# List of top-scoring protein chains for t2k-100-30-str 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 1e0tA 470 5.56e-05 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1edt 271 4.38e-04 2ebn c.1.8.5 28993 1ff9A 450 1.38e-03 1ff9A c.2.1.3 30039 d.81.1.2 39954 1uroA 367 1.39e-03 1uroA c.1.22.1 29675 2ebn 289 1.63e-03 2ebn c.1.8.5 28990 1db3A 372 2.92e-03 1db3A c.2.1.2 29813 1f6dA 376 3.51e-03 1f6dA c.87.1.3 35467 6mhtA 327 6.45e-03 6mhtA c.66.1.10 34226 1eqjA 511 7.47e-03 1ejjA c.105.1.1 59495 c.76.1.3 59496 1pfkA 320 7.52e-03 3pfk c.89.1.1 35575 1gjwA 637 8.03e-03 b.71.1.1 60582 c.1.8.1 60583 1gjuA 637 8.07e-03 b.71.1.1 60580 c.1.8.1 60581 1wetA 340 8.80e-03 1qpzA a.35.1.5 17093 c.93.1.1 35670 1ejjA 511 1.05e-02 1ejjA c.105.1.1 59422 c.76.1.3 59423 2pfkA 320 1.07e-02 3pfk c.89.1.1 35577 1qpzA 340 1.09e-02 1qpzA a.35.1.5 17097 c.93.1.1 35673 1hmy 327 1.40e-02 6mhtA c.66.1.10 34229 1jl2A 156 1.48e-02 c.55.3.1 66822 3mhtA 327 1.63e-02 6mhtA c.66.1.10 34234 1hp1A 516 1.75e-02 1ush 550 2.08e-02 1ush d.114.1.1 40923 d.159.1.2 42079 1lvk 762 2.19e-02 1lvk b.34.3.1 24576 c.37.1.9 32173 1qfcA 306 3.59e-02 1uteA d.159.1.1 42077 1ad1A 266 3.62e-02 1aj2 c.1.21.1 29668 1d0yA 761 3.66e-02 1lvk b.34.3.1 24581 c.37.1.9 32178 1byb 495 3.72e-02 1byb c.1.8.2 28790 1j8mF 297 3.76e-02 1ng1 a.24.13.1 62742 c.37.1.10 62743 1korA 400 4.00e-02 1fecA 490 4.06e-02 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1gpjA 404 4.11e-02 a.151.1.1 65451 c.2.1.10 65452 d.58.39.1 65453 1vid 221 4.44e-02 1vid c.66.1.1 34178 1bif 469 4.50e-02 1bif c.37.1.7 31961 c.60.1.4 34003 1lvl 458 4.66e-02 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1kewA 361 4.74e-02 c.2.1.2 68544 1dosA 358 5.28e-02 1dosA c.1.10.2 29175 1f75A 249 5.44e-02 1f75A c.101.1.1 59662 1cydA 244 5.51e-02 1cydA c.2.1.2 29825 1qvbA 481 5.53e-02 1qvbA c.1.8.4 28983 1mnd 762 5.83e-02 1lvk b.34.3.1 24591 c.37.1.9 32188 1eudB 396 5.84e-02 2scuB c.23.4.1 31150 d.142.1.4 41571 1iqrA 420 6.14e-02 a.99.1.1 66275 c.28.1.1 66276 2reb 352 6.46e-02 2reb c.37.1.11 32282 d.48.1.1 38767 1hdoA 206 6.72e-02 1he2A c.2.1.2 60965 1bglA 1023 6.89e-02 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.1.1 24358 c.1.8.3 28857 6pfkA 319 7.07e-02 3pfk c.89.1.1 35583 1aogA 485 7.23e-02 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1ewkA 490 7.62e-02 1ewkA c.93.1.1 35712 1jz8A 1023 7.85e-02 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.1.1 67833 c.1.8.3 67834 1i3kA 348 7.96e-02 1xel c.2.1.2 61595 1iirA 415 8.01e-02 1iirA c.87.1.5 62453 1dp0A 1023 