# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1c7qA 445 2.58e-03 2pgi c.80.1.2 35307 2pgi 445 3.89e-03 2pgi c.80.1.2 35308 1bouB 302 6.73e-02 1bouB c.56.6.1 33859 1gt8D 1025 7.52e-02 1onrA 316 8.81e-02 1onrA c.1.10.1 29169 1b8gA 429 9.13e-02 1b8gA c.67.1.4 34499 1h7xA 1025 9.54e-02 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1srvA 145 9.57e-02 1derA c.8.5.1 30817 1h7xB 1025 1.13e-01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1h7wA 1025 1.13e-01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1h7wB 1025 1.18e-01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1qopA 268 1.19e-01 2tysA c.1.2.4 28570 1h7xC 1025 1.22e-01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1gt8B 1025 1.27e-01 1gt8C 1025 1.31e-01 1gt8A 1025 1.38e-01 1gthC 1025 1.43e-01 1gthA 1025 1.45e-01 1h7wD 1025 1.46e-01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1h7xD 1025 2.01e-01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 2wsyA 268 2.27e-01 2tysA c.1.2.4 28588 1gteA 1025 2.45e-01 1gthB 1025 2.67e-01 1bksA 268 2.89e-01 2tysA c.1.2.4 28585 1bif 469 3.13e-01 1bif c.37.1.7 31961 c.60.1.4 34003 1eudA 311 3.57e-01 2scuA c.2.1.8 30312 c.23.4.1 31140 2tysA 268 4.17e-01 2tysA c.1.2.4 28572 1c7nA 399 4.78e-01 1d2fA c.67.1.3 34413 2cevA 299 4.94e-01 1d3vA c.42.1.1 32576 9ldtA 332 5.76e-01 3ldh c.2.1.5 30154 d.162.1.1 42121 1f5sA 211 5.98e-01 1f5sA c.108.1.4 59656 1j97A 211 5.98e-01 1f5sA c.108.1.4 62753 1kzhA 555 6.01e-01 6ldh 330 6.03e-01 3ldh c.2.1.5 30161 d.162.1.1 42128 1gteD 1025 6.15e-01 1gthD 1025 6.20e-01 1jeoA 180 7.37e-01 c.80.1.3 66611 1l7mA 211 1.07e+00 1bfd 528 1.28e+00 1bfd c.31.1.3 31745 c.36.1.1 31801 c.36.1.1 31802 1kid 203 1.38e+00 1derA c.8.5.1 30771 1aa8A 347 1.63e+00 1an9A c.4.1.2 30619 d.16.1.3 37906 1mucA 373 1.80e+00 1mucA c.1.11.2 29236 d.54.1.1 38880 1ec7A 446 1.80e+00 1bqg c.1.11.2 29218 d.54.1.1 38862 1jgtA 513 1.84e+00 c.26.2.1 66684 d.153.1.1 66685 1l2qA 458 1.84e+00 1l2rA 458 1.90e+00 1pprM 312 1.90e+00 1pprM a.131.1.1 19502 a.131.1.1 19503 1ceqA 316 2.03e+00 1ceqA c.2.1.5 30163 d.162.1.1 42130 1jpmA 366 2.10e+00 c.1.11.2 67031 d.54.1.1 67032 1an9A 340 2.13e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1ewkA 490 2.24e+00 1ewkA c.93.1.1 35712 1chuA 540 2.25e+00 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1pdo 135 2.30e+00 1pdo c.54.1.1 33376 1qmgA 524 2.57e+00 1qmgA a.100.1.2 18785 c.2.1.6 30182 1inlA 296 2.59e+00 c.66.1.17 66220 1id1A 153 2.62e+00 1id1A c.2.1.9 62286 1jdfA 447 2.73e+00 c.1.11.2 62897 d.54.1.1 62898 4gr1 478 2.90e+00 3grs c.3.1.5 