# 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 1dnlA 199 1.06e-09 1ci0A b.45.1.1 25753 1g79A 218 1.72e-09 1ci0A b.45.1.1 25752 1nrgA 261 3.46e-06 b.45.1.1 80694 1axj 122 2.64e-05 1axj b.45.1.1 25749 1flmA 122 3.27e-05 1axj b.45.1.1 25747 1ci0A 228 1.94e-02 1ci0A b.45.1.1 25750 1ukkA 142 1.67e-01 d.227.1.1 -11206 1ko3A 230 4.27e-01 d.157.1.1 -11454 1gal 583 9.49e-01 1gpeA c.3.1.2 30386 d.16.1.1 37950 1t5yA 190 9.53e-01 1cf3A 583 9.61e-01 1gpeA c.3.1.2 30385 d.16.1.1 37949 1tin 69 1.16e+00 2sniI d.40.1.1 38580 1lq9A 112 1.17e+00 d.58.4.3 78129 1a26 361 1.28e+00 1a26 a.41.1.1 17412 d.166.1.2 42274 1nftA 329 1.48e+00 1nnt c.94.1.2 35881 1n9lA 109 1.61e+00 d.110.3.6 85468 1orrA 347 1.62e+00 c.2.1.2 -5776 1knqA 175 1.64e+00 c.37.1.17 72786 1lldA 319 1.82e+00 3ldh c.2.1.5 30177 d.162.1.1 42144 1ojrA 274 1.88e+00 c.74.1.1 -8441 1ea0A 1479 2.12e+00 b.80.4.1 64854 c.1.4.1 64855 d.153.1.1 64856 1tfaA 329 2.19e+00 1nnt c.94.1.2 35880 1jenA 267 2.30e+00 1jenA 1r6lA 239 2.45e+00 d.14.1.4 -9057 d.101.1.1 -10747 1ejhA 190 2.49e+00 1ejhA d.86.1.1 40147 1d8hA 311 2.65e+00 1d8iA d.63.1.1 39544 1efyA 350 2.72e+00 1a26 a.41.1.1 17413 d.166.1.2 42275 1f1xA 322 2.83e+00 d.32.1.3 83208 d.32.1.3 83209 1i52A 236 2.90e+00 1i52A c.68.1.13 61767 1g5tA 196 2.90e+00 1g5rA c.37.1.11 32366 1v4xA 144 3.02e+00 1gt7A 274 3.04e+00 c.74.1.1 70398 1iejA 332 3.34e+00 1nnt c.94.1.2 62328 1tbaB 180 3.36e+00 1ytbA d.129.1.1 41286 d.129.1.1 41287 1josA 128 3.47e+00 d.52.7.1 84191 1e8oB 106 3.87e+00 1914 d.49.1.1 38775 1bo4B 168 4.03e+00 1bo4A d.108.1.1 40799 1d8iA 311 4.20e+00 1d8iA d.63.1.1 39541 1f2tB 148 4.40e+00 1f2tB 1kvkA 395 4.45e+00 d.14.1.5 73060 d.58.26.3 73061 1qg3A 195 4.73e+00 1qg3A b.1.2.1 21993 b.1.2.1 21994 1g5rA 196 5.01e+00 1g5rA c.37.1.11 32367 1nr4A 71 5.07e+00 d.9.1.1 -8957 1fthA 122 5.17e+00 d.150.1.2 60028 1nd4A 264 5.26e+00 d.144.1.6 -11381 1bo4A 168 5.30e+00 1bo4A d.108.1.1 40798 1cg5A 141 5.53e+00 1abwA a.1.1.2 15406 1nnt 328 5.63e+00 1nnt c.94.1.2 35884 1plq 258 5.68e+00 1plq d.131.1.2 41388 d.131.1.2 41389 1v84A 253 5.71e+00 1k3sA 113 5.80e+00 d.198.1.1 68120 1cdwA 179 5.87e+00 1ytbA d.129.1.1 41212 d.129.1.1 41213 1dyr 206 5.91e+00 1aoeA c.71.1.1 34916 1gvuA 329 6.10e+00 b.50.1.2 70619 1q15A 503 6.30e+00 c.26.2.1 -6625 d.153.1.1 -11400 1pjxA 314 6.46e+00 1qnaA 200 6.51e+00 1ytbA d.129.1.1 41226 d.129.1.1 41227 1k92A 455 6.61e+00 c.26.2.1 68325 d.210.1.1 68326 5er2E 330 6.81e+00 2er7E b.50.1.2 26783 5croA 66 6.98e+00 1orc a.35.1.2 17044 1dm1A 146 7.27e+00 2fal a.1.1.2 15153 1cvrA 