8.06e-02 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.1.1 24346 c.1.8.3 28845 1jpnA 296 8.42e-02 a.24.13.1 67039 c.37.1.10 67040 1cr5A 189 8.89e-02 1cr5A b.52.2.3 26931 d.31.1.1 38465 1dbqA 289 9.01e-02 1qpzA c.93.1.1 35666 1qh8A 478 9.13e-02 1qguA c.92.2.3 35633 4pfk 319 9.15e-02 3pfk c.89.1.1 35582 1ir6A 424 9.44e-02 1qguA 478 9.60e-02 1qguA c.92.2.3 35625 3pfk 319 9.74e-02 3pfk c.89.1.1 35581 1he2A 206 1.06e-01 1he2A c.2.1.2 60966 1bdb 277 1.08e-01 1bdb c.2.1.2 29874 1ew2A 513 1.14e-01 1b8jA c.76.1.1 59525 1qp8A 303 1.28e-01 1qp8A c.2.1.4 30092 c.23.12.1 31352 1reqB 637 1.33e-01 1reqB c.1.19.1 29621 c.23.6.1 31248 2gbp 309 1.35e-01 1gca c.93.1.1 35657 1qhtA 775 1.38e-01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1vom 762 1.45e-01 1lvk b.34.3.1 24577 c.37.1.9 32174 1qh3A 260 1.53e-01 1qh5A d.157.1.2 42059 2rn2 155 1.62e-01 2rn2 c.55.3.1 33551 2minA 491 1.68e-01 1qguA c.92.2.3 35609 1bqcA 302 1.71e-01 1bqcA c.1.8.3 28831 1uteA 313 1.71e-01 1uteA d.159.1.1 42078 1broA 277 1.72e-01 1brt c.69.1.12 34700 1jztA 246 1.76e-01 c.104.1.1 63319 1qr6A 584 1.77e-01 1qr6A c.2.1.7 30293 c.58.1.3 33941 1f8rA 498 1.78e-01 1f8rA c.3.1.2 30410 d.16.1.5 37974 1jw9B 249 1.82e-01 c.111.1.1 67377 1gca 309 1.89e-01 1gca c.93.1.1 35659 1i9sA 210 1.90e-01 1i9sA c.45.1.1 62099 1k1eA 180 1.94e-01 c.108.1.5 67995 1ng1 294 2.12e-01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1h65A 270 2.14e-01 c.37.1.8 65640 1k3rA 268 2.15e-01 2scuB 388 2.17e-01 2scuB c.23.4.1 31141 d.142.1.4 41562 1qnf 484 2.22e-01 1qnf a.99.1.1 18777 c.28.1.1 31632 2ng1 293 2.26e-01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1brt 277 2.31e-01 1brt c.69.1.12 34699 2ts1 419 2.41e-01 2ts1 c.26.1.1 31564 1a8q 274 2.43e-01 1brt c.69.1.12 34702 1gmlA 178 2.49e-01 1d4fA 431 2.54e-01 1b3rA c.2.1.4 30110 c.23.12.3 31370 1reqD 637 2.55e-01 1reqB c.1.19.1 29623 c.23.6.1 31250 1qh5A 260 2.55e-01 1qh5A d.157.1.2 42057 1tr1A 447 2.68e-01 1e70M c.1.8.4 28957 1km4A 247 2.77e-01 1b3rA 431 2.78e-01 1b3rA c.2.1.4 30106 c.23.12.3 31366 2masA 314 2.94e-01 2masA c.70.1.1 34810 3minC 491 3.22e-01 1qguA c.92.2.3 35607 1qrrA 394 3.23e-01 1qrrA c.2.1.2 29824 7a3hA 303 3.28e-01 7a3hA c.1.8.3 28817 1a3h 300 3.28e-01 7a3hA c.1.8.3 28819 1fpzA 212 3.50e-01 1fpzA c.45.1.1 59976 1efvB 255 3.59e-01 1efvB c.29.1.1 31634 1f0kA 364 3.60e-01 1f0kA c.87.1.2 35465 1gm5A 780 3.69e-01 a.29.4.1 65298 b.40.4.9 65299 c.37.1.13 65300 c.37.1.13 65301 1b57A 358 3.79e-01 1dosA c.1.10.2 29177 4ts1A 319 3.82e-01 2ts1 c.26.1.1 31565 1kjqA 391 3.94e-01 1ez1A 392 