30461 c.3.1.5 30462 d.87.1.1 40162 3grs 478 2.97e+00 3grs c.3.1.5 30441 c.3.1.5 30442 d.87.1.1 40152 1lgyA 269 3.19e+00 3tgl c.69.1.17 34758 1fohA 664 3.48e+00 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1kaeA 434 3.76e+00 3vtk 343 3.95e+00 1qhiA c.37.1.1 31884 1gpjA 404 4.02e+00 a.151.1.1 65451 c.2.1.10 65452 d.58.39.1 65453 1ej2A 181 4.05e+00 1f9aA c.26.1.3 59414 1yveI 524 4.13e+00 1qmgA a.100.1.2 18789 c.2.1.6 30186 1a27 289 4.20e+00 1fds c.2.1.2 29839 1ex2A 189 4.28e+00 1ex2A c.51.4.2 33225 2scuA 288 4.54e+00 2scuA c.2.1.8 30303 c.23.4.1 31131 1ecpA 238 4.56e+00 1ecpA c.56.2.1 33775 1hwyA 501 4.69e+00 1hwyA c.2.1.7 30262 c.58.1.1 33910 1yveJ 524 4.72e+00 1qmgA a.100.1.2 18790 c.2.1.6 30187 1bqg 451 4.90e+00 1bqg c.1.11.2 29217 d.54.1.1 38861 1nhs 447 5.09e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1qhhA 167 5.24e+00 1pjr c.37.1.13 32393 1fdt 327 5.37e+00 1fds c.2.1.2 29841 1k9sA 237 5.42e+00 c.56.2.1 68359 2cmd 312 5.45e+00 2cmd c.2.1.5 30135 d.162.1.1 42102 1qq7A 253 5.52e+00 1qq5A c.108.1.1 43329 1qq5A 253 5.60e+00 1qq5A c.108.1.1 43327 1jq3A 296 5.89e+00 c.66.1.17 67079 1chmA 401 5.97e+00 1chmA c.55.2.1 33545 d.127.1.1 41142 1kqpA 271 6.11e+00 1dcfA 136 6.11e+00 1dcfA c.23.1.2 31124 2nsyA 271 6.12e+00 2nsyA c.26.2.1 31612 1nsyA 271 6.12e+00 2nsyA c.26.2.1 31614 1aq6A 253 6.16e+00 1qq5A c.108.1.1 43331 1jjyA 636 6.53e+00 1jjyA e.26.1.2 63141 1xxbA 78 6.54e+00 1xxaA d.74.2.1 39706 1fxkC 133 6.55e+00 1fxkC a.2.5.1 15702 1hg3A 225 6.64e+00 1hg3A c.1.1.1 61025 1ek0A 170 6.66e+00 1ctqA c.37.1.8 32076 2nacA 393 6.76e+00 2nadA c.2.1.4 30088 c.23.12.1 31348 1ih8A 271 6.78e+00 2nsyA c.26.2.1 62377 1hkcA 917 6.88e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1fbaA 361 6.93e+00 1fbaA c.1.10.1 29120 1eulA 994 6.97e+00 1eulA f.2.1.10 43726 1fds 327 7.04e+00 1fds c.2.1.2 29838 1ofgA 381 7.07e+00 1ofgA c.2.1.3 30064 d.81.1.5 39979 1l3lA 234 7.24e+00 1a6f 119 7.33e+00 1a6f d.14.1.2 37564 2liv 344 7.37e+00 2liv c.93.1.1 35708 1cliA 345 7.44e+00 1cliA d.79.4.1 39816 d.139.1.1 41459 1k89 449 7.98e+00 1k89 c.2.1.7 30218 c.58.1.1 33866 1fs5A 266 8.00e+00 c.35.1.1 65044 1fsfA 266 8.03e+00 c.35.1.1 65047 1deaA 266 8.26e+00 1deaA c.35.1.1 31760 1nhp 447 8.32e+00 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1lk5A 229 8.60e+00 1asyA 490 8.63e+00 1b8aA b.40.4.1 25242 d.104.1.1 40763 1joa 447 8.64e+00 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1ig0A 319 9.06e+00 1ig0A b.82.6.1 62354 c.100.1.1 62355 1dguA 183 9.17e+00 1dguA a.39.1.5 17333 1jztA 246 9.39e+00 c.104.1.1 63319 1d1gA 168 