435 7.32e+00 1cvrA b.1.18.12 21949 c.17.1.2 31006 1e1aA 314 7.59e+00 1e1aA b.68.6.1 59155 1de4C 640 7.59e+00 1cx8B a.48.2.1 17779 c.8.4.1 30760 c.56.5.5 33848 1hymA 45 7.61e+00 1hymA d.40.1.1 38581 1ytbA 180 7.68e+00 1ytbA d.129.1.1 41276 d.129.1.1 41277 1ukgA 252 7.76e+00 b.29.1.1 -3390 1j5qA 437 8.02e+00 b.121.2.3 77084 b.121.2.3 77085 1prxA 224 8.06e+00 1prxA c.47.1.10 33076 1epnE 330 8.42e+00 2er7E b.50.1.2 26780 1i3cA 149 8.45e+00 c.23.1.1 71112 1oewA 329 8.54e+00 b.50.1.2 86924 9ldtA 332 8.74e+00 3ldh c.2.1.5 30154 d.162.1.1 42121 1b8aA 438 8.86e+00 1b8aA b.40.4.1 25244 d.104.1.1 40765 1bkcA 255 9.25e+00 1bkcA d.92.1.10 40331 1agx 331 9.89e+00 4pgaA c.88.1.1 35564 2er7E 330 9.97e+00 2er7E b.50.1.2 26779 1gpeA 587 1.03e+01 1gpeA c.3.1.2 30387 d.16.1.1 37951 1iwhB 146 1.04e+01 a.1.1.2 76883 1diwA 441 1.08e+01 1a8d b.29.1.6 24264 b.42.4.2 25609 1kuuA 202 1.09e+01 d.153.2.1 73019 1clvI 32 1.12e+01 1qfdA g.3.2.1 44075 1kr4A 125 1.13e+01 d.58.5.2 72889 1n3oA 252 1.13e+01 b.29.1.1 79967 1opd 85 1.13e+01 1ptf d.94.1.1 40560 1uocA 289 1.15e+01 unknown_sccs -7671 1j4wA 174 1.17e+01 d.51.1.1 71529 d.51.1.1 71530 1dixA 208 1.17e+01 1bk7A d.124.1.1 41122 1j71A 334 1.18e+01 1eagA b.50.1.2 62669 1jwqA 179 1.22e+01 unknown_sccs -7897 1b6rA 355 1.25e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1copD 66 1.26e+01 1orc a.35.1.2 17058 1nq7A 244 1.26e+01 a.123.1.1 -1682 1eonA 245 1.34e+01 1rvaA c.52.1.2 33238 1viaA 175 1.35e+01 c.37.1.2 -7021 1kjvB 100 1.37e+01 b.1.1.2 77423 1ri6A 343 1.38e+01 unknown_sccs -4621 1kr7A 110 1.38e+01 a.1.1.4 72890 1ns5A 155 1.39e+01 c.116.1.3 80705 1f0iA 504 1.40e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1btl 263 1.41e+01 1btl e.3.1.1 42691 1nhs 447 1.41e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1plr 258 1.43e+01 1plq d.131.1.2 41390 d.131.1.2 41391 1aw8E 91 1.46e+01 1aw8B 1fqgA 263 1.46e+01 1btl e.3.1.1 42699 1gcvB 136 1.47e+01 1cg5B a.1.1.2 15589 6ldh 330 1.47e+01 3ldh c.2.1.5 30161 d.162.1.1 42128 1k4wA 252 1.48e+01 a.123.1.1 72068 1trkA 680 1.52e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1sx5A 244 1.53e+01 c.52.1.2 -7551 1v0wA 506 1.58e+01 2fal 147 1.61e+01 2fal a.1.1.2 15150 1azo 232 1.61e+01 1azo c.52.1.14 33329 1ah2 269 1.61e+01 1gci c.41.1.1 32542 1qrrA 394 1.62e+01 1qrrA c.2.1.2 29824 1rkqA 282 1.63e+01 c.108.1.10 -6847 2prd 174 1.64e+01 2prd b.40.5.1 25435 1gppA 237 1.65e+01 b.86.1.2 76262 1hx0A 496 1.66e+01 b.71.1.1 61346 c.1.8.1 61347 1bkcE 256 1.67e+01 1bkcA d.92.1.10 40333 1nhp 447 