3.94e-01 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1iq0A 592 4.13e-01 a.27.1.1 66257 c.26.1.1 66258 d.67.2.1 66259 1kbqA 273 4.22e-01 c.23.5.3 68391 1j8dA 180 4.23e-01 c.108.1.5 66433 1e4iA 447 4.26e-01 1e70M c.1.8.4 59225 1eyzA 392 4.37e-01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1g8oA 310 4.37e-01 1g8oA c.68.1.9 60375 1g8lA 411 4.54e-01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1psdA 409 4.64e-01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1bs2A 607 4.70e-01 1bs2A a.27.1.1 16930 c.26.1.1 31597 d.67.2.1 39563 1el5A 389 4.90e-01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1g5aA 628 4.96e-01 b.71.1.1 65152 c.1.8.1 65153 1hwyA 501 5.01e-01 1hwyA c.2.1.7 30262 c.58.1.1 33910 1g59A 468 5.04e-01 a.97.1.1 60257 c.26.1.1 60258 1fds 327 5.08e-01 1fds c.2.1.2 29838 1azwA 313 5.12e-01 1qtrA c.69.1.7 34658 1i9gA 280 5.36e-01 c.66.1.13 62090 5tmpA 213 5.37e-01 5tmpA c.37.1.1 31931 1qgoA 264 5.42e-01 1qgoA c.92.1.2 35596 1tpt 440 5.48e-01 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1k4vA 289 5.74e-01 1a8s 273 5.81e-01 1brt c.69.1.12 34710 1bd0A 388 5.90e-01 1bd0A b.49.2.1 26480 c.1.6.1 28642 1ek6A 348 5.93e-01 1xel c.2.1.2 29800 1gw9A 388 6.08e-01 1b93A 152 6.08e-01 1b93A c.24.1.2 31507 1f7uA 607 6.22e-01 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1lldA 319 6.24e-01 3ldh c.2.1.5 30177 d.162.1.1 42144 1yasA 257 6.58e-01 1qj4A c.69.1.20 34801 1gln 468 6.64e-01 1gln a.97.1.1 18752 c.26.1.1 31588 1dvjC 246 6.70e-01 1dvjA c.1.2.3 28548 1qj4A 257 6.78e-01 1qj4A c.69.1.20 34796 1hzyA 332 6.78e-01 1pscA c.1.9.3 61468 1i0dA 332 6.78e-01 1pscA c.1.9.3 61487 2udpA 338 6.91e-01 1xel c.2.1.2 29791 2xis 387 7.14e-01 4xis c.1.15.3 29427 1rpxA 230 7.20e-01 1rpxA c.1.2.2 28536 1eno 312 7.36e-01 1enp c.2.1.2 29905 1xel 338 7.42e-01 1xel c.2.1.2 29786 1enp 312 7.46e-01 1enp c.2.1.2 29906 1udb 338 7.55e-01 1xel c.2.1.2 29787 7odcA 424 7.63e-01 7odcA b.49.2.1 26488 c.1.6.1 28650 3csuA 310 7.76e-01 3csuA c.78.1.1 35094 c.78.1.1 35095 1e0cA 271 7.85e-01 1e0cA c.46.1.2 32717 c.46.1.2 32718 1udc 338 7.89e-01 1xel c.2.1.2 29785 1eulA 994 8.01e-01 1eulA f.2.1.10 43726 1nal1 297 8.08e-01 1nal3 1b43A 340 8.19e-01 1a76 a.60.7.1 18092 c.53.1.2 33362 1dvjA 246 8.20e-01 1dvjA c.1.2.3 28546 4xis 387 8.29e-01 4xis c.1.15.3 29421 1scuA 288 8.36e-01 2scuA c.2.1.8 30307 c.23.4.1 31135 1gpmA 525 8.39e-01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1b7bA 310 8.40e-01 1b7bA c.73.1.1 34963 1c14A 262 8.53e-01 1eny c.2.1.2 29927 1f6yA 262 8.64e-01 1f6yA c.1.21.2 29673 