9.79e+00 1d1gA c.71.1.1 34889 1je0A 236 9.81e+00 c.56.2.1 66581 1tplA 426 9.99e+00 1ax4A c.67.1.2 34387 1ylvA 342 1.01e+01 1b4kA c.1.10.3 29180 1guzA 310 1.02e+01 c.2.1.5 65586 d.162.1.1 65587 1e5dA 402 1.03e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 1g97A 459 1.03e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1i50K 120 1.04e+01 d.74.3.2 61765 1xxcA 78 1.06e+01 1xxaA d.74.2.1 39712 1hrdA 449 1.08e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1h7nA 342 1.09e+01 1b4kA c.1.10.3 60726 1aye 401 1.10e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1i58A 189 1.11e+01 1b3qA d.122.1.3 61773 1bgvA 449 1.12e+01 1k89 c.2.1.7 30217 c.58.1.1 33865 1kl7A 514 1.14e+01 1evyA 366 1.15e+01 1evyA a.100.1.6 18811 c.2.1.6 30215 1hskA 326 1.18e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1ig3A 263 1.20e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1g9mG 321 1.27e+01 1gc1G d.172.1.1 42492 1yasA 257 1.35e+01 1qj4A c.69.1.20 34801 1k75A 434 1.37e+01 c.82.1.2 68253 1e19A 314 1.38e+01 1b7bA c.73.1.1 34967 1kyqA 274 1.38e+01 2nadA 393 1.38e+01 2nadA c.2.1.4 30090 c.23.12.1 31350 1dgkN 917 1.44e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1hwxA 501 1.45e+01 1hwyA c.2.1.7 30250 c.58.1.1 33898 1mgtA 174 1.46e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1hkbA 917 1.47e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1qpzA 340 1.51e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1srrA 124 1.51e+01 1dz3A c.23.1.1 31110 4ts1A 319 1.55e+01 2ts1 c.26.1.1 31565 1qj4A 257 1.56e+01 1qj4A c.69.1.20 34796 1bykA 255 1.56e+01 1bykA c.93.1.1 35706 1czaN 917 1.57e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1fnnA 389 1.58e+01 1fnnA a.4.5.11 16129 c.37.1.13 32426 1af7 274 1.58e+01 1af7 a.58.1.1 17928 c.66.1.8 34203 1i60A 278 1.59e+01 1fd9A 213 1.63e+01 1fd9A d.26.1.1 59771 1jeyB 565 1.63e+01 1jeqB e.31.1.2 62925 1fsz 372 1.67e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1km4A 247 1.70e+01 1fj2A 232 1.70e+01 1auoA c.69.1.14 34720 1jmxA 494 1.74e+01 a.3.1.7 66901 a.3.1.7 66902 b.1.1.6 66903 b.1.1.6 66904 b.61.4.1 66905 1dd3A 128 1.75e+01 1dd3C a.108.1.1 19031 d.45.1.1 38760 1nulA 152 1.76e+01 1nulA c.61.1.1 34011 1akr 147 1.78e+01 1rcf c.23.5.1 31152 1d3vA 323 1.80e+01 1d3vA c.42.1.1 32559 1bc5A 269 1.83e+01 1af7 a.58.1.1 17929 c.66.1.8 34204 1huxA 270 1.84e+01 1huxA c.55.1.5 61278 1qhaA 917 1.85e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 2chsA 127 1.90e+01 2chsA d.79.1.2 39764 2act 220 1.90e+01 1cs8A d.3.1.1 37002 1a4uA 254 1.94e+01 1b16A c.2.1.2 29878 1ypcI 