347 2.57e+01 1taxA c.1.8.3 28899 1f21A 155 2.58e+01 2rn2 c.55.3.1 33550 1qgoA 264 2.59e+01 1qgoA c.92.1.2 35596 1bcsA 263 2.61e+01 1ivyA c.69.1.5 34647 1gqoB 143 2.61e+01 c.23.13.1 76296 1kx9A 112 2.62e+01 unknown_sccs 77602 1ajsA 412 2.63e+01 1ajsA c.67.1.1 34276 1xxaA 78 2.65e+01 1xxaA d.74.2.1 39700 1whtA 256 2.66e+01 1ivyA c.69.1.5 34646 1ky3A 182 2.69e+01 c.37.1.8 73193 1thg 544 2.74e+01 1thg c.69.1.17 34763 1imbA 277 2.74e+01 1imbA e.7.1.1 42957 2hhmA 276 2.75e+01 1imbA e.7.1.1 42955 9apiA 347 2.76e+01 1ovaA e.1.1.1 42630 1mo0A 275 2.84e+01 c.1.1.1 79329 1gqoN 143 2.84e+01 c.23.13.1 76308 1k0fA 277 2.87e+01 c.92.2.2 71974 1gqoP 143 2.90e+01 c.23.13.1 76310 1uqrA 154 2.91e+01 c.23.13.1 -6455 1gqoI 143 2.91e+01 c.23.13.1 76303 1sep 261 2.91e+01 1oaa c.2.1.2 29830 1gqoO 143 2.92e+01 c.23.13.1 76309 1f8mA 429 2.98e+01 1dquA c.1.12.7 29315 1mai 131 2.99e+01 1mai b.55.1.1 26951 2scuA 288 3.03e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1eqnA 321 3.06e+01 1dd9A e.13.1.1 43256 1lwdA 413 3.07e+01 c.77.1.1 78265 1k0nA 241 3.07e+01 a.45.1.1 67953 c.47.1.5 67954 1jwiB 125 3.12e+01 d.169.1.1 67384 1qb0A 211 3.17e+01 1c25 c.46.1.1 32699 1ntr 124 3.18e+01 1dbwA c.23.1.1 31092 1amoA 615 3.22e+01 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1mxa 383 3.23e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1iyeA 309 3.24e+01 e.17.1.1 83786 1oaa 259 3.25e+01 1oaa c.2.1.2 29829 1ogiA 303 3.28e+01 b.43.4.2 -4042 c.25.1.1 -6587 1c25 161 3.31e+01 1c25 c.46.1.1 32698 1xxcA 78 3.31e+01 1xxaA d.74.2.1 39712 1j8fA 323 3.32e+01 1j8fA c.31.1.5 62738 1go3E 187 3.40e+01 b.40.4.5 83054 d.230.1.1 83055 1vhvA 268 3.40e+01 c.90.1.1 -8619 1mc3A 296 3.41e+01 c.68.1.6 78943 3vub 101 3.43e+01 3vub b.34.6.1 24613 1m2oA 768 3.44e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1bymA 97 3.44e+01 1bi0 b.34.1.2 24458 1fsz 372 3.47e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1uouA 474 3.49e+01 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1ns5A 155 3.51e+01 c.116.1.3 80705 2ay1A 394 3.51e+01 1ajsA c.67.1.1 34357 1ec7A 446 3.55e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1fvyA 31 3.59e+01 1fvyA j.15.1.1 46157 1kk9A 221 3.64e+01 d.115.1.1 77432 1go2A 304 3.77e+01 b.43.4.2 76243 c.25.1.1 76244 1dun 134 3.78e+01 1dun b.85.4.1 28371 1b2rA 304 3.78e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1n8vA 112 3.82e+01 unknown_sccs 85457 1pb1A 416 3.83e+01 c.77.1.1 88014 1kk1A 410 3.84e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1jfrA 262 3.86e+01 1jfrA c.69.1.16 34724 1gqoT 143 3.87e+01 c.23.13.1 76314 1mek 120 3.87e+01 1erv c.47.1.2 32775 1xbrA 184 3.92e+01 1xbrA b.2.5.4 22458 1ur1A 378 3.97e+01 c.1.8.3 -5311 1xyzA 347 3.98e+01 1taxA c.1.8.3 28804 2trxA 108 3.98e+01 1thx c.47.1.1 32719