1gg4A 452 8.81e-01 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 1tgoA 773 8.99e-01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1fdyA 297 9.00e-01 1nal3 c.1.10.1 29071 1dd9A 338 9.01e-01 1dd9A e.13.1.1 43254 1d4aA 273 9.26e-01 1d4aA c.23.5.3 31219 1frb 315 9.27e-01 1frb c.1.7.1 28665 2dhqA 146 9.30e-01 2dhqA c.23.13.1 31382 1l9fA 389 9.32e-01 1vrtA 560 9.40e-01 1rthA c.55.3.1 33574 e.8.1.2 43023 1efpB 252 9.44e-01 1efvB c.29.1.1 31636 1ig3A 263 9.52e-01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1gv4A 528 9.56e-01 2nsyA 271 9.77e-01 2nsyA c.26.2.1 31612 1eceA 358 9.88e-01 1eceA c.1.8.3 28813 1ih8A 271 1.00e+00 2nsyA c.26.2.1 62377 1sftA 388 1.01e+00 1bd0A b.49.2.1 26482 c.1.6.1 28644 1oasA 322 1.03e+00 1oasA c.79.1.1 35293 1g5cA 170 1.04e+00 1g5cA c.53.2.1 60264 1d7kA 421 1.04e+00 7odcA b.49.2.1 26486 c.1.6.1 28648 1fdt 327 1.05e+00 1fds c.2.1.2 29841 3xis 387 1.07e+00 4xis c.1.15.3 29423 2gar 212 1.07e+00 2gar c.65.1.1 34161 1nsyA 271 1.08e+00 2nsyA c.26.2.1 31614 1kqpA 271 1.08e+00 1qsgA 265 1.09e+00 1eny c.2.1.2 29935 1d7oA 297 1.11e+00 1enp c.2.1.2 29907 1g6sA 427 1.12e+00 1eps d.68.2.2 39584 1c3oE 1073 1.13e+00 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1bqg 451 1.13e+00 1bqg c.1.11.2 29217 d.54.1.1 38861 1kvs 338 1.14e+00 1xel c.2.1.2 29799 1pscA 365 1.14e+00 1pscA c.1.9.3 29058 2hdhA 293 1.15e+00 2hdhA a.100.1.3 18795 c.2.1.6 30199 1id1A 153 1.16e+00 1id1A c.2.1.9 62286 1ezwA 349 1.17e+00 1ezwA c.1.16.3 29558 1js1X 324 1.17e+00 1d3gA 367 1.17e+00 1d3gA c.1.4.1 28600 4tmkA 213 1.24e+00 5tmpA c.37.1.1 31930 1jj7A 260 1.26e+00 c.37.1.12 63114 1efvA 315 1.26e+00 1efvA c.29.1.1 31633 c.31.1.2 31728 1jkxA 212 1.26e+00 c.65.1.1 66813 1g7tA 594 1.29e+00 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1jdc 429 1.31e+00 1jdc b.71.1.1 27789 c.1.8.1 28776 1dtwB 342 1.32e+00 1qs0B c.36.1.3 31828 c.48.1.2 33102 1f21A 155 1.36e+00 2rn2 c.55.3.1 33550 1a2zA 220 1.37e+00 1a2zA c.56.4.1 33794 1d4oA 184 1.38e+00 1d4oA c.31.1.4 31748 1keeE 1073 1.41e+00 a.92.1.1 68508 c.24.1.1 68509 c.30.1.1 68510 c.30.1.1 68511 d.142.1.2 68512 d.142.1.2 68513 1xyzA 347 1.42e+00 1taxA c.1.8.3 28804 1cnv 299 1.45e+00 1cnv c.1.8.5 28989 1hdr 244 1.45e+00 1dhr c.2.1.2 29837 1qrdA 273 1.46e+00 1d4aA c.23.5.3 31217 1ecfA 504 1.47e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 1eywA 331 1.47e+00 1pscA c.1.9.3 29057 1zfjA 491 1.49e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 2scuA 288 1.51e+00 2scuA c.2.1.8 30303 c.23.4.1 31131 1nal3 297 1.55e+00 1nal3 1a27 289 1.55e+00 1fds c.2.1.2 29839 1g2iA 166 1.55e+00 1g2iA c.23.16.2 31438 1taq 832 1.56e+00 1taq a.60.7.1 18082 c.53.