1.67e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1orc 71 1.70e+01 1orc a.35.1.2 17054 1ermA 263 1.73e+01 1btl e.3.1.1 42690 1rvaA 244 1.75e+01 1rvaA c.52.1.2 33240 1o0xA 262 1.75e+01 d.127.1.1 80755 3ldh 330 1.78e+01 3ldh i.12.1.1 46015 1tlk 154 1.80e+01 1tlk b.1.1.4 21707 1hxmA 229 1.80e+01 1hxmA b.1.1.1 61367 b.1.1.2 61368 1ytbB 180 1.81e+01 1ytbA d.129.1.1 41278 d.129.1.1 41279 3gcb 470 1.82e+01 3gcb d.3.1.1 37032 2u1a 88 1.82e+01 2u1a d.58.7.1 39164 1q4rA 112 1.83e+01 d.58.4.4 -9943 1b6sA 355 1.83e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1ejeA 192 1.84e+01 1ejeA b.45.1.2 25757 1tl2A 236 1.88e+01 1tl2A b.67.1.1 27541 1i24A 404 1.90e+01 c.2.1.2 83663 1hl8A 449 1.90e+01 unknown_sccs -4690 unknown_sccs -5361 1led 243 1.92e+01 1led b.29.1.1 24039 1bg2 325 1.96e+01 1bg2 c.37.1.9 32189 1fhgA 154 1.96e+01 1tlk b.1.1.4 21706 1gci 269 1.99e+01 1gci c.41.1.1 32503 1n6aA 259 2.07e+01 b.76.2.1 80121 b.85.7.1 80122 1scs 237 2.09e+01 1nls b.29.1.1 23930 1kwaB 88 2.13e+01 1kwaA b.36.1.1 24773 1mrzA 293 2.13e+01 b.43.5.1 -4048 c.26.1.3 -6616 1o7tA 309 2.13e+01 c.94.1.1 86645 1myt 146 2.14e+01 1a6m a.1.1.2 15207 1fo5A 85 2.15e+01 1fo5A c.47.1.1 59922 1iujA 106 2.17e+01 unknown_sccs -9953 1skoA 143 2.18e+01 1irdB 146 2.19e+01 a.1.1.2 66287 2kinA 238 2.21e+01 1bg2 c.37.1.9 32190 1smd 496 2.22e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1aw8B 91 2.26e+01 1aw8B 1q0sA 259 2.28e+01 c.66.1.28 -8110 1k5dC 386 2.30e+01 c.10.1.2 68170 1od5A 492 2.30e+01 b.82.1.2 86832 b.82.1.2 86833 1vokA 200 2.30e+01 1ytbA d.129.1.1 41242 d.129.1.1 41243 1l8bA 190 2.31e+01 d.86.1.1 73683 1jpdX 324 2.32e+01 c.1.11.2 67014 d.54.1.1 67015 1ub4C 85 2.33e+01 b.129.1.1 88401 1i7wB 151 2.34e+01 1i7wB j.71.1.1 61910 1n25A 368 2.34e+01 c.37.1.20 85264 1nu0A 138 2.36e+01 unknown_sccs -7658 1q52A 314 2.36e+01 c.14.1.3 -6246 1aoeA 192 2.37e+01 1aoeA c.71.1.1 34923 1poh 85 2.39e+01 1ptf d.94.1.1 40553 4gatA 66 2.45e+01 1gatA g.39.1.1 45100 1hl9A 449 2.48e+01 unknown_sccs -4694 unknown_sccs -5365 1hbkA 94 2.49e+01 1aca a.11.1.1 60887 1joa 447 2.49e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1udsA 255 2.51e+01 d.14.1.4 -9055 d.101.1.1 -10745 1df3A 162 2.52e+01 1mup b.60.1.1 27134 1gpuA 680 2.52e+01 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1oa4A 222 2.53e+01 b.29.1.11 86731 1m40A 263 2.55e+01 e.3.1.1 74437 1uw4A 91 2.62e+01 unknown_sccs -10038 1mba 147 2.62e+01 2fal a.1.1.2 15149 1pqhA 143 2.63e+01 b.52.2.1 -4318 1kwsA 261 2.67e+01 c.68.1.7 73083 1hg8A 349 2.67e+01 b.80.1.3 65830 1l6pA 125 2.69e+01 b.1.17.1 