64 1.97e+01 2sniI d.40.1.1 38570 1agx 331 2.00e+01 4pgaA c.88.1.1 35564 1djnA 729 2.02e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1mroB 442 2.03e+01 1mroB a.89.1.1 18531 d.58.31.2 39449 1aszB 490 2.05e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1cjbA 231 2.05e+01 1qk3A c.61.1.1 34079 1fp6A 289 2.06e+01 1cp2A c.37.1.10 32243 1h65A 270 2.06e+01 c.37.1.8 65640 1a3c 181 2.09e+01 1a3c c.61.1.1 34095 2tmdA 729 2.12e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1h6dA 433 2.12e+01 c.2.1.3 65656 d.81.1.5 65657 1k3fA 253 2.13e+01 c.56.2.1 68105 1b5tA 275 2.17e+01 1b5tA c.1.23.1 29676 1pytA 94 2.18e+01 1pytA d.58.3.1 39064 1hyuA 521 2.22e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1gm6A 175 2.22e+01 1h8eD 482 2.25e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1dptA 117 2.27e+01 1dptA d.80.1.3 39862 1kq4A 232 2.30e+01 d.207.1.1 68791 1gesA 450 2.31e+01 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1pjcA 361 2.33e+01 1sayA c.2.1.4 30101 c.23.12.2 31361 6pfkA 319 2.36e+01 3pfk c.89.1.1 35583 1aw5 326 2.38e+01 1b4kA c.1.10.3 29181 1sayA 361 2.38e+01 1sayA c.2.1.4 30102 c.23.12.2 31362 1bzyA 217 2.38e+01 1qk3A c.61.1.1 34071 1jk7A 323 2.38e+01 1auiA d.159.1.3 63144 1c8uA 285 2.41e+01 1c8uA d.38.1.3 38547 d.38.1.3 38548 1lldA 319 2.42e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 1adjA 421 2.43e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1rlaA 323 2.44e+01 1d3vA c.42.1.1 32561 1g6q2 328 2.46e+01 1g6q2 1dixA 208 2.48e+01 1bk7A d.124.1.1 41122 1innA 166 2.49e+01 1j98A d.185.1.2 62608 1a8q 274 2.52e+01 1brt c.69.1.12 34702 1dbfA 127 2.52e+01 2chsA d.79.1.2 39761 1fpxA 352 2.55e+01 1fpxA a.4.5.29 59950 c.66.1.12 59951 1fg7A 356 2.60e+01 1gewA c.67.1.1 59819 1c3pA 375 2.61e+01 1c3pA c.42.1.2 32606 1que 303 2.61e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1edg 380 2.70e+01 1edg c.1.8.3 28807 1wab 232 2.70e+01 1wab c.23.10.3 31341 1jeqB 565 2.71e+01 1jeqB e.31.1.2 62922 1brlB 324 2.71e+01 1lucA c.1.16.1 29554 1i7qB 193 2.72e+01 1qdlB c.23.16.1 61902 1ldg 316 2.77e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1wetA 340 2.78e+01 1qpzA a.35.1.5 17093 c.93.1.1 35670 1bd3A 243 2.84e+01 1bd3A c.61.1.1 34098 1pjbA 361 2.87e+01 1sayA c.2.1.4 30103 c.23.12.2 31363 1d5yA 292 2.96e+01 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1d9tA 289 2.98e+01 1deaA c.35.1.1 31767 1lx7A 253 2.98e+01 1ihvA 52 3.02e+01 1ihvA b.34.7.1 24629 8abp 306 3.02e+01 8abp c.93.1.1 35647 1f3lA 321 3.04e+01 1g6q2 c.66.1.6 59630 1jsrA 327 3.05e+01 c.88.1.1 67237 1rgs 288 3.08e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1b87A 181 3.11e+01 1b87A d.108.1.1 40797 1klpA 115 3.15e+01 1hrkA 359 3.15e+01 1hrkA c.92.1.1 61228 1qk4A 233 3.17e+01 1qk3A c.61.1.1 34037 1ecfB 504 3.18e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1ct9A 553 3.18e+01 1ct9A c.26.2.1 31616 d.153.1.1 41834 1dhy 292 3.19e+01 1han d.32.1.3 38504 d.32.1.3 38505 1ars 396 3.19e+01 1ajsA c.67.1.1 34287 1prxA 224 3.20e+01 1prxA c.47.1.10 33076 1b3qA 379 3.22e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1lucB 324 3.25e+01 1lucA c.1.16.1 29548 1dvjC 246 3.27e+01 1dvjA c.1.2.3 28548 2lbp 346 3.30e+01 2liv c.93.1.1 35709 1ejjA 511 3.31e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1hfoA 113 3.33e+01 d.80.1.3 61006 3grx 82 3.34e+01 1aba c.47.1.1 32769 1hbnB 442 3.34e+01 1mroB a.89.1.1 60900 d.58.31.2 60901 1dpe 507 3.36e+01 1dpe c.94.1.1 35799 1kp9B 287 3.37e+01 c.66.1.18 68734 1ii2A 524 3.38e+01 c.91.1.1 66146 c.109.1.1 66147 1c8bA 371 3.38e+01 1c8bA c.56.1.2 59082 1ecfA 504 3.43e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 3adk 195 3.45e+01 1zin c.37.1.1 31885 1ca9A 192 3.45e+01 1d0aB b.8.1.1 23244 h.1.2.1 45451 1khbA 625 3.48e+01 c.91.1.1 68606 c.109.1.1 68607 1d2iA 223 3.53e+01 1d2iA c.52.1.5 33297 1dfmA 223 3.54e+01 1d2iA c.52.1.5 33295 1h4vB 421 3.54e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1dosA 358 3.55e+01 1dosA c.1.10.2 29175 1ktbA 405 3.61e+01 1b9yC 246 3.61e+01 1b9yC c.47.1.6 33052 1ktgA 138 3.63e+01 1dppA 507 3.63e+01 1dpe c.94.1.1 35800 1qo2A 241 3.63e+01 1qo2A c.1.2.1 28533 1bu5A 147 3.67e+01 5nul c.23.5.1 31155 1poxA 585 3.69e+01 1poxA c.31.1.3 31731 c.36.1.1 31793 c.36.1.1 31794 1f1eA 154 3.71e+01 a.22.1.2 64927 1iw2A 182 3.72e+01 1k2yX 463 3.75e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 c.84.1.1 68066 1go4A 205 3.78e+01 1maz 221 3.78e+01 1maz f.1.4.1 43393 1oatA 439 3.78e+01 2dkb c.67.1.4 34461 1hnnA 282 3.79e+01 c.66.1.15 65895 1h75A 81 3.79e+01 1h75A c.47.1.1 60716 1b1cA 181 3.79e+01 1amoA c.23.5.2 31212 1fjmA 330 3.80e+01 1auiA d.159.1.3 42082 1taq 832 3.81e+01 1taq a.60.7.1 18082 c.53.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 3pfk 319 3.81e+01 3pfk c.89.1.1 35581 1hr6A 475 3.84e+01 1hr6A d.185.1.1 61164 d.185.1.1 61165 1a0p 290 3.89e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 1k8kA 418 3.89e+01 c.55.1.1 68305 c.55.1.1 68306 1lf7A 182 3.89e+01 1qjwA 365 3.90e+01 1bvwA c.6.1.1 30657 1qkkA 155 3.90e+01 1dbwA c.23.1.1 31104 1l0oA 150 3.91e+01 1b16A 254 3.94e+01 1b16A c.2.1.2 29875 1dciA 275 3.96e+01 1dciA c.14.1.3 30918