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1etu 394 1.59e+00 1efcA c.37.1.8 64737 1qlwA 328 1.60e+00 1qlwA c.69.1.15 34722 1kl7A 514 1.60e+00 1g7sA 594 1.60e+00 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1bl3A 160 1.61e+00 1b9dA c.55.3.2 33655 4enl 436 1.67e+00 4enl c.1.11.1 29202 d.54.1.1 38846 1ihuA 589 1.67e+00 c.37.1.10 62394 c.37.1.10 62395 1kyqA 274 1.68e+00 1c3oA 1073 1.68e+00 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1cipA 353 1.68e+00 1cipA a.66.1.1 18210 c.37.1.8 32093 1pymA 295 1.69e+00 1pymA c.1.12.4 29308 1jyeA 349 1.70e+00 c.93.1.1 67455 1duvG 333 1.70e+00 1othA c.78.1.1 35228 c.78.1.1 35229 1c0pA 363 1.71e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 1gzgA 337 1.73e+00 1c0dA 358 1.73e+00 1eceA c.1.8.3 28815 1ecfB 504 1.77e+00 1ecfB c.61.1.1 34054 d.153.1.1 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1g5tA 196 3.47e+01 1g5rA c.37.1.11 32366 1yacA 208 3.48e+01 1yacA c.33.1.2 31757 1u9aA 160 3.49e+01 1u9aA d.20.1.1 38333 1jhdA 396 3.49e+01 b.58.1.2 66712 c.26.1.5 66713 1ffkM 148 3.50e+01 1ffkM a.94.1.1 18740 1qb7A 236 3.51e+01 1qb7A c.61.1.1 34087 1qd9A 124 3.52e+01 1qu9A d.79.1.1 39758 1bj4A 470 3.54e+01 1bj4A c.67.1.4 34479 1h77A 605 3.54e+01 1a4mA 349 3.54e+01 1a4mA c.1.9.1 29014 1rhs 296 3.55e+01 1rhs c.46.1.2 32703 c.46.1.2 32704 3eugA 229 3.57e+01 3eugA c.18.1.1 31018 1gegA 256 3.59e+01 1ybvA c.2.1.2 29888 1dbuA 158 3.59e+01 1dbuA d.116.1.1 40930 1fc4A 401 3.59e+01 1bs0A c.67.1.4 59760 1qamA 244 3.61e+01 2ercA c.66.1.9 34220 1rpmA 278 3.62e+01 2shpA c.45.1.2 32679 1qumA 285 3.63e+01 1qumA c.1.15.1 29393 1l4uA 176 3.64e+01 1jx2B 315 3.66e+01 c.37.1.8 67404 1rhd 293 3.68e+01 1rhs c.46.1.2 32715 c.46.1.2 32716 1gqwA 283 3.70e+01 1tkaA 678 3.70e+01 1trkA c.36.1.2 31815 c.36.1.2 31816 c.48.1.1 33096 7timA 247 3.73e+01 1amk c.1.1.1 28457 1dqaA 467 3.75e+01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1k8tA 510 3.75e+01 e.9.1.4 68316 1b8oA 284 3.75e+01 1b8oA c.56.2.1 33762 1f7cA 231 3.80e+01 1f7cA a.116.1.1 19107 1e15A 499 3.81e+01 1e15A b.72.2.1 27810 c.1.8.5 29006 d.26.3.1 38440 1cf9A 753 3.84e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1g8kA 825 3.91e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 2tysB 397 3.94e+01 2tysB c.79.1.1 35272 1k94A 165 3.97e+01 a.39.1.7 68333 1lkxA 697 3.97e+01 1pbn 289 3.98e+01 1b8oA c.56.2.1 33771 1eny 268 4.00e+01 1eny c.2.1.2 29910 1efnB 152 4.00e+01 1efnB d.102.1.1 40699