73626 1hzoA 271 2.72e+01 e.3.1.1 71092 1qntA 176 2.73e+01 1sfe a.4.2.1 16074 c.55.7.1 33749 1gcb 454 2.74e+01 3gcb d.3.1.1 37034 2rveA 244 2.77e+01 1rvaA c.52.1.2 33283 1r8hA 87 2.78e+01 d.58.8.1 -10041 1fggA 261 2.84e+01 1fggA c.68.1.7 34576 1tkaA 678 2.88e+01 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 1bdb 277 2.92e+01 1bdb c.2.1.2 29874 1iyaA 187 2.93e+01 1aky 221 2.95e+01 1zin c.37.1.1 31896 g.41.2.1 45197 1nls 237 3.03e+01 1nls b.29.1.1 23928 1gaxA 862 3.04e+01 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 1d0hA 469 3.05e+01 1a8d b.29.1.6 24265 b.42.4.2 25610 1efcA 393 3.06e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1a8d 452 3.06e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 1cdzA 96 3.09e+01 1cdzA c.15.1.1 30925 1qa7B 217 3.11e+01 1havA b.47.1.4 26426 1d6mA 653 3.14e+01 1d6mA e.10.1.1 43248 1gca 309 3.14e+01 1gca c.93.1.1 35659 1qp2A 70 3.22e+01 1pse b.34.4.2 24596 1spgB 147 3.23e+01 1cg5B a.1.1.2 15588 1qfxA 460 3.23e+01 1qfxA c.60.1.2 33994 1ufyA 122 3.26e+01 d.79.1.2 88489 1pvmA 184 3.27e+01 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1o5iA 249 3.40e+01 c.2.1.2 -5833 1kriA 186 3.41e+01 b.29.1.14 72897 1a8y 367 3.43e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1jljA 189 3.44e+01 c.57.1.1 63169 1yrgB 385 3.45e+01 1yrgA c.10.1.2 30855 1m3yA 413 3.45e+01 b.121.2.3 78579 b.121.2.3 78580 1s7jA 262 3.46e+01 d.21.1.2 -9424 1mpyA 307 3.47e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1ewkA 490 3.47e+01 1ewkA c.93.1.1 35712 1bywA 110 3.47e+01 1bywA d.110.3.6 40912 1o4uA 285 3.48e+01 c.1.17.1 86624 d.41.2.1 86625 1mt6A 280 3.50e+01 b.76.2.1 79446 b.85.7.1 79447 1ej1A 190 3.52e+01 1ejhA d.86.1.1 40144 1yrgA 385 3.52e+01 1yrgA c.10.1.2 30854 1obpA 159 3.52e+01 1obpA b.60.1.1 27092 1s4zC 30 3.55e+01 1vkxA 273 3.58e+01 1a3qA b.1.18.1 21941 b.2.5.3 22454 1ihcA 188 3.59e+01 1di6A c.57.1.1 62379 1fnmA 691 3.61e+01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1cx8A 639 3.66e+01 1cx8B a.48.2.1 17782 c.8.4.1 30763 c.56.5.5 33851 1cx8B 639 3.77e+01 1cx8B a.48.2.1 17783 c.8.4.1 30764 c.56.5.5 33852 1pt1A 143 3.77e+01 b.52.2.1 -4322 2gbp 309 3.78e+01 1gca c.93.1.1 35657 1pse 69 3.81e+01 1pse b.34.4.2 24595 1d2nA 272 3.82e+01 1d2nA c.37.1.20 32428 3il8 72 3.82e+01 1tvxA d.9.1.1 37356 1iqrA 420 3.84e+01 a.99.1.1 66275 c.28.1.1 66276 1iarB 207 3.85e+01 1iarB b.1.2.1 22037 b.1.2.1 22038 1q9jA 422 3.86e+01 1gnxA 479 3.86e+01 c.1.8.4 76241 1odeA 122 3.90e+01 d.79.1.2 86846 1gt91 357 3.94e+01 1ltlA 279 3.97e+01 